Zinc in PDB 7ot2: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J

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

All present enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J:
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 4J, PDB code: 7ot2 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) 54.91 / 2.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.017, 92.839, 87.933, 90, 108.99, 90
R / Rfree (%) 19.4 / 25.3

Other elements in 7ot2:

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

Fluorine (F) 6 atoms
Strontium (Sr) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J (pdb code 7ot2). 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 4J, PDB code: 7ot2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7ot2

Go back to Zinc Binding Sites List in 7ot2
Zinc binding site 1 out of 2 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J


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 4J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1603

b:92.5
occ:1.00
SG A:CYS1453 2.4 101.6 1.0
SG A:CYS1448 2.4 87.4 1.0
SG A:CYS1495 2.5 103.2 1.0
SG A:CYS1497 2.6 115.6 1.0
CB A:CYS1448 3.1 87.0 1.0
CB A:CYS1453 3.2 105.0 1.0
CB A:CYS1495 3.3 108.4 1.0
CB A:CYS1497 3.7 113.8 1.0
N A:CYS1448 3.8 90.4 1.0
CA A:CYS1448 4.0 85.5 1.0
N A:CYS1497 4.3 108.4 1.0
CE1 A:PHE1447 4.4 95.8 1.0
CD1 A:PHE1447 4.4 90.1 1.0
OD1 A:ASN1500 4.5 122.1 1.0
CA A:CYS1497 4.7 113.4 1.0
CA A:CYS1495 4.7 106.4 1.0
CA A:CYS1453 4.7 106.5 1.0
C A:CYS1448 4.9 89.4 1.0
CB A:ASN1500 4.9 109.1 1.0
C A:PHE1447 4.9 89.8 1.0
N A:VAL1496 4.9 103.9 1.0

Zinc binding site 2 out of 2 in 7ot2

Go back to Zinc Binding Sites List in 7ot2
Zinc binding site 2 out of 2 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J


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 4J within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1603

b:107.6
occ:1.00
SG B:CYS1453 2.2 180.7 1.0
SG B:CYS1495 2.4 106.9 1.0
SG B:CYS1448 2.6 116.3 1.0
SG B:CYS1497 2.7 138.7 1.0
CB B:CYS1453 3.0 135.5 1.0
CB B:CYS1497 3.1 134.0 1.0
CB B:CYS1495 3.4 119.3 1.0
CB B:CYS1448 3.6 121.9 1.0
N B:CYS1497 3.9 134.5 1.0
N B:CYS1448 4.0 118.3 1.0
CA B:CYS1497 4.1 142.6 1.0
CD1 B:PHE1447 4.4 108.6 1.0
CA B:CYS1448 4.5 123.2 1.0
CE1 B:PHE1447 4.5 118.1 1.0
CA B:CYS1453 4.5 126.7 1.0
N B:VAL1496 4.6 117.9 1.0
CA B:CYS1495 4.8 115.5 1.0
C B:VAL1496 4.9 133.2 1.0
CG2 B:VAL1496 4.9 112.1 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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