Zinc in PDB 2cjb: Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with Serine

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

The structure of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with Serine, PDB code: 2cjb 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)	19.94 / 2.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.933, 96.933, 270.503, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 27.2

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

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with Serine (pdb code 2cjb). 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 Serine, PDB code: 2cjb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with Serine


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 Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1503 b:83.2 occ:1.00 OE2 A:GLU355 2.0 88.8 1.0 SG A:CYS461 2.4 94.5 1.0 SG A:CYS306 2.5 0.2 1.0 N A:SER1505 2.7 92.7 1.0 CA A:SER1505 3.1 92.9 1.0 CB A:CYS461 3.1 92.0 1.0 CD A:GLU355 3.2 90.1 1.0 CB A:SER1505 3.2 92.6 1.0 CB A:CYS306 3.5 97.7 1.0 CZ2 A:TRP396 3.5 0.6 1.0 OE1 A:GLU355 3.9 93.8 1.0 CH2 A:TRP396 3.9 0.6 1.0 CE2 A:TRP396 4.0 1.0 1.0 OG A:SER1505 4.0 91.2 1.0 O A:ALA304 4.2 95.8 1.0 O A:HOH2033 4.2 56.2 1.0 CG A:GLU355 4.3 88.8 1.0 NE1 A:TRP396 4.4 0.1 1.0 CA A:CYS461 4.6 91.7 1.0 C A:SER1505 4.6 93.2 1.0 CZ3 A:TRP396 4.6 1.0 1.0 CD2 A:TRP396 4.7 0.6 1.0 N A:CYS306 4.7 96.7 1.0 CA A:CYS306 4.7 97.4 1.0 C A:CYS461 4.9 91.8 1.0 N A:SER462 5.0 92.1 1.0 CE3 A:TRP396 5.0 0.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase Complexed with Serine


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 Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1503 b:81.1 occ:1.00 OE2 B:GLU355 2.0 94.8 1.0 SG B:CYS461 2.1 94.9 1.0 N B:SER1505 2.2 74.5 1.0 SG B:CYS306 2.5 0.7 1.0 CA B:SER1505 3.0 74.3 1.0 CB B:CYS461 3.1 94.9 1.0 CD B:GLU355 3.2 94.7 1.0 CB B:SER1505 3.3 73.8 1.0 CB B:CYS306 3.5 99.2 1.0 OE1 B:GLU355 3.8 96.1 1.0 OG B:SER1505 3.8 73.0 1.0 O B:ALA304 3.9 95.5 1.0 CH2 B:TRP396 3.9 0.7 1.0 CZ2 B:TRP396 3.9 0.5 1.0 CG B:GLU355 4.4 91.4 1.0 N B:CYS306 4.4 98.2 1.0 CE2 B:TRP396 4.4 0.5 1.0 CZ3 B:TRP396 4.4 0.5 1.0 C B:SER1505 4.4 74.3 1.0 CA B:CYS461 4.5 94.6 1.0 CA B:CYS306 4.6 99.2 1.0 O B:HOH2037 4.7 59.5 1.0 C B:CYS461 4.7 94.1 1.0 N B:SER462 4.8 93.8 1.0 CD2 B:TRP396 4.9 0.1 1.0 CE3 B:TRP396 4.9 0.2 1.0 O B:ILE356 5.0 90.0 1.0 O B:SER1505 5.0 74.0 1.0

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