Zinc in PDB 4h2u: Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp

The structure of Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp, PDB code: 4h2u was solved by M.Luic, I.Weygand-Durasevic, N.Ivic, M.Mocibob, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.32 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.709, 100.904, 104.266, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.9

The structure of Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp (pdb code 4h2u). 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 Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp, PDB code: 4h2u:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp


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 Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:27.5 occ:0.72 OE1 A:GLU176 1.9 34.1 1.0 SG A:CYS131 2.3 28.6 1.0 O A:HOH655 2.4 45.0 1.0 SG A:CYS279 2.5 30.1 1.0 CD A:GLU176 2.9 22.1 1.0 CB A:CYS131 3.1 16.6 1.0 OE2 A:GLU176 3.2 26.9 1.0 CB A:CYS279 3.4 23.3 1.0 C43 C:PNS1000 3.6 49.4 1.0 S44 C:PNS1000 3.9 61.9 1.0 CG A:GLU176 4.2 18.1 1.0 CA A:CYS131 4.3 22.5 1.0 N A:CYS131 4.3 17.4 1.0 OH A:TYR135 4.5 30.5 1.0 C42 C:PNS1000 4.5 46.0 1.0 NE2 A:HIS257 4.6 28.5 1.0 CE1 A:HIS257 4.7 28.9 1.0 CB A:GLU176 4.7 17.3 1.0 CA A:CYS279 4.9 24.0 1.0 ND2 A:ASN255 5.0 26.1 1.0 CG2 A:VAL178 5.0 20.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp


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 Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:31.3 occ:0.71 OE1 B:GLU176 1.9 34.3 1.0 SG B:CYS131 2.4 32.7 1.0 SG B:CYS279 2.5 33.5 1.0 CD B:GLU176 2.8 25.6 1.0 O B:HOH652 2.8 45.8 1.0 OE2 B:GLU176 3.1 27.7 1.0 CB B:CYS131 3.1 20.7 1.0 S44 D:PNS1000 3.3 77.9 1.0 C43 D:PNS1000 3.4 56.8 1.0 CB B:CYS279 3.4 24.9 1.0 CG B:GLU176 4.1 22.0 1.0 N B:CYS131 4.3 19.9 1.0 CA B:CYS131 4.4 23.1 1.0 CB B:GLU176 4.6 15.5 1.0 OH B:TYR135 4.6 28.8 1.0 NE2 B:HIS257 4.6 26.5 1.0 CE1 B:HIS257 4.7 25.0 1.0 CA B:CYS279 4.9 21.8 1.0 C42 D:PNS1000 4.9 59.6 1.0

M.Mocibob, N.Ivic, M.Luic, I.Weygand-Durasevic. Adaptation of Aminoacyl-Trna Synthetase Catalytic Core to Carrier Protein Aminoacylation. Structure V. 21 614 2013.
ISSN: ISSN 0969-2126
PubMed: 23541895
DOI: 10.1016/J.STR.2013.02.017