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Calcium in PDB 7f9d: Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96

Enzymatic activity of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96

All present enzymatic activity of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96:
6.1.1.15; 6.1.1.17;

Protein crystallography data

The structure of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96, PDB code: 7f9d was solved by Y.Manickam, N.Malhotra, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.13 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.49, 106.13, 145.55, 90, 90, 90
R / Rfree (%) 18.7 / 26.3

Other elements in 7f9d:

The structure of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 6 atoms
Fluorine (F) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96 (pdb code 7f9d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96, PDB code: 7f9d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7f9d

Go back to Calcium Binding Sites List in 7f9d
Calcium binding site 1 out of 4 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1903

b:72.9
occ:1.00
 O A:HOH2050 2.4 59.2 1.0
OE1 A:GLU1100 2.6 81.1 1.0
O A:ASP1096 2.8 43.6 1.0
O A:HOH2017 3.0 51.7 1.0
OD1 A:ASP1096 3.5 61.5 1.0
CD A:GLU1100 3.6 72.8 1.0
C A:ASP1096 3.9 47.1 1.0
OE2 A:GLU1100 4.0 83.2 1.0
CG A:ASP1096 4.0 57.8 1.0
OD2 A:ASP1096 4.4 58.9 1.0
CA A:ASP1096 4.6 56.7 1.0
OE1 A:GLU1154 4.6 93.0 1.0
N A:PHE1097 4.9 46.5 1.0
CA A:PHE1097 4.9 48.5 1.0
CB A:ASP1096 4.9 54.0 1.0
CG A:GLU1100 4.9 51.1 1.0

Calcium binding site 2 out of 4 in 7f9d

Go back to Calcium Binding Sites List in 7f9d
Calcium binding site 2 out of 4 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1904

b:60.6
occ:0.91
 O A:HOH2039 2.5 55.6 1.0
OE2 A:GLU1450 2.5 65.0 1.0
OE1 A:GLU1450 3.0 62.9 1.0
CD A:GLU1450 3.1 57.7 1.0
OD1 A:ASN1500 4.0 46.8 1.0
ND2 A:ASN1500 4.0 54.7 1.0
CG A:ASN1500 4.3 47.7 1.0
CG A:GLU1450 4.6 50.1 1.0

Calcium binding site 3 out of 4 in 7f9d

Go back to Calcium Binding Sites List in 7f9d
Calcium binding site 3 out of 4 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1905

b:80.4
occ:1.00
 OD1 A:ASP1466 2.7 81.9 1.0
O A:LEU1467 3.1 72.4 1.0
CG A:ASP1466 3.6 76.0 1.0
OD2 A:ASP1466 3.8 81.5 1.0
C A:LEU1467 3.9 70.8 1.0
CA A:GLU1468 4.4 64.1 1.0
N A:GLU1468 4.4 71.9 1.0
O A:ASP1466 4.6 67.0 1.0
C A:ASP1466 4.7 65.9 1.0
N A:LEU1467 4.8 78.2 1.0
CA A:LEU1467 5.0 73.4 1.0
CB A:ASP1466 5.0 64.4 1.0

Calcium binding site 4 out of 4 in 7f9d

Go back to Calcium Binding Sites List in 7f9d
Calcium binding site 4 out of 4 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1604

b:83.4
occ:1.00
 O B:ASP1096 2.7 54.6 1.0
OE2 B:GLU1100 2.8 76.1 1.0
OE1 B:GLU1100 3.5 77.5 1.0
CD B:GLU1100 3.6 69.9 1.0
C B:ASP1096 3.8 47.3 1.0
OD2 B:ASP1096 3.9 66.9 1.0
OD1 B:ASP1096 3.9 70.9 1.0
CG B:ASP1096 4.0 66.6 1.0
CA B:ASP1096 4.5 51.3 1.0
N B:PHE1097 4.8 41.6 1.0
CB B:ASP1096 4.8 62.0 1.0
CA B:PHE1097 4.9 42.2 1.0

Reference:

N.Malhotra, Y.Manickam, A.Sharma. Hsprs with Atp Binding Pocket Inhibitor To Be Published.
Page generated: Wed Jul 9 22:04:18 2025

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