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Samarium in PDB 5g3s: The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative

Enzymatic activity of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative

All present enzymatic activity of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative:
1.4.3.23;

Protein crystallography data

The structure of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative, PDB code: 5g3s was solved by J.Krausze, J.Rabe, J.Moser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.880, 87.070, 78.020, 90.00, 112.95, 90.00
R / Rfree (%) 16.5 / 18.8

Other elements in 5g3s:

The structure of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative also contains other interesting chemical elements:

Mercury (Hg) 12 atoms
Chlorine (Cl) 3 atoms

Samarium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Samarium atom in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative (pdb code 5g3s). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 11 binding sites of Samarium where determined in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative, PDB code: 5g3s:
Jump to Samarium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Samarium binding site 1 out of 11 in 5g3s

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Samarium binding site 1 out of 11 in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative


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Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm419

b:47.6
occ:0.61
 HH12 B:ARG201 2.0 56.0 1.0
OE1 A:GLU324 2.6 53.1 1.0
NH1 B:ARG201 2.7 46.6 1.0
HH22 B:ARG201 2.7 55.8 1.0
OE2 A:GLU324 2.8 55.5 1.0
O A:HOH2180 2.9 26.8 1.0
O A:HOH2152 3.1 41.2 1.0
CD A:GLU324 3.1 52.9 1.0
HH11 B:ARG201 3.2 56.0 1.0
NH2 B:ARG201 3.2 46.5 1.0
CZ B:ARG201 3.3 45.7 1.0
HH12 B:ARG35 3.8 50.6 1.0
HH21 B:ARG201 4.0 55.8 1.0
HH22 B:ARG35 4.0 48.2 1.0
NH1 B:ARG35 4.3 40.1 1.0
HA A:GLU324 4.4 54.3 1.0
NE B:ARG201 4.5 43.8 1.0
NH2 B:ARG35 4.5 42.2 1.0
CG A:GLU324 4.6 49.2 1.0
CZ B:ARG35 4.7 40.5 1.0
HH11 B:ARG35 4.8 50.6 1.0
HG2 A:GLU324 5.0 59.0 1.0

Samarium binding site 2 out of 11 in 5g3s

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Samarium binding site 2 out of 11 in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm420

b:35.0
occ:1.00
 HZ1 A:LYS101 1.8 29.5 1.0
NE2 A:HIS97 2.4 21.2 1.0
CL A:CL437 2.7 42.1 1.0
NZ A:LYS101 2.7 24.6 1.0
O A:HOH2181 2.8 31.1 1.0
HZ3 A:LYS101 3.1 29.5 1.0
HZ2 A:LYS101 3.1 29.5 1.0
CD2 A:HIS97 3.3 20.3 1.0
HD3 A:LYS101 3.3 29.3 1.0
HD2 A:HIS97 3.4 24.3 1.0
CE1 A:HIS97 3.4 22.4 1.0
CE A:LYS101 3.6 24.1 1.0
HE1 A:HIS97 3.6 26.8 1.0
HE2 A:LYS101 3.7 28.9 1.0
CD A:LYS101 3.9 24.4 1.0
HD2 A:LYS101 4.1 29.3 1.0
CG A:HIS97 4.5 20.4 1.0
HE3 A:LYS101 4.5 28.9 1.0
ND1 A:HIS97 4.5 22.1 1.0
OE1 A:GLN129 4.6 35.0 1.0
O A:HOH2069 4.7 25.2 1.0
HE22 A:GLN129 4.8 41.9 1.0
HG13 A:VAL98 5.0 25.9 1.0

Samarium binding site 3 out of 11 in 5g3s

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Samarium binding site 3 out of 11 in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative


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Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm421

b:29.7
occ:1.00
 HN3 A:TRS438 1.6 30.0 1.0
ND1 A:HIS361 2.5 24.8 1.0
O3 A:NO3435 2.5 26.7 1.0
N A:TRS438 2.6 25.0 1.0
H22 A:TRS438 2.6 34.2 1.0
O3 A:TRS438 2.7 30.9 1.0
HB2 A:HIS361 2.8 28.8 1.0
CL A:CL436 2.9 23.8 1.0
HN2 A:TRS438 3.0 30.0 1.0
HN1 A:TRS438 3.1 30.0 1.0
O2 A:NO3435 3.2 27.8 1.0
N A:NO3435 3.2 27.0 1.0
C A:TRS438 3.2 27.1 1.0
H A:HIS361 3.2 26.1 1.0
C2 A:TRS438 3.3 28.5 1.0
CG A:HIS361 3.3 25.5 1.0
HB1 A:ALA360 3.5 20.7 1.0
HO3 A:TRS438 3.5 37.1 1.0
CE1 A:HIS361 3.5 25.2 1.0
C3 A:TRS438 3.5 29.4 1.0
CB A:HIS361 3.5 24.0 1.0
HE1 A:HIS361 3.7 30.2 1.0
O A:HOH2160 3.7 29.6 1.0
N A:HIS361 3.8 21.7 1.0
O2 A:TRS438 3.8 30.2 1.0
H32 A:TRS438 3.9 35.3 1.0
CA A:HIS361 4.2 23.7 1.0
H21 A:TRS438 4.2 34.2 1.0
HB3 A:HIS361 4.3 28.8 1.0
HO2 A:TRS438 4.3 36.3 1.0
O1 A:NO3435 4.4 35.4 1.0
CB A:ALA360 4.4 17.2 1.0
H31 A:TRS438 4.4 35.3 1.0
OG A:SER244 4.5 21.4 1.0
CD2 A:HIS361 4.5 27.3 1.0
O A:HOH2159 4.5 23.8 1.0
NE2 A:HIS361 4.5 26.9 1.0
H A:ALA360 4.6 19.6 1.0
C A:ALA360 4.6 18.0 1.0
C1 A:TRS438 4.7 25.0 1.0
HB2 A:ALA360 4.8 20.7 1.0
C A:HIS361 4.9 22.6 1.0
N A:ALA360 4.9 16.4 1.0
CA A:ALA360 4.9 17.1 1.0
HG A:SER244 4.9 25.7 1.0
O A:HIS361 4.9 22.4 1.0
HB3 A:ALA360 5.0 20.7 1.0
H11 A:TRS438 5.0 30.0 1.0

Samarium binding site 4 out of 11 in 5g3s

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Samarium binding site 4 out of 11 in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm422

b:0.1
occ:0.80
 HD1 A:HIS97 1.9 26.6 1.0
ND1 A:HIS97 2.6 22.1 1.0
O A:HOH2182 3.0 31.5 1.0
HE1 A:HIS97 3.1 26.8 1.0
CE1 A:HIS97 3.2 22.4 1.0
OE1 A:GLN100 3.4 35.5 1.0
HB2 A:GLN100 3.5 33.5 1.0
O A:HOH2068 3.5 21.1 1.0
HA A:HIS97 3.6 25.4 1.0
CG A:HIS97 3.7 20.4 1.0
O A:HIS97 4.0 20.1 1.0
HB2 A:HIS97 4.1 24.7 1.0
HB3 A:GLN100 4.1 33.5 1.0
CA A:HIS97 4.2 21.2 1.0
CB A:GLN100 4.2 27.9 1.0
CB A:HIS97 4.3 20.6 1.0
HB2 A:LYS101 4.3 25.4 1.0
NE2 A:HIS97 4.4 21.2 1.0
CD A:GLN100 4.6 33.1 1.0
C A:HIS97 4.6 20.2 1.0
CD2 A:HIS97 4.7 20.3 1.0
H A:LYS101 4.7 23.4 1.0
N A:LYS101 4.9 19.5 1.0

Samarium binding site 5 out of 11 in 5g3s

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Samarium binding site 5 out of 11 in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 5 of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm423

b:0.9
occ:1.00
 NE2 A:HIS116 2.5 40.6 1.0
HD2 A:HIS116 3.0 46.7 1.0
CD2 A:HIS116 3.1 38.9 1.0
CE1 A:HIS116 3.7 41.0 1.0
HE1 A:HIS116 4.0 49.2 1.0
HH12 A:ARG127 4.4 47.5 1.0
CG A:HIS116 4.4 37.8 1.0
HD3 A:ARG112 4.5 42.9 1.0
HH11 A:ARG127 4.6 47.5 1.0
NH1 A:ARG127 4.6 39.6 1.0
ND1 A:HIS116 4.6 40.0 1.0
HB3 A:ARG112 4.9 37.7 1.0

