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Zinc in PDB 7ot0: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H

Enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H

All present enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H:
6.1.1.15; 6.1.1.17;

Protein crystallography data

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H, PDB code: 7ot0 was solved by L.Pang, J.Zitko, S.V.Strelkov, S.D.Weeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.44 / 2.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.163, 93.458, 87.484, 90, 108.61, 90
R / Rfree (%) 19.7 / 25

Other elements in 7ot0:

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H also contains other interesting chemical elements:

Strontium (Sr) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H (pdb code 7ot0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H, PDB code: 7ot0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7ot0

Go back to Zinc Binding Sites List in 7ot0
Zinc binding site 1 out of 2 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1603

b:104.1
occ:1.00
SG A:CYS1448 2.3 75.6 1.0
SG A:CYS1453 2.3 84.6 1.0
SG A:CYS1495 2.4 82.5 1.0
SG A:CYS1497 2.4 105.3 1.0
CB A:CYS1453 3.3 79.4 1.0
CB A:CYS1495 3.3 85.0 1.0
CB A:CYS1448 3.4 80.4 1.0
CB A:CYS1497 3.5 100.2 1.0
N A:CYS1448 4.0 81.5 1.0
N A:CYS1497 4.3 94.1 1.0
CE1 A:PHE1447 4.3 79.8 1.0
CA A:CYS1448 4.3 80.4 1.0
CD1 A:PHE1447 4.3 70.0 1.0
CA A:CYS1497 4.5 101.7 1.0
CA A:CYS1495 4.7 86.5 1.0
CB A:ASN1500 4.7 109.0 1.0
OD1 A:ASN1500 4.8 125.2 1.0
CA A:CYS1453 4.8 71.8 1.0
N A:VAL1496 4.9 85.7 1.0
C A:CYS1495 5.0 87.6 1.0

Zinc binding site 2 out of 2 in 7ot0

Go back to Zinc Binding Sites List in 7ot0
Zinc binding site 2 out of 2 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1603

b:115.0
occ:1.00
SG B:CYS1495 2.4 95.7 1.0
SG B:CYS1448 2.4 109.9 1.0
SG B:CYS1497 2.5 129.1 1.0
SG B:CYS1453 2.6 121.6 1.0
CB B:CYS1453 3.2 116.5 1.0
CB B:CYS1495 3.3 103.5 1.0
CB B:CYS1497 3.5 125.1 1.0
CB B:CYS1448 3.6 112.5 1.0
CE1 B:PHE1447 4.1 89.1 1.0
N B:CYS1448 4.2 105.7 1.0
N B:CYS1497 4.2 121.6 1.0
CD1 B:PHE1447 4.3 84.8 1.0
CA B:CYS1497 4.5 123.5 1.0
CA B:CYS1448 4.5 115.0 1.0
CA B:CYS1453 4.7 112.8 1.0
CA B:CYS1495 4.7 112.1 1.0
N B:VAL1496 4.9 117.7 1.0

Reference:

L.Pang, S.D.Weeks, S.V.Strelkov, J.Zitko, A.Van Aerschot. Towards Novel 3-Aminopyrazinamide-Based Prolyl-Trna Synthetase Inhibitors: in Silico Modelling, Thermal Shift Assay and Structural Studies Int J Mol Sci 2021.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS22157793
Page generated: Sun Aug 22 09:53:04 2021

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