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Strontium in PDB 7ot3: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B

Enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B

All present enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B:
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 3B, PDB code: 7ot3 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) 54.77 / 2.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.871, 92.422, 87.26, 90, 108.88, 90
R / Rfree (%) 21.8 / 27.6

Other elements in 7ot3:

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 2 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B (pdb code 7ot3). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 4 binding sites of Strontium where determined in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B, PDB code: 7ot3:
Jump to Strontium binding site number: 1; 2; 3; 4;

Strontium binding site 1 out of 4 in 7ot3

Go back to Strontium Binding Sites List in 7ot3
Strontium binding site 1 out of 4 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1604

b:184.2
occ:1.00
O A:HOH1713 2.7 138.4 1.0
O A:HOH1704 2.7 157.7 1.0
O A:ASP1220 2.9 137.7 1.0
C A:ASP1220 3.8 87.3 1.0
CA A:ASP1220 4.1 99.0 1.0
CB A:ASP1220 4.1 112.6 1.0
OE2 A:GLU1212 4.1 144.1 1.0
NZ A:LYS1215 4.3 98.4 1.0
OD1 A:ASP1220 4.5 140.6 1.0
CG A:ASP1220 4.7 133.4 1.0
N A:TYR1221 4.9 86.8 1.0

Strontium binding site 2 out of 4 in 7ot3

Go back to Strontium Binding Sites List in 7ot3
Strontium binding site 2 out of 4 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1605

b:233.3
occ:1.00
O A:HOH1712 2.6 220.3 1.0
O A:HOH1708 2.6 169.4 1.0
O A:HOH1714 2.7 234.5 1.0
O A:GLY1072 2.8 98.5 1.0
C A:GLY1072 3.8 91.7 1.0
CA A:GLY1072 4.2 82.0 1.0
OE1 A:GLU1074 4.2 108.8 1.0
CD A:GLU1074 4.3 97.3 1.0
CG A:GLU1074 4.5 90.1 1.0
OE2 A:GLU1074 4.8 114.4 1.0
N A:VAL1073 4.9 85.0 1.0

Strontium binding site 3 out of 4 in 7ot3

Go back to Strontium Binding Sites List in 7ot3
Strontium binding site 3 out of 4 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1606

b:237.5
occ:1.00
OD1 A:ASP1096 2.7 109.5 1.0
O A:HOH1711 2.7 113.3 1.0
O A:ASP1096 2.9 111.0 1.0
OE1 A:GLU1100 3.2 149.2 1.0
CG A:ASP1096 3.9 111.5 1.0
C A:ASP1096 3.9 83.5 1.0
CA A:ASP1096 4.2 93.4 1.0
CD A:GLU1100 4.4 140.4 1.0
CB A:ASP1096 4.7 88.1 1.0
OD2 A:ASP1096 4.8 100.9 1.0
CG A:PRO1099 4.9 121.2 1.0

Strontium binding site 4 out of 4 in 7ot3

Go back to Strontium Binding Sites List in 7ot3
Strontium binding site 4 out of 4 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1604

b:256.1
occ:1.00
OD1 B:ASP1096 2.7 152.3 1.0
O B:ASP1096 3.2 156.2 1.0
CG B:ASP1096 3.9 132.0 1.0
C B:ASP1096 4.0 142.6 1.0
CG B:PRO1099 4.1 132.7 1.0
CA B:ASP1096 4.1 136.6 1.0
CB B:ASP1096 4.6 127.9 1.0
OD2 B:ASP1096 4.8 120.8 1.0
CD B:PRO1099 4.8 119.1 1.0
O B:ALA1095 4.9 119.8 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: Sat Aug 21 17:34:10 2021

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