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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy