Zinc in PDB 4yye: Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with the Canonical Trnathr and Threonyl Sulfamoyl Adenylate

Enzymatic activity of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with the Canonical Trnathr and Threonyl Sulfamoyl Adenylate

All present enzymatic activity of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with the Canonical Trnathr and Threonyl Sulfamoyl Adenylate:
6.1.1.3;

Protein crystallography data

The structure of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with the Canonical Trnathr and Threonyl Sulfamoyl Adenylate, PDB code: 4yye was solved by K.M.Holman, M.Simonovic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.45 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.021, 77.228, 86.157, 63.86, 75.04, 89.39
R / Rfree (%) 16 / 20.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with the Canonical Trnathr and Threonyl Sulfamoyl Adenylate (pdb code 4yye). 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 the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with the Canonical Trnathr and Threonyl Sulfamoyl Adenylate, PDB code: 4yye:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4yye

Go back to Zinc Binding Sites List in 4yye
Zinc binding site 1 out of 2 in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with the Canonical Trnathr and Threonyl Sulfamoyl Adenylate


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 the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with the Canonical Trnathr and Threonyl Sulfamoyl Adenylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:19.0
occ:1.00
SG A:CYS133 1.8 39.2 1.0
NE2 A:HIS184 2.1 15.4 1.0
ND1 A:HIS319 2.1 17.5 1.0
N A:TSB502 2.2 14.7 1.0
OG1 A:TSB502 2.3 16.7 1.0
CE1 A:HIS319 3.0 18.6 1.0
CA A:TSB502 3.0 17.4 1.0
CE1 A:HIS184 3.0 18.3 1.0
CD2 A:HIS184 3.1 17.6 1.0
CB A:TSB502 3.2 16.3 1.0
CG A:HIS319 3.2 17.4 1.0
CB A:CYS133 3.3 28.6 1.0
CB A:HIS319 3.6 16.5 1.0
O A:HOH617 3.8 15.7 1.0
NE2 A:HIS319 4.1 19.2 1.0
ND1 A:HIS184 4.2 19.7 1.0
CG A:HIS184 4.2 17.0 1.0
N A:CYS133 4.2 20.6 1.0
CD2 A:HIS319 4.2 17.9 1.0
CA A:CYS133 4.2 22.2 1.0
OD1 A:ASP182 4.3 17.9 1.0
CG2 A:TSB502 4.3 18.4 1.0
OD2 A:ASP182 4.4 23.9 1.0
OH A:TYR270 4.4 19.6 1.0
C A:TSB502 4.4 18.0 1.0
CA A:HIS319 4.6 15.7 1.0
CG A:ASP182 4.8 21.1 1.0
NE2 A:GLN292 4.9 19.9 1.0
O A:TSB502 4.9 16.0 1.0
SD A:MET131 4.9 28.9 1.0

Zinc binding site 2 out of 2 in 4yye

Go back to Zinc Binding Sites List in 4yye
Zinc binding site 2 out of 2 in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with the Canonical Trnathr and Threonyl Sulfamoyl Adenylate


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 the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with the Canonical Trnathr and Threonyl Sulfamoyl Adenylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:19.1
occ:1.00
NE2 B:HIS184 2.0 17.9 1.0
ND1 B:HIS319 2.1 19.6 1.0
SG B:CYS133 2.2 22.7 1.0
N B:TSB502 2.2 15.6 1.0
OG1 B:TSB502 2.4 14.1 1.0
CE1 B:HIS184 3.0 16.1 1.0
CA B:TSB502 3.0 14.0 1.0
CD2 B:HIS184 3.0 18.0 1.0
CE1 B:HIS319 3.1 20.2 1.0
CG B:HIS319 3.2 14.9 1.0
CB B:TSB502 3.2 17.9 1.0
CB B:HIS319 3.5 14.3 1.0
CB B:CYS133 3.6 20.1 1.0
O B:HOH610 3.8 15.3 1.0
ND1 B:HIS184 4.1 18.7 1.0
CG B:HIS184 4.2 19.3 1.0
OH B:TYR270 4.2 22.3 1.0
NE2 B:HIS319 4.2 17.7 1.0
CA B:CYS133 4.3 19.0 1.0
OD2 B:ASP182 4.3 22.5 1.0
CD2 B:HIS319 4.3 15.8 1.0
N B:CYS133 4.3 18.4 1.0
OD1 B:ASP182 4.3 17.2 1.0
C B:TSB502 4.4 15.2 1.0
CG2 B:TSB502 4.4 13.9 1.0
CA B:HIS319 4.5 12.2 1.0
CG B:ASP182 4.8 20.3 1.0
O B:TSB502 4.8 19.3 1.0
CZ B:TYR270 5.0 22.2 1.0
OE1 B:GLN292 5.0 24.2 1.0

Reference:

K.M.Holman, J.Wu, J.Ling, M.Simonovic. The Crystal Structure of Yeast Mitochondrial Thrrs in Complex with the Canonical Threonine Trna. Nucleic Acids Res. V. 44 1428 2016.
ISSN: ESSN 1362-4962
PubMed: 26704982
DOI: 10.1093/NAR/GKV1501
Page generated: Wed Dec 16 05:58:36 2020

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