Zinc in PDB 3vrh: Crystal Structure of PH0300

The structure of Crystal Structure of PH0300, PDB code: 3vrh was solved by H.Nakagawa, M.Kuratani, S.Goto-Ito, T.Ito, S.I.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.24 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.071, 70.071, 128.636, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.4

The binding sites of Zinc atom in the Crystal Structure of PH0300 (pdb code 3vrh). 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 PH0300, PDB code: 3vrh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PH0300


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 PH0300 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:34.1 occ:1.00 ND1 A:HIS25 2.2 33.5 1.0 SG A:CYS3 2.4 29.0 1.0 SG A:CYS22 2.5 33.0 1.0 SG A:CYS6 2.5 35.6 1.0 CE1 A:HIS25 3.1 36.2 1.0 CB A:CYS3 3.1 34.9 1.0 CG A:HIS25 3.2 34.9 1.0 CB A:CYS22 3.4 35.0 1.0 CB A:HIS25 3.6 30.6 1.0 CB A:CYS6 3.6 36.0 1.0 N A:CYS6 3.9 32.1 1.0 N A:CYS22 4.1 33.9 1.0 NE2 A:HIS25 4.2 37.2 1.0 CA A:CYS6 4.3 39.2 1.0 CD2 A:HIS25 4.3 37.9 1.0 CA A:CYS22 4.3 33.7 1.0 C A:PHE5 4.4 36.8 1.0 NH1 A:ARG8 4.6 41.1 1.0 CB A:PHE5 4.6 37.2 1.0 CA A:CYS3 4.6 34.3 1.0 N A:HIS25 4.6 32.6 1.0 N A:PHE5 4.7 35.6 1.0 CB A:ARG8 4.7 44.0 1.0 CA A:PHE5 4.7 38.6 1.0 CA A:HIS25 4.8 30.3 1.0 C A:CYS6 4.8 40.3 1.0 O A:PHE5 5.0 34.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PH0300


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 PH0300 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:40.0 occ:1.00 SG A:CYS287 2.4 37.6 1.0 SG A:CYS275 2.6 45.2 1.0 SG A:CYS272 2.6 39.4 1.0 SG A:CYS284 2.7 42.3 1.0 CB A:CYS287 3.2 39.4 1.0 CB A:CYS272 3.3 43.1 1.0 CB A:CYS284 3.5 44.6 1.0 CB A:CYS275 3.5 41.8 1.0 N A:CYS275 3.8 42.4 1.0 N A:CYS284 4.1 48.9 1.0 OH A:TYR137 4.2 32.3 1.0 N A:CYS287 4.3 35.7 1.0 CA A:CYS275 4.3 39.1 1.0 CA A:CYS284 4.3 48.9 1.0 CB A:ILE274 4.3 46.9 1.0 CA A:CYS287 4.3 34.8 1.0 CE2 A:TYR137 4.6 33.8 1.0 CA A:CYS272 4.7 47.8 1.0 C A:ILE274 4.8 46.1 1.0 CZ A:TYR137 4.8 36.0 1.0 O A:HOH565 4.8 39.9 1.0 C A:CYS284 4.9 42.4 1.0 CA A:ILE274 4.9 49.5 1.0 N A:ILE274 4.9 46.4 1.0 N A:ARG276 4.9 47.1 1.0 C A:CYS275 4.9 43.3 1.0 CG2 A:ILE274 4.9 49.6 1.0 O A:HOH516 5.0 36.6 1.0 O A:CYS284 5.0 42.3 1.0

H.Nakagawa, M.Kuratani, S.Goto-Ito, T.Ito, K.Katsura, T.Terada, M.Shirouzu, S.I.Sekine, N.Shigi, S.Yokoyama. Crystallographic and Mutational Studies on the Trna Thiouridine Synthetase Ttua. Proteins 2013.
ISSN: ESSN 1097-0134
PubMed: 23444054
DOI: 10.1002/PROT.24273