Zinc in PDB 4h2y: Crystal Structure of Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Atp

The structure of Crystal Structure of Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Atp, PDB code: 4h2y 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)	46.08 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.863, 101.587, 103.424, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21

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

Magnesium

(Mg)

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 Atp (pdb code 4h2y). 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 Atp, PDB code: 4h2y:
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 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 Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:38.8 occ:0.39 OE1 A:GLU176 1.9 37.1 1.0 SG A:CYS279 2.6 35.0 1.0 O A:HOH626 2.6 54.0 1.0 SG A:CYS131 2.7 35.4 1.0 CD A:GLU176 2.9 23.1 1.0 OE2 A:GLU176 3.1 34.1 1.0 CB A:CYS131 3.2 20.8 1.0 CB A:CYS279 3.6 16.8 1.0 S44 D:PNS101 3.7 63.3 1.0 CG A:GLU176 4.2 18.4 1.0 CA A:CYS131 4.4 18.0 1.0 N A:CYS131 4.4 17.5 1.0 NE2 A:HIS257 4.4 27.1 1.0 CE1 A:HIS257 4.5 25.6 1.0 OH A:TYR135 4.6 28.6 1.0 O A:HOH629 4.8 50.3 1.0 CB A:GLU176 4.8 13.5 1.0 O A:HOH633 4.9 34.3 1.0 CA A:CYS279 5.0 21.4 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 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 Engineered Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Carrier Protein From Agrobacterium Tumefaciens and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:32.7 occ:0.57 OE1 B:GLU176 1.9 37.6 1.0 SG B:CYS279 2.4 30.9 1.0 SG B:CYS131 2.6 38.1 1.0 O B:HOH676 2.7 41.7 1.0 CD B:GLU176 2.9 24.9 1.0 OE2 B:GLU176 3.2 32.8 1.0 CB B:CYS131 3.3 21.7 1.0 CB B:CYS279 3.4 23.3 1.0 S44 C:PNS101 3.5 80.0 1.0 CG B:GLU176 4.3 19.3 1.0 N B:CYS131 4.5 17.4 1.0 CA B:CYS131 4.5 20.3 1.0 ND2 B:ASN255 4.7 33.7 1.0 CE1 B:HIS257 4.7 26.1 1.0 OH B:TYR135 4.7 35.0 1.0 NE2 B:HIS257 4.7 27.4 1.0 CB B:GLU176 4.7 17.9 1.0 CA B:CYS279 4.8 19.6 1.0 C43 C:PNS101 4.9 57.2 1.0 O B:HOH677 5.0 43.8 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