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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

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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

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