Atomistry » Zinc » PDB 1g45-1gkq » 1gax
Atomistry »
  Zinc »
    PDB 1g45-1gkq »
      1gax »

Zinc in PDB 1gax: Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue

Enzymatic activity of Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue:
6.1.1.9;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue, PDB code: 1gax was solved by S.Fukai, O.Nureki, S.Sekine, A.Shimada, J.Tao, D.G.Vassylyev, S.Yokoyama, Riken Structural Genomics/Proteomics Initiative(Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 411.810, 411.810, 81.970, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 27.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue (pdb code 1gax). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue, PDB code: 1gax:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1gax

Go back to Zinc Binding Sites List in 1gax
Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue


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 Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn998

b:54.1
occ:1.00
 SG A:CYS344 2.5 50.9 1.0
SG A:CYS347 2.5 77.7 1.0
SG A:CYS176 2.6 54.9 1.0
SG A:CYS179 2.6 68.6 1.0
CB A:CYS347 2.7 63.9 1.0
CB A:CYS344 3.1 57.2 1.0
CG A:ARG178 3.4 81.3 1.0
CB A:CYS176 3.6 47.7 1.0
CB A:CYS179 3.8 70.2 1.0
CA A:CYS347 3.9 60.1 1.0
N A:CYS347 4.0 54.7 1.0
CB A:ARG178 4.1 75.4 1.0
N A:CYS179 4.1 71.0 1.0
CA A:CYS344 4.6 59.6 1.0
C A:CYS347 4.6 62.4 1.0
CA A:CYS179 4.6 68.7 1.0
C A:ARG346 4.6 52.1 1.0
CD A:ARG178 4.7 86.4 1.0
N A:GLY348 4.9 63.0 1.0
O A:CYS344 5.0 62.9 1.0
C A:ARG178 5.0 71.1 1.0

Zinc binding site 2 out of 4 in 1gax

Go back to Zinc Binding Sites List in 1gax
Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue


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 Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn999

b:42.8
occ:1.00
 SG A:CYS438 2.3 61.7 1.0
CB A:CYS420 2.3 46.6 1.0
SG A:CYS441 2.6 38.0 1.0
SG A:CYS417 2.8 25.0 1.0
N A:CYS441 2.9 34.8 1.0
CB A:CYS441 2.9 40.4 1.0
CB A:CYS417 3.1 41.3 1.0
CB A:CYS438 3.3 51.6 1.0
SG A:CYS420 3.3 65.3 1.0
CA A:CYS420 3.4 44.9 1.0
CB A:ALA440 3.4 26.9 1.0
N A:CYS420 3.4 40.0 1.0
CA A:CYS441 3.5 38.1 1.0
C A:ALA440 3.9 36.8 1.0
CA A:ALA440 4.2 38.2 1.0
CB A:ALA422 4.2 43.8 1.0
C A:CYS420 4.2 48.2 1.0
C A:CYS441 4.4 45.5 1.0
N A:ALA440 4.5 41.3 1.0
N A:GLN421 4.6 50.5 1.0
N A:ALA422 4.6 52.3 1.0
N A:GLY442 4.6 46.9 1.0
CA A:CYS417 4.7 45.9 1.0
C A:ASP419 4.7 44.6 1.0
CA A:CYS438 4.7 45.0 1.0
O A:CYS420 4.9 49.6 1.0
O A:ALA440 5.0 31.3 1.0
C A:CYS438 5.0 39.6 1.0
CA A:ALA422 5.0 49.6 1.0

Zinc binding site 3 out of 4 in 1gax

Go back to Zinc Binding Sites List in 1gax
Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue


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 Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn998

b:65.4
occ:1.00
 SG B:CYS347 2.3 76.4 1.0
SG B:CYS344 2.5 58.7 1.0
SG B:CYS176 2.5 60.0 1.0
SG B:CYS179 2.6 65.1 1.0
CB B:CYS347 3.1 76.3 1.0
CB B:CYS344 3.1 62.2 1.0
CB B:CYS179 3.5 65.8 1.0
N B:CYS179 3.8 68.4 1.0
CB B:ARG178 3.8 76.7 1.0
N B:CYS347 3.9 72.8 1.0
CB B:CYS176 4.0 52.3 1.0
CA B:CYS347 4.0 75.5 1.0
CG B:ARG178 4.1 81.7 1.0
CA B:CYS179 4.3 63.7 1.0
CA B:CYS344 4.6 64.9 1.0
C B:CYS347 4.7 77.4 1.0
C B:ARG178 4.8 70.0 1.0
CA B:ARG178 4.8 70.5 1.0
N B:GLY348 4.8 76.6 1.0
O B:CYS176 5.0 50.6 1.0

Zinc binding site 4 out of 4 in 1gax

Go back to Zinc Binding Sites List in 1gax
Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Thermus Thermophilus Valyl-Trna Synthetase Complexed with Trna(Val) and Valyl-Adenylate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn999

b:39.0
occ:1.00
 SG B:CYS438 2.2 45.5 1.0
CB B:CYS420 2.5 44.7 1.0
SG B:CYS417 2.6 17.1 1.0
SG B:CYS441 2.7 47.2 1.0
CB B:CYS417 2.9 39.6 1.0
CB B:CYS441 3.0 37.7 1.0
CB B:CYS438 3.1 42.0 1.0
N B:CYS441 3.3 30.8 1.0
N B:CYS420 3.5 40.8 1.0
SG B:CYS420 3.5 59.6 1.0
CA B:CYS420 3.5 46.2 1.0
CA B:CYS441 3.7 35.0 1.0
CB B:ALA440 4.0 33.9 1.0
CB B:ALA422 4.1 43.1 1.0
C B:CYS420 4.2 53.9 1.0
CA B:CYS417 4.4 43.9 1.0
C B:ALA440 4.4 36.5 1.0
N B:ALA422 4.4 51.8 1.0
N B:GLN421 4.5 57.4 1.0
C B:CYS441 4.5 42.9 1.0
CA B:CYS438 4.6 38.6 1.0
CA B:ALA440 4.6 38.5 1.0
N B:GLY442 4.7 44.3 1.0
C B:ASP419 4.7 47.4 1.0
N B:ALA440 4.8 41.6 1.0
CA B:ALA422 4.9 47.0 1.0

Reference:

S.Fukai, O.Nureki, S.Sekine, A.Shimada, J.Tao, D.G.Vassylyev, S.Yokoyama. Structural Basis For Double-Sieve Discrimination of L-Valine From L-Isoleucine and L-Threonine By the Complex of Trna(Val) and Valyl-Trna Synthetase. Cell(Cambridge,Mass.) V. 103 793 2000.
ISSN: ISSN 0092-8674
PubMed: 11114335
DOI: 10.1016/S0092-8674(00)00182-3
Page generated: Sun Oct 13 01:28:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy