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Zinc in PDB 2cj9: Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate

Enzymatic activity of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate

All present enzymatic activity of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate:
6.1.1.11;

Protein crystallography data

The structure of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate, PDB code: 2cj9 was solved by S.Bilokapic, T.Maier, D.Ahel, I.Gruic-Sovulj, D.Soll, I.Weygand-Durasevic, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.93 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 96.713, 96.713, 270.302, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 24.8

Other elements in 2cj9:

The structure of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate (pdb code 2cj9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate, PDB code: 2cj9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2cj9

Go back to Zinc Binding Sites List in 2cj9
Zinc binding site 1 out of 2 in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1503

b:51.6
occ:1.00
 OE2 A:GLU355 1.9 58.8 1.0
N10 A:SSA1505 2.3 42.3 1.0
SG A:CYS461 2.4 63.8 1.0
SG A:CYS306 2.6 62.0 1.0
CD A:GLU355 3.1 58.9 1.0
CA A:SSA1505 3.2 41.8 1.0
CB A:CYS461 3.2 62.0 1.0
CB A:CYS306 3.2 60.2 1.0
CB A:SSA1505 3.3 41.3 1.0
CZ2 A:TRP396 3.7 79.6 1.0
OE1 A:GLU355 3.8 60.2 1.0
O A:ALA304 3.9 60.6 1.0
CH2 A:TRP396 3.9 79.5 1.0
OG A:SSA1505 3.9 42.6 1.0
CE2 A:TRP396 4.2 79.7 1.0
CG A:GLU355 4.2 58.7 1.0
O A:HOH2080 4.3 40.1 1.0
CA A:CYS306 4.5 60.6 1.0
N A:CYS306 4.5 60.4 1.0
CZ3 A:TRP396 4.5 79.5 1.0
C9 A:SSA1505 4.5 41.9 1.0
CA A:CYS461 4.6 62.0 1.0
O A:HOH2119 4.6 45.7 1.0
NE1 A:TRP396 4.8 79.6 1.0
CD2 A:TRP396 4.8 79.7 1.0
O9 A:SSA1505 4.9 41.8 1.0
C A:CYS461 4.9 61.6 1.0
CE3 A:TRP396 4.9 79.5 1.0

Zinc binding site 2 out of 2 in 2cj9

Go back to Zinc Binding Sites List in 2cj9
Zinc binding site 2 out of 2 in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with An Analog of Seryladenylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1503

b:51.3
occ:1.00
 OE2 B:GLU355 2.1 60.2 1.0
N10 B:SSA1505 2.3 41.5 1.0
SG B:CYS461 2.4 65.0 1.0
SG B:CYS306 2.6 63.1 1.0
CB B:CYS461 3.1 63.9 1.0
CA B:SSA1505 3.1 40.9 1.0
CD B:GLU355 3.2 59.9 1.0
CB B:SSA1505 3.2 40.3 1.0
CB B:CYS306 3.3 62.1 1.0
OG B:SSA1505 3.6 41.4 1.0
OE1 B:GLU355 3.7 60.8 1.0
CZ2 B:TRP396 3.8 77.6 1.0
O B:ALA304 3.8 60.9 1.0
CH2 B:TRP396 4.1 77.4 1.0
CE2 B:TRP396 4.3 78.2 1.0
CG B:GLU355 4.3 60.4 1.0
N B:CYS306 4.5 61.7 1.0
O B:HOH2115 4.5 44.4 1.0
CA B:CYS306 4.5 62.5 1.0
C9 B:SSA1505 4.5 40.9 1.0
CA B:CYS461 4.5 63.8 1.0
O B:HOH2161 4.5 51.2 1.0
CZ3 B:TRP396 4.7 77.4 1.0
NE1 B:TRP396 4.8 78.3 1.0
C B:ALA304 4.9 60.8 1.0
C B:CYS461 4.9 63.6 1.0
O9 B:SSA1505 4.9 40.3 1.0
CD2 B:TRP396 4.9 78.0 1.0

Reference:

S.Bilokapic, T.Maier, D.Ahel, I.Gruic-Sovulj, D.Soll, I.Weygand-Durasevic, N.Ban. Structure of the Unusual Seryl-Trna Synthetase Reveals A Distinct Zinc-Dependent Mode of Substrate Recognition Embo J. V. 25 2498 2006.
ISSN: ISSN 0261-4189
PubMed: 16675947
DOI: 10.1038/SJ.EMBOJ.7601129
Page generated: Wed Aug 20 01:43:47 2025

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