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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 1v4p

Go back to Zinc Binding Sites List in 1v4p
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 1v4p

Go back to Zinc Binding Sites List in 1v4p
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 1v4p

Go back to Zinc Binding Sites List in 1v4p
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

Reference:

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
Page generated: Mon Jan 25 16:14:52 2021

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