Zinc in PDB 1v4p: Crystal Structure of Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3

All present enzymatic activity of Crystal Structure of Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3:
6.1.1.7;

The structure of Crystal Structure of Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3, PDB code: 1v4p was solved by J.Ishijima, K.Yutani, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.04 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.802, 97.861, 60.872, 90.00, 96.51, 90.00
R / Rfree (%)	20.6 / 22.7

The binding sites of Zinc atom in the Crystal Structure of Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3 (pdb code 1v4p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3, PDB code: 1v4p:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3


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 Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:16.6 occ:1.00 NE2 A:HIS13 2.1 14.6 1.0 NE2 A:HIS120 2.1 17.9 1.0 NE2 A:HIS9 2.1 18.3 1.0 SG A:CYS116 2.3 17.4 1.0 CD2 A:HIS120 3.0 19.5 1.0 CD2 A:HIS13 3.0 14.6 1.0 CE1 A:HIS9 3.0 16.7 1.0 CD2 A:HIS9 3.0 18.5 1.0 CE1 A:HIS13 3.0 17.3 1.0 CE1 A:HIS120 3.1 20.1 1.0 CB A:CYS116 3.3 17.2 1.0 CG A:HIS120 4.1 20.8 1.0 CG2 A:VAL106 4.1 20.6 1.0 ND1 A:HIS9 4.1 18.6 1.0 ND1 A:HIS13 4.1 18.1 1.0 ND1 A:HIS120 4.2 20.7 1.0 CG A:HIS9 4.2 17.9 1.0 CG A:HIS13 4.2 15.3 1.0 CB A:LYS118 4.4 26.9 1.0 CA A:CYS116 4.7 16.7 1.0 N A:LYS118 4.9 26.0 1.0 OD1 A:ASN114 4.9 15.1 1.0 O A:HIS9 4.9 17.0 1.0 CB A:VAL106 5.0 21.1 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3


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 Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:13.3 occ:1.00 NE2 B:HIS120 2.0 15.3 1.0 NE2 B:HIS13 2.0 12.2 1.0 NE2 B:HIS9 2.1 12.5 1.0 SG B:CYS116 2.3 14.7 1.0 CE1 B:HIS9 2.9 15.8 1.0 CE1 B:HIS120 3.0 15.4 1.0 CD2 B:HIS120 3.0 14.9 1.0 CD2 B:HIS13 3.0 12.6 1.0 CE1 B:HIS13 3.0 16.0 1.0 CD2 B:HIS9 3.1 13.9 1.0 CB B:CYS116 3.3 14.1 1.0 ND1 B:HIS120 4.1 15.8 1.0 ND1 B:HIS9 4.1 14.2 1.0 CG B:HIS120 4.1 15.0 1.0 ND1 B:HIS13 4.1 14.8 1.0 CG B:HIS13 4.2 12.4 1.0 CG B:HIS9 4.2 12.6 1.0 CG2 B:VAL106 4.3 16.5 1.0 CB B:LYS118 4.5 19.4 1.0 O B:HOH1100 4.6 29.4 1.0 CA B:CYS116 4.7 14.1 1.0 O B:HOH1098 4.9 27.4 1.0 O B:HIS9 4.9 12.6 1.0 N B:LYS118 5.0 18.4 1.0 O B:LYS118 5.0 17.3 1.0 OD1 B:ASN114 5.0 15.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Alanyl-Trna Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:11.5 occ:1.00 NE2 C:HIS13 2.0 8.1 1.0 NE2 C:HIS120 2.0 11.2 1.0 NE2 C:HIS9 2.1 13.1 1.0 SG C:CYS116 2.3 10.7 1.0 CE1 C:HIS120 3.0 12.8 1.0 CE1 C:HIS13 3.0 13.0 1.0 CD2 C:HIS13 3.0 10.4 1.0 CD2 C:HIS120 3.0 12.0 1.0 CE1 C:HIS9 3.1 12.4 1.0 CD2 C:HIS9 3.1 10.4 1.0 CB C:CYS116 3.3 12.0 1.0 ND1 C:HIS13 4.1 13.8 1.0 ND1 C:HIS120 4.1 14.4 1.0 CG C:HIS13 4.1 10.8 1.0 CG C:HIS120 4.2 12.7 1.0 ND1 C:HIS9 4.2 11.4 1.0 CG2 C:VAL106 4.2 14.8 1.0 CG C:HIS9 4.2 10.4 1.0 CB C:LYS118 4.5 14.0 1.0 O C:HOH1049 4.6 24.5 1.0 CA C:CYS116 4.7 11.9 1.0 OD1 C:ASN114 4.9 12.8 1.0 O C:HIS9 4.9 9.7 1.0 N C:LYS118 5.0 12.3 1.0

J.Ishijima, Y.Uchida, C.Kuroishi, C.Tuzuki, N.Takahashi, N.Okazaki, K.Yutani, M.Miyano. Crystal Structure of Alanyl-Trna Synthetase Editing-Domain Homolog (PH0574) From A Hyperthermophile, Pyrococcus Horikoshii OT3 at 1.45 A Resolution Proteins V. 62 1133 2006.
ISSN: ISSN 0887-3585
PubMed: 16374837
DOI: 10.1002/PROT.20760