Zinc in PDB 4h2w: Crystal Structure of Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Amp

The structure of Crystal Structure of Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Amp, PDB code: 4h2w 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)	45.76 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.695, 101.248, 102.997, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.6

The structure of Crystal Structure of Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Amp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Amp (pdb code 4h2w). 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 Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Amp, PDB code: 4h2w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Amp


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 Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:25.9 occ:0.37 OE1 A:GLU176 1.9 34.1 1.0 SG A:CYS279 2.4 26.6 1.0 O A:HOH661 2.7 54.5 1.0 SG A:CYS131 2.7 33.1 1.0 CD A:GLU176 2.8 21.9 1.0 OE2 A:GLU176 3.1 36.2 1.0 CB A:CYS131 3.2 19.0 1.0 CB A:CYS279 3.4 16.4 1.0 S44 D:PNS101 3.8 57.8 1.0 CG A:GLU176 4.2 16.6 1.0 CA A:CYS131 4.4 19.2 1.0 N A:CYS131 4.5 17.6 1.0 NE2 A:HIS257 4.5 22.9 1.0 CE1 A:HIS257 4.5 21.3 1.0 C43 D:PNS101 4.5 64.7 1.0 OH A:TYR135 4.6 26.1 1.0 CB A:GLU176 4.7 12.8 1.0 CA A:CYS279 4.8 14.3 1.0 ND2 A:ASN255 4.9 29.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Amp


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 Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:21.0 occ:0.53 OE1 B:GLU176 1.9 32.5 1.0 O B:HOH520 2.1 44.9 1.0 SG B:CYS279 2.4 24.3 1.0 SG B:CYS131 2.5 30.8 1.0 CD B:GLU176 2.8 24.0 1.0 OE2 B:GLU176 3.0 26.1 1.0 CB B:CYS131 3.2 20.3 1.0 CB B:CYS279 3.3 17.1 1.0 S44 C:PNS101 4.1 61.1 1.0 CG B:GLU176 4.2 19.2 1.0 CA B:CYS131 4.4 15.9 1.0 N B:CYS131 4.4 13.7 1.0 C43 C:PNS101 4.6 55.5 1.0 OH B:TYR135 4.6 27.7 1.0 CB B:GLU176 4.7 15.5 1.0 CE1 B:HIS257 4.7 19.7 1.0 CA B:CYS279 4.8 20.1 1.0 NE2 B:HIS257 4.8 21.2 1.0 ND2 B:ASN255 4.8 19.4 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