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Zinc in PDB 1h4s: Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg) and A Prolyl-Adenylate Analogue

Enzymatic activity of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg) and A Prolyl-Adenylate Analogue

All present enzymatic activity of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg) and A Prolyl-Adenylate Analogue:
6.1.1.15;

Protein crystallography data

The structure of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg) and A Prolyl-Adenylate Analogue, PDB code: 1h4s was solved by A.Yaremchuk, M.Tukalo, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20 / 2.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 140.780, 140.780, 236.970, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg) and A Prolyl-Adenylate Analogue (pdb code 1h4s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg) and A Prolyl-Adenylate Analogue, PDB code: 1h4s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1h4s

Go back to Zinc Binding Sites List in 1h4s
Zinc binding site 1 out of 2 in the Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg) and A Prolyl-Adenylate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg) and A Prolyl-Adenylate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn490

b:50.9
occ:1.00
 SG A:CYS432 2.3 45.4 1.0
SG A:CYS458 2.3 42.7 1.0
SG A:CYS427 2.4 52.7 1.0
SG A:CYS461 2.4 59.4 1.0
CB A:CYS432 3.2 44.0 1.0
CB A:CYS458 3.2 44.4 1.0
CB A:CYS427 3.3 41.6 1.0
CB A:CYS461 3.3 55.2 1.0
N A:CYS461 3.7 56.4 1.0
NE2 A:HIS426 3.9 42.5 1.0
N A:CYS427 3.9 49.1 1.0
CA A:CYS461 4.1 56.0 1.0
CD2 A:HIS426 4.2 42.5 1.0
CA A:CYS427 4.2 50.0 1.0
CE1 A:HIS426 4.3 42.0 1.0
NH2 A:ARG463 4.6 62.7 1.0
CA A:CYS432 4.7 45.9 1.0
CA A:CYS458 4.7 47.8 1.0
CG A:HIS426 4.7 37.8 1.0
ND1 A:HIS426 4.7 40.0 1.0
CB A:ARG460 4.8 48.5 1.0
C A:ARG460 4.8 54.5 1.0
NE A:ARG463 4.9 55.2 1.0
C A:CYS461 4.9 54.2 1.0
N A:ARG460 5.0 42.2 1.0

Zinc binding site 2 out of 2 in 1h4s

Go back to Zinc Binding Sites List in 1h4s
Zinc binding site 2 out of 2 in the Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg) and A Prolyl-Adenylate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg) and A Prolyl-Adenylate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn490

b:65.6
occ:1.00
 SG B:CYS427 2.3 55.6 1.0
SG B:CYS432 2.3 63.0 1.0
SG B:CYS458 2.3 64.9 1.0
SG B:CYS461 2.4 71.4 1.0
CB B:CYS427 3.2 51.3 1.0
CB B:CYS432 3.2 60.2 1.0
CB B:CYS458 3.2 61.6 1.0
CB B:CYS461 3.3 64.3 1.0
N B:CYS461 3.7 64.4 1.0
N B:CYS427 3.8 48.8 1.0
CA B:CYS461 4.1 64.6 1.0
CA B:CYS427 4.1 52.4 1.0
NE2 B:HIS426 4.2 54.7 1.0
CE1 B:HIS426 4.3 56.3 1.0
CD2 B:HIS426 4.5 51.8 1.0
ND1 B:HIS426 4.6 55.8 1.0
CA B:CYS458 4.7 60.5 1.0
CA B:CYS432 4.7 58.1 1.0
NH2 B:ARG463 4.7 98.1 1.0
CG B:HIS426 4.8 53.0 1.0
C B:ARG460 4.8 64.4 1.0
N B:GLY462 4.8 62.0 1.0
C B:CYS461 4.9 66.6 1.0
CB B:ARG460 4.9 59.8 1.0
NE B:ARG463 4.9 90.9 1.0
C B:HIS426 5.0 49.3 1.0
N B:ARG460 5.0 60.6 1.0

Reference:

A.Yaremchuk, M.Tukalo, M.Grotli, S.Cusack. A Succession of Substrate Induced Conformational Changes Ensures the Amino Acid Specificity of Thermus Thermophilus Prolyl-Trna Synthetase: Comparison with Histidyl-Trna Synthetase J.Mol.Biol. V. 309 989 2001.
ISSN: ISSN 0022-2836
PubMed: 11399074
DOI: 10.1006/JMBI.2001.4712
Page generated: Fri Sep 25 21:47:40 2020
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