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Samarium in PDB 5nsj: GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus

Protein crystallography data

The structure of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus, PDB code: 5nsj was solved by A.Shimon, O.Shani, R.Diskin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.32 / 2.25
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 128.024, 128.352, 45.966, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.9

Samarium Binding Sites:

The binding sites of Samarium atom in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus (pdb code 5nsj). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 7 binding sites of Samarium where determined in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus, PDB code: 5nsj:
Jump to Samarium binding site number: 1; 2; 3; 4; 5; 6; 7;

Samarium binding site 1 out of 7 in 5nsj

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Samarium binding site 1 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm305

b:41.5
occ:1.00
 SM A:SM308 1.7 62.9 0.6
O A:HOH469 2.2 20.7 1.0
OE2 A:GLU137 2.8 79.4 1.0
CB A:ASN134 3.0 0.6 1.0
OE1 A:GLU137 3.3 77.8 1.0
CD A:GLU137 3.4 66.2 1.0
CB A:ASP136 3.6 70.1 1.0
CA A:ASN134 4.0 0.9 1.0
CG A:ASN134 4.1 0.9 1.0
ND2 A:ASN134 4.1 0.2 1.0
N A:ASP136 4.4 62.9 1.0
OD2 A:ASP136 4.4 83.8 1.0
CG A:ASP136 4.5 76.8 1.0
CA A:ASP136 4.6 63.2 1.0
C A:ASN134 4.7 88.3 1.0
CG A:GLU137 4.7 66.1 1.0
N A:GLN135 4.9 91.1 1.0
N A:GLU137 4.9 64.1 1.0

Samarium binding site 2 out of 7 in 5nsj

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Samarium binding site 2 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm306

b:68.0
occ:1.00
 CA A:GLU137 3.2 64.5 1.0
O A:HOH466 3.3 29.3 1.0
N A:ARG138 3.4 34.5 1.0
NE1 A:TRP102 3.4 23.8 1.0
N A:LEU139 3.4 25.1 1.0
C A:GLU137 3.5 79.2 1.0
CB A:GLU137 3.6 70.6 1.0
CZ2 A:TRP102 3.6 28.2 1.0
CB A:LEU139 3.7 27.3 1.0
CG A:LEU139 3.7 25.0 1.0
CE2 A:TRP102 3.9 23.2 1.0
CD1 A:LEU139 4.1 25.3 1.0
CA A:LEU139 4.2 24.9 1.0
C A:ARG138 4.4 32.3 1.0
CA A:ARG138 4.4 30.9 1.0
O A:GLU137 4.4 67.1 1.0
O A:ASP136 4.4 70.2 1.0
CG A:ARG138 4.4 35.5 1.0
N A:GLU137 4.5 64.1 1.0
CD1 A:TRP102 4.6 26.0 1.0
CH2 A:TRP102 4.9 26.3 1.0
C A:ASP136 4.9 69.7 1.0
C A:LEU139 4.9 30.7 1.0
CB A:ARG138 5.0 28.1 1.0
CG A:GLU137 5.0 66.1 1.0

Samarium binding site 3 out of 7 in 5nsj

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Samarium binding site 3 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm307

b:11.8
occ:0.07
 NE2 A:HIS155 2.4 34.4 1.0
CD2 A:HIS155 3.0 34.4 1.0
CE1 A:HIS156 3.3 27.6 1.0
NE2 A:HIS156 3.4 27.7 1.0
CE1 A:HIS155 3.6 36.5 1.0
ND1 A:HIS156 4.2 27.5 1.0
CG A:HIS155 4.2 33.9 1.0
CD2 A:HIS156 4.4 27.0 1.0
ND1 A:HIS155 4.5 36.3 1.0
CG A:HIS156 4.8 29.4 1.0

Samarium binding site 4 out of 7 in 5nsj

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Samarium binding site 4 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm308

b:62.9
occ:0.63
 SM A:SM305 1.7 41.5 1.0
OE2 A:GLU137 2.3 79.4 1.0
CB A:ASN134 2.7 0.6 1.0
O A:HOH469 3.1 20.7 1.0
ND2 A:ASN134 3.1 0.2 1.0
CD A:GLU137 3.4 66.2 1.0
CG A:ASN134 3.4 0.9 1.0
OE1 A:GLU137 3.9 77.8 1.0
CA A:ASN134 4.0 0.9 1.0
OD1 A:ASN134 4.6 0.0 1.0
CG A:GLU137 4.6 66.1 1.0
N A:ASN134 4.9 0.6 1.0
ND2 A:ASN133 4.9 68.8 1.0
O A:HOH422 4.9 23.3 1.0

Samarium binding site 5 out of 7 in 5nsj

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Samarium binding site 5 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 5 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm305

b:31.9
occ:0.74
 OE2 A:GLU180 2.0 63.0 1.0
CB B:ASP136 2.8 38.4 1.0
OE1 B:GLU137 3.0 55.6 1.0
O B:HOH412 3.0 31.2 1.0
CD A:GLU180 3.1 64.1 1.0
OD2 B:ASP136 3.1 49.4 1.0
CG B:ASP136 3.4 50.9 1.0
OE2 B:GLU137 3.5 45.9 1.0
CD B:GLU137 3.6 41.9 1.0
CG A:GLU180 3.8 55.9 1.0
O A:HOH456 3.8 13.3 1.0
O A:CYS201 3.8 27.4 1.0
CB B:ASN134 3.9 45.5 1.0
OE1 A:GLU180 4.0 66.1 1.0
CA B:ASP136 4.1 45.6 1.0
N B:ASP136 4.3 53.6 1.0
ND1 A:HIS204 4.6 25.4 1.0
OD1 B:ASP136 4.6 55.6 1.0
O A:SER203 4.7 29.4 1.0
N B:GLU137 4.7 42.9 1.0
ND2 B:ASN134 4.7 44.6 1.0
C B:ASP136 4.7 44.8 1.0
CE1 A:HIS204 4.8 26.6 1.0
CG B:ASN134 4.8 46.9 1.0
CA B:ASN134 4.9 50.3 1.0
C A:CYS201 5.0 23.4 1.0

Samarium binding site 6 out of 7 in 5nsj

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Samarium binding site 6 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 6 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm306

b:0.5
occ:1.00
 O B:HOH489 2.5 35.5 1.0
CE1 B:HIS156 2.6 61.6 1.0
NE2 B:HIS155 2.8 72.3 1.0
ND1 B:HIS156 3.5 59.7 1.0
NE2 B:HIS156 3.5 61.2 1.0
CE1 B:HIS155 3.7 71.0 1.0
CD2 B:HIS155 3.8 69.0 1.0
O B:HOH514 4.3 23.4 1.0
CG B:HIS156 4.7 53.1 1.0
CD2 B:HIS156 4.7 54.4 1.0
O B:HOH555 4.7 77.4 1.0
ND1 B:HIS155 4.8 66.4 1.0
CG B:HIS155 4.9 65.7 1.0

Samarium binding site 7 out of 7 in 5nsj

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Samarium binding site 7 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 7 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm307

b:7.4
occ:0.15
 O B:HOH441 1.9 5.0 1.0
O B:HOH459 2.9 21.6 1.0
NE1 B:TRP102 3.5 36.0 1.0
CZ2 B:TRP102 3.7 21.8 1.0
CE2 B:TRP102 3.9 22.7 1.0
CD1 B:LEU139 4.2 23.8 1.0
CG B:LEU139 4.3 30.4 1.0
CA B:GLU137 4.3 33.8 1.0
CB B:LEU139 4.4 27.2 1.0
CB B:GLU137 4.4 31.6 1.0
CB B:ALA100 4.6 26.8 1.0
N B:ARG138 4.6 32.1 1.0
N B:LEU139 4.6 19.9 1.0
CD1 B:TRP102 4.7 38.7 1.0
C B:GLU137 4.7 35.3 1.0
CH2 B:TRP102 4.9 20.0 1.0
O B:PRO97 5.0 28.4 1.0

Reference:

A.Shimon, O.Shani, R.Diskin. Structural Basis For Receptor Selectivity By the Whitewater Arroyo Mammarenavirus. J. Mol. Biol. V. 429 2825 2017.
ISSN: ESSN 1089-8638
PubMed: 28736175
DOI: 10.1016/J.JMB.2017.07.011
Page generated: Wed Dec 16 02:10:09 2020

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