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Zinc in PDB 1evk: Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with the Ligand Threonine

Enzymatic activity of Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with the Ligand Threonine

All present enzymatic activity of Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with the Ligand Threonine:
6.1.1.3;

Protein crystallography data

The structure of Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with the Ligand Threonine, PDB code: 1evk was solved by R.Sankaranarayanan, A.C.Dock-Bregeon, B.Rees, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.050, 117.340, 87.080, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with the Ligand Threonine (pdb code 1evk). 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 A Truncated Form of Threonyl-Trna Synthetase with the Ligand Threonine, PDB code: 1evk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1evk

Go back to Zinc Binding Sites List in 1evk
Zinc binding site 1 out of 2 in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with the Ligand Threonine


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 A Truncated Form of Threonyl-Trna Synthetase with the Ligand Threonine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:40.7
occ:1.00
NE2 A:HIS385 2.3 35.8 1.0
ND1 A:HIS511 2.5 44.5 1.0
SG A:CYS334 2.5 37.7 1.0
O A:HOH842 3.1 48.4 1.0
CD2 A:HIS385 3.1 35.8 1.0
CE1 A:HIS385 3.3 35.3 1.0
CB A:CYS334 3.4 34.2 1.0
CG A:HIS511 3.4 44.5 1.0
CE1 A:HIS511 3.4 45.8 1.0
CB A:HIS511 3.6 42.2 1.0
O A:HOH673 3.7 36.9 1.0
CA A:CYS334 4.0 33.5 1.0
N A:CYS334 4.2 32.1 1.0
OD1 A:ASP383 4.2 49.0 1.0
CG A:HIS385 4.3 35.4 1.0
OD2 A:ASP383 4.3 48.2 1.0
ND1 A:HIS385 4.4 36.6 1.0
NE2 A:HIS511 4.5 45.6 1.0
CD2 A:HIS511 4.5 45.5 1.0
CA A:HIS511 4.6 40.8 1.0
CG A:ASP383 4.7 46.1 1.0

Zinc binding site 2 out of 2 in 1evk

Go back to Zinc Binding Sites List in 1evk
Zinc binding site 2 out of 2 in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with the Ligand Threonine


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 A Truncated Form of Threonyl-Trna Synthetase with the Ligand Threonine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:22.4
occ:1.00
NE2 B:HIS385 2.2 21.0 1.0
ND1 B:HIS511 2.3 19.6 1.0
N B:THR801 2.3 22.1 1.0
OG1 B:THR801 2.5 24.8 1.0
SG B:CYS334 2.5 20.8 1.0
CD2 B:HIS385 3.1 15.6 1.0
CA B:THR801 3.1 21.4 1.0
CG B:HIS511 3.2 20.8 1.0
CE1 B:HIS511 3.2 19.9 1.0
CE1 B:HIS385 3.2 17.8 1.0
CB B:THR801 3.3 23.7 1.0
CB B:CYS334 3.4 19.3 1.0
CB B:HIS511 3.5 17.9 1.0
O B:HOH806 3.8 19.4 1.0
OD2 B:ASP383 4.1 20.7 1.0
OH B:TYR462 4.2 24.1 1.0
CG B:HIS385 4.3 20.5 1.0
NE2 B:HIS511 4.3 22.0 1.0
ND1 B:HIS385 4.3 18.3 1.0
CD2 B:HIS511 4.3 22.2 1.0
CA B:CYS334 4.3 20.5 1.0
N B:CYS334 4.3 18.4 1.0
OD1 B:ASP383 4.4 18.0 1.0
C B:THR801 4.5 22.0 1.0
CG2 B:THR801 4.5 24.1 1.0
CA B:HIS511 4.6 21.4 1.0
CG B:ASP383 4.7 21.6 1.0
OE1 B:GLN484 4.8 24.1 1.0
CZ B:TYR462 4.8 24.4 1.0
O B:THR801 4.9 22.4 1.0
SD B:MET332 5.0 22.8 1.0

Reference:

R.Sankaranarayanan, A.C.Dock-Bregeon, B.Rees, M.Bovee, J.Caillet, P.Romby, C.S.Francklyn, D.Moras. Zinc Ion Mediated Amino Acid Discrimination By Threonyl-Trna Synthetase. Nat.Struct.Biol. V. 7 461 2000.
ISSN: ISSN 1072-8368
PubMed: 10881191
DOI: 10.1038/75856
Page generated: Wed Dec 16 02:48:35 2020

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