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Samarium in PDB 5ktj: Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme

Protein crystallography data

The structure of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme, PDB code: 5ktj was solved by L.A.Nguyen, J.Wang, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.27 / 2.97
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.190, 85.190, 256.540, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25.7

Other elements in 5ktj:

The structure of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme also contains other interesting chemical elements:

Cobalt (Co) 10 atoms
Magnesium (Mg) 19 atoms

Samarium Binding Sites:

The binding sites of Samarium atom in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme (pdb code 5ktj). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 10 binding sites of Samarium where determined in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme, PDB code: 5ktj:
Jump to Samarium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Samarium binding site 1 out of 10 in 5ktj

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Samarium binding site 1 out of 10 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm101

b:0.0
occ:1.00
 OP2 A:C41 2.0 0.7 1.0
O A:HOH212 2.3 68.0 1.0
OP2 A:G42 2.3 0.4 1.0
O A:HOH205 2.5 83.1 1.0
P A:C41 3.4 0.7 1.0
P A:G42 3.5 0.4 1.0
O3' A:C41 3.7 0.3 1.0
OP1 A:C41 4.0 0.5 1.0
O3' A:G40 4.2 1.0 1.0
OP1 A:G42 4.3 0.1 1.0
N7 A:G43 4.3 0.6 1.0
O5' A:C41 4.4 0.1 1.0
O2' A:G40 4.4 0.9 1.0
C3' A:C41 4.5 0.7 1.0
OP2 A:G43 4.5 0.4 1.0
O5' A:G42 4.8 0.6 1.0
N7 A:G42 4.9 0.3 1.0
C8 A:G42 5.0 0.6 1.0

Samarium binding site 2 out of 10 in 5ktj

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Samarium binding site 2 out of 10 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm102

b:0.6
occ:1.00
 O3' A:C22 2.6 0.5 1.0
OP2 A:C22 2.6 0.1 1.0
C5' A:C22 3.3 0.3 1.0
C3' A:C22 3.3 0.6 1.0
OP2 A:A23 3.6 0.6 1.0
P A:A23 3.7 0.4 1.0
C4' A:C22 3.8 1.0 1.0
P A:C22 3.8 0.1 1.0
O5' A:C22 4.0 0.0 1.0
MG A:MG107 4.5 0.8 1.0
O5' A:A23 4.6 0.2 1.0
OP1 A:A23 4.8 0.1 1.0
OP1 A:C22 4.8 0.7 1.0
C2' A:C22 4.8 0.9 1.0
O3' A:A21 4.9 0.6 1.0

Samarium binding site 3 out of 10 in 5ktj

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Samarium binding site 3 out of 10 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm103

b:0.5
occ:0.50
 OP1 A:G32 3.6 0.7 1.0
OP2 A:G32 4.5 0.4 1.0
P A:G32 4.5 0.4 1.0
O4 A:U30 4.5 0.6 1.0

Samarium binding site 4 out of 10 in 5ktj

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Samarium binding site 4 out of 10 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm104

b:0.4
occ:0.50
 N6 A:NCO113 4.1 0.8 1.0
OP1 A:G47 4.5 0.6 1.0

Samarium binding site 5 out of 10 in 5ktj

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Samarium binding site 5 out of 10 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 5 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm105

b:0.9
occ:1.00
 OP2 A:U18 3.5 0.9 1.0
O5' A:U18 3.7 0.4 1.0
P A:U18 3.9 0.2 1.0
OP1 A:U18 4.0 0.0 1.0
MG A:MG108 4.0 0.9 1.0
C5' A:U18 4.1 0.8 1.0

Samarium binding site 6 out of 10 in 5ktj

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Samarium binding site 6 out of 10 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 6 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sm101

b:0.7
occ:1.00
 O C:HOH204 2.0 68.7 1.0
OP2 C:C41 2.1 0.7 1.0
O C:HOH220 2.3 80.1 1.0
OP2 C:G42 2.3 93.0 1.0
O C:HOH202 2.8 64.9 1.0
O C:HOH206 3.1 0.8 1.0
P C:C41 3.5 0.3 1.0
P C:G42 3.6 0.5 1.0
O3' C:G40 3.9 0.9 1.0
O3' C:C41 3.9 0.9 1.0
O5' C:C41 4.2 0.2 1.0
OP1 C:G42 4.5 0.3 1.0
C3' C:C41 4.6 0.8 1.0
O2' C:G40 4.6 0.1 1.0
O5' C:G42 4.7 0.8 1.0
OP1 C:C41 4.7 0.7 1.0
N7 C:G43 4.9 97.2 1.0

Samarium binding site 7 out of 10 in 5ktj

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Samarium binding site 7 out of 10 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 7 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sm102

b:0.2
occ:0.50
 N7 C:G50 3.4 0.1 1.0
O6 C:G50 3.9 0.8 1.0
N6 C:A49 4.1 0.1 1.0
C5 C:G50 4.3 0.1 1.0
C8 C:G50 4.4 0.5 1.0
N7 C:A49 4.4 0.4 1.0
C6 C:G50 4.4 0.8 1.0
C6 C:A49 4.5 0.6 1.0
C5 C:A49 4.6 0.3 1.0
OP2 C:G50 5.0 0.1 1.0

Samarium binding site 8 out of 10 in 5ktj

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Samarium binding site 8 out of 10 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 8 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sm103

b:0.9
occ:1.00
 MG C:MG107 3.9 0.7 1.0
OP1 C:A46 4.3 0.7 1.0

Samarium binding site 9 out of 10 in 5ktj

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Samarium binding site 9 out of 10 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 9 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sm104

b:0.8
occ:1.00
 O3' C:C22 3.9 0.1 1.0
OP2 C:A23 4.0 0.8 1.0
N7 C:G24 4.2 0.2 1.0
O6 C:G24 4.3 0.3 1.0
P C:A23 4.6 0.0 1.0
OP2 C:C22 4.9 0.4 1.0

Samarium binding site 10 out of 10 in 5ktj

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Samarium binding site 10 out of 10 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 10 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sm101

b:0.4
occ:0.30
 OP2 D:A15 2.5 0.6 1.0
P D:A15 3.9 0.7 1.0
O5' D:A15 4.3 0.0 1.0
OP2 D:A14 4.6 0.8 1.0
C8 D:A15 4.7 0.0 1.0
N7 D:A15 4.7 0.6 1.0
O5' D:A14 4.7 0.5 1.0
OP1 D:A15 4.8 0.1 1.0
O3' D:A14 5.0 0.5 1.0

Reference:

L.A.Nguyen, J.Wang, T.A.Steitz. Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme. Proc. Natl. Acad. Sci. V. 114 1021 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28096403
DOI: 10.1073/PNAS.1611191114
Page generated: Wed Dec 16 02:10:05 2020

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