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Zinc in PDB 3ugt: Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form

Enzymatic activity of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form

All present enzymatic activity of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form:
6.1.1.3;

Protein crystallography data

The structure of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form, PDB code: 3ugt was solved by K.M.Peterson, J.Ling, I.Simonovic, C.Cho, D.Soll, M.Simonovic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.11 / 3.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 154.083, 157.939, 237.041, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 27.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form (pdb code 3ugt). 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 the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form, PDB code: 3ugt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3ugt

Go back to Zinc Binding Sites List in 3ugt
Zinc binding site 1 out of 4 in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form


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 - Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:70.2
occ:1.00
 ND1 A:HIS319 2.5 74.8 1.0
NE2 A:HIS184 2.5 75.8 1.0
SG A:CYS133 2.8 84.9 1.0
CD2 A:HIS184 3.2 75.1 1.0
CE1 A:HIS319 3.2 75.8 1.0
CG A:HIS319 3.5 78.0 1.0
CE1 A:HIS184 3.5 75.4 1.0
OD1 A:ASP182 3.5 82.4 1.0
OD2 A:ASP182 3.6 81.5 1.0
CB A:HIS319 3.9 76.2 1.0
CG A:ASP182 3.9 80.8 1.0
CB A:CYS133 4.1 85.8 1.0
CG A:HIS184 4.3 76.3 1.0
NE2 A:HIS319 4.3 77.1 1.0
CA A:CYS133 4.4 85.0 1.0
ND1 A:HIS184 4.4 74.0 1.0
CD2 A:HIS319 4.5 79.1 1.0
CA A:HIS319 4.5 76.8 1.0
O A:GLY183 4.5 78.2 1.0
N A:CYS133 4.5 84.7 1.0

Zinc binding site 2 out of 4 in 3ugt

Go back to Zinc Binding Sites List in 3ugt
Zinc binding site 2 out of 4 in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form


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 - Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:92.3
occ:1.00
 ND1 B:HIS319 2.5 95.5 1.0
NE2 B:HIS184 2.6 89.8 1.0
SG B:CYS133 2.8 0.2 1.0
CG B:HIS319 3.1 98.6 1.0
CE1 B:HIS319 3.3 95.7 1.0
CE1 B:HIS184 3.4 91.0 1.0
CB B:HIS319 3.5 95.5 1.0
CD2 B:HIS184 3.5 90.1 1.0
CB B:CYS133 3.8 0.5 1.0
CD2 B:HIS319 4.1 1.0 1.0
NE2 B:HIS319 4.1 98.7 1.0
CA B:CYS133 4.1 98.0 1.0
ND1 B:HIS184 4.4 87.2 1.0
CA B:HIS319 4.4 95.5 1.0
CG B:HIS184 4.5 88.0 1.0
N B:CYS133 4.6 97.7 1.0
OE1 B:GLN292 4.9 0.2 1.0

Zinc binding site 3 out of 4 in 3ugt

Go back to Zinc Binding Sites List in 3ugt
Zinc binding site 3 out of 4 in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form


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 the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn463

b:59.4
occ:1.00
 NE2 C:HIS184 2.4 62.6 1.0
SG C:CYS133 2.7 83.5 1.0
CE1 C:HIS184 3.0 65.2 1.0
CG C:HIS319 3.2 65.2 1.0
CB C:HIS319 3.4 65.2 1.0
CD2 C:HIS184 3.5 64.7 1.0
OD1 C:ASP182 3.5 65.4 1.0
ND1 C:HIS319 3.6 68.1 1.0
CD2 C:HIS319 3.6 64.2 1.0
CB C:CYS133 4.0 78.6 1.0
CA C:CYS133 4.1 76.3 1.0
CE1 C:HIS319 4.1 70.5 1.0
O C:ASN132 4.1 81.3 1.0
NE2 C:HIS319 4.1 70.8 1.0
N C:CYS133 4.2 76.9 1.0
ND1 C:HIS184 4.2 63.7 1.0
CA C:HIS319 4.3 64.8 1.0
CG C:ASP182 4.4 68.3 1.0
CG C:HIS184 4.4 64.8 1.0
OD2 C:ASP182 4.4 70.9 1.0
C C:ASN132 4.4 78.8 1.0
CE C:MET131 4.6 95.4 1.0

Zinc binding site 4 out of 4 in 3ugt

Go back to Zinc Binding Sites List in 3ugt
Zinc binding site 4 out of 4 in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form


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 the Yeast Mitochondrial Threonyl-Trna Synthetase - Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn463

b:1.0
occ:1.00
 CE1 D:HIS184 2.6 98.6 1.0
SG D:CYS133 2.7 91.0 1.0
CB D:HIS319 2.9 0.6 1.0
CD2 D:HIS319 2.9 0.8 1.0
CG D:HIS319 2.9 0.1 1.0
ND1 D:HIS184 3.0 99.9 1.0
CB D:CYS133 3.6 92.2 1.0
NE2 D:HIS184 3.6 98.8 1.0
NE2 D:HIS319 3.9 0.1 1.0
CA D:HIS319 4.0 99.7 1.0
ND1 D:HIS319 4.0 0.1 1.0
CG D:HIS184 4.1 96.3 1.0
CA D:CYS133 4.3 90.3 1.0
CE1 D:HIS319 4.4 0.5 1.0
CD2 D:HIS184 4.5 97.3 1.0
CE D:MET317 4.5 1.0 1.0
N D:HIS319 4.8 99.6 1.0
N D:CYS133 4.8 92.5 1.0
OD1 D:ASP182 4.8 91.8 1.0

Reference:

J.Ling, K.M.Peterson, I.Simonovic, C.Cho, D.Soll, M.Simonovic. Yeast Mitochondrial Threonyl-Trna Synthetase Recognizes Trna Isoacceptors By Distinct Mechanisms and Promotes Cun Codon Reassignment. Proc.Natl.Acad.Sci.Usa V. 109 3281 2012.
ISSN: ISSN 0027-8424
PubMed: 22343532
DOI: 10.1073/PNAS.1200109109
Page generated: Wed Dec 16 04:54:39 2020

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