Samarium binding site 6 out of 11 in 5g3s

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Samarium binding site 6 out of 11 in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 6 of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm424

b:73.2
occ:0.71
 HG2 A:GLN3 2.6 55.1 1.0
HE21 A:GLN3 2.6 54.8 1.0
NE2 A:GLN3 2.9 45.7 1.0
HA A:GLN3 2.9 71.0 1.0
CD A:GLN3 3.2 45.2 1.0
CG A:GLN3 3.3 46.0 1.0
HE22 A:GLN3 3.3 54.8 1.0
O A:LYS2 3.5 62.8 1.0
CA A:GLN3 3.7 59.2 1.0
HH22 A:ARG35 3.8 53.1 1.0
O A:HOH2001 3.8 38.2 1.0
CB A:GLN3 3.9 45.7 1.0
OE1 A:GLN3 4.0 44.4 1.0
C A:LYS2 4.0 63.1 1.0
HG3 A:GLN3 4.1 55.1 1.0
N A:GLN3 4.1 61.6 1.0
HH12 A:ARG35 4.1 51.4 1.0
HB3 A:GLN3 4.1 54.8 1.0
HA B:GLU324 4.2 43.0 1.0
CG B:GLU324 4.2 37.4 1.0
H A:SER4 4.5 48.7 1.0
H A:LYS2 4.6 82.3 1.0
NH2 A:ARG35 4.6 42.8 1.0
H A:GLN3 4.7 73.9 1.0
HB2 A:GLN3 4.8 54.8 1.0
HB3 B:GLU324 4.9 43.8 1.0
NH1 A:ARG35 4.9 44.2 1.0
C A:GLN3 4.9 55.6 1.0
CB B:GLU324 5.0 36.5 1.0
N A:LYS2 5.0 68.5 1.0

Samarium binding site 7 out of 11 in 5g3s

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Samarium binding site 7 out of 11 in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 7 of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm425

b:0.3
occ:0.96
 NE2 A:HIS163 2.6 22.2 1.0
O A:HOH2168 3.2 50.4 1.0
O A:HOH2036 3.3 35.0 1.0
O A:HOH2145 3.3 27.8 1.0
O A:HOH2184 3.4 35.9 1.0
O A:HOH2183 3.4 37.1 1.0
CE1 A:HIS163 3.5 22.8 1.0
CD2 A:HIS163 3.6 20.9 1.0
HE1 A:HIS163 3.7 27.4 1.0
HD2 A:HIS163 3.7 25.1 1.0
HE1 A:TYR143 3.7 24.1 1.0
CE1 A:TYR143 4.2 20.1 1.0
HD1 A:TYR143 4.3 22.6 1.0
HZ2 A:TRP397 4.4 30.2 1.0
CD1 A:TYR143 4.5 18.8 1.0
O A:HOH2169 4.6 35.8 1.0
OH A:TYR309 4.7 19.4 1.0
ND1 A:HIS163 4.7 22.1 1.0
HG22 A:VAL363 4.7 36.2 1.0
CG A:HIS163 4.7 20.6 1.0
HH21 A:ARG64 4.8 23.2 1.0
CZ2 A:TRP397 4.8 25.2 1.0
HH A:TYR309 4.9 23.3 1.0
HE1 A:TRP397 5.0 30.4 1.0

Samarium binding site 8 out of 11 in 5g3s

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Samarium binding site 8 out of 11 in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 8 of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm419

b:60.5
occ:1.00
 HZ1 B:LYS101 1.9 32.2 1.0
NE2 B:HIS97 2.6 23.5 1.0
O B:HOH2189 2.7 31.4 1.0
NZ B:LYS101 2.7 26.8 1.0
HZ2 B:LYS101 3.0 32.2 1.0
HD2 B:HIS97 3.1 27.5 1.0
HZ3 B:LYS101 3.1 32.2 1.0
CD2 B:HIS97 3.2 22.9 1.0
HD3 B:LYS101 3.5 32.9 1.0
CE B:LYS101 3.7 26.8 1.0
HE2 B:LYS101 3.8 32.1 1.0
CE1 B:HIS97 3.8 25.9 1.0
CD B:LYS101 4.1 27.4 1.0
HE1 B:HIS97 4.1 31.0 1.0
HD2 B:LYS101 4.4 32.9 1.0
CG B:HIS97 4.5 23.7 1.0
HE3 B:LYS101 4.6 32.1 1.0
HG13 B:VAL98 4.7 24.4 1.0
OE1 B:GLN129 4.7 37.6 1.0
ND1 B:HIS97 4.7 25.9 1.0
HE22 B:GLN129 4.8 45.3 1.0
O B:HOH2080 4.9 27.9 1.0

Samarium binding site 9 out of 11 in 5g3s

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Samarium binding site 9 out of 11 in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 9 of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm420

b:35.2
occ:1.00
 HN2 B:TRS433 1.8 45.5 1.0
H32 B:TRS433 1.9 45.5 1.0
H22 B:TRS433 2.3 43.7 1.0
O3 B:NO3431 2.5 29.5 1.0
ND1 B:HIS361 2.5 24.8 1.0
N B:TRS433 2.7 37.9 1.0
C3 B:TRS433 2.7 37.9 1.0
HB2 B:HIS361 2.8 27.2 1.0
CL B:CL432 2.9 23.3 1.0
C B:TRS433 2.9 35.9 1.0
O2 B:NO3431 3.0 29.5 1.0
C2 B:TRS433 3.0 36.4 1.0
N B:NO3431 3.1 30.0 1.0
HN3 B:TRS433 3.3 45.5 1.0
CG B:HIS361 3.4 24.2 1.0
HN1 B:TRS433 3.4 45.5 1.0
H B:HIS361 3.4 26.7 1.0
O3 B:TRS433 3.4 39.0 1.0
CB B:HIS361 3.5 22.6 1.0
CE1 B:HIS361 3.5 25.8 1.0
H31 B:TRS433 3.6 45.5 1.0
HB1 B:ALA360 3.6 24.1 1.0
HE1 B:HIS361 3.7 31.0 1.0
O B:HOH2029 3.8 38.5 1.0
HO3 B:TRS433 3.8 46.8 1.0
H21 B:TRS433 3.8 43.7 1.0
N B:HIS361 3.9 22.2 1.0
HG B:SER244 3.9 30.1 1.0
O2 B:TRS433 3.9 37.1 1.0
CA B:HIS361 4.2 22.7 1.0
HB3 B:HIS361 4.3 27.2 1.0
O1 B:NO3431 4.3 36.7 1.0
HO2 B:TRS433 4.4 44.5 1.0
O A:HOH2123 4.4 23.9 1.0
C1 B:TRS433 4.4 32.0 1.0
O B:HOH2195 4.5 42.0 1.0
CD2 B:HIS361 4.5 25.9 1.0
CB B:ALA360 4.5 20.1 1.0
NE2 B:HIS361 4.6 27.4 1.0
OG B:SER244 4.6 25.0 1.0
H B:ALA360 4.6 22.8 1.0
C B:ALA360 4.7 20.4 1.0
O1 B:TRS433 4.9 27.8 1.0
C B:HIS361 4.9 21.9 1.0
N B:ALA360 4.9 19.0 1.0
H12 B:TRS433 4.9 38.4 1.0
HB2 B:ALA360 4.9 24.1 1.0
CA B:ALA360 5.0 19.6 1.0
O B:HIS361 5.0 22.1 1.0
H11 B:TRS433 5.0 38.4 1.0

Samarium binding site 10 out of 11 in 5g3s

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Samarium binding site 10 out of 11 in the The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 10 of The Structure of the L-Tryptophan Oxidase Vioa From Chromobacterium Violaceum - Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm421

b:0.2
occ:0.80
 NE2 B:HIS163 2.5 21.0 1.0
O B:HOH2160 3.0 27.2 1.0
O B:HOH2180 3.3 36.0 1.0
O B:HOH2190 3.4 39.8 1.0
HE1 B:TYR143 3.4 21.5 1.0
CE1 B:HIS163 3.4 21.2 1.0
O B:HOH2040 3.5 40.5 1.0
CD2 B:HIS163 3.5 19.8 1.0
O B:HOH2191 3.5 42.2 1.0
HE1 B:HIS163 3.6 25.4 1.0
HD2 B:HIS163 3.6 23.7 1.0
HH B:TYR309 3.7 25.2 1.0
CE1 B:TYR143 3.9 17.9 1.0
HD1 B:TYR143 4.0 21.9 1.0
CD1 B:TYR143 4.2 18.2 1.0
OH B:TYR309 4.3 21.0 1.0
ND1 B:HIS163 4.6 21.0 1.0
HG22 B:VAL363 4.6 35.0 1.0
CG B:HIS163 4.6 20.1 1.0
HH21 B:ARG64 4.6 20.3 1.0
HZ2 B:TRP397 4.6 26.5 1.0
CZ B:TYR143 4.8 19.0 1.0
CZ2 B:TRP397 5.0 22.1 1.0
HB B:VAL363 5.0 33.7 1.0
HE2 B:TYR309 5.0 22.0 1.0

Reference:

J.Fuller, R.Roepke, J.Krausze, K.E.Rennhack, N.P.Daniel, W.Blankenfeldt, S.Schulz, D.Jahn, J.Moser. Biosynthesis of Violacein: Structure and Function of L-Tryptophan Oxidase Vioa Chromobacterium Violaceum J.Biol.Chem. V. 291 20068 2016.
ISSN: ISSN 0021-9258
PubMed: 27466367
DOI: 10.1074/JBC.M116.741561
Page generated: Thu Oct 10 13:53:22 2024

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