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Calcium in PDB 7f99: 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: 7f99 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) 78.25 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.471, 91.518, 83.335, 90, 110.11, 90
R / Rfree (%) 18.1 / 22.8

Other elements in 7f99:

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

Chlorine (Cl) 3 atoms
Zinc (Zn) 2 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 7f99). 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: 7f99:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7f99

Go back to Calcium Binding Sites List in 7f99
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:81.1
occ:1.00
 O A:HOH2218 2.5 40.4 1.0
O A:HOH2163 2.8 53.9 1.0
OE1 A:GLN1378 2.8 57.8 1.0
OG A:SER1376 2.9 74.1 1.0
O A:SER1376 3.2 52.0 1.0
CD A:GLN1378 3.8 60.1 1.0
CB A:SER1376 4.2 66.2 1.0
C A:SER1376 4.3 55.2 1.0
CB A:GLN1378 4.6 56.2 1.0
CG A:GLN1378 4.7 54.2 1.0
NE2 A:GLN1378 4.7 56.3 1.0
CA A:SER1376 4.8 59.0 1.0

Calcium binding site 2 out of 4 in 7f99

Go back to Calcium Binding Sites List in 7f99
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:51.6
occ:0.77
 O A:HOH2145 2.3 61.7 1.0
OE2 A:GLU1100 2.4 61.4 1.0
O A:ASP1096 2.5 36.6 1.0
O A:HOH2031 2.6 64.1 1.0
CD A:GLU1100 3.2 56.7 1.0
OE1 A:GLU1100 3.2 56.9 1.0
OD2 A:ASP1096 3.4 63.7 1.0
O A:HOH2119 3.5 61.2 1.0
C A:ASP1096 3.7 36.5 1.0
CG A:ASP1096 4.2 56.1 1.0
O A:HOH2015 4.3 44.3 1.0
O A:HOH2112 4.4 49.8 1.0
CA A:PHE1097 4.4 31.1 1.0
CA A:ASP1096 4.5 37.2 1.0
N A:PHE1097 4.5 31.2 1.0
CG A:GLU1100 4.7 42.5 1.0
OD1 A:ASP1096 4.8 67.1 1.0
CB A:ASP1096 4.8 41.9 1.0
OE1 A:GLU1154 4.9 47.8 1.0

Calcium binding site 3 out of 4 in 7f99

Go back to Calcium Binding Sites List in 7f99
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:60.8
occ:1.00
 OE1 A:GLU1264 2.4 55.0 1.0
O A:HOH2217 2.8 57.5 1.0
CD A:GLU1264 3.5 56.6 1.0
O A:HOH2193 3.6 62.9 1.0
OE2 A:GLU1264 4.3 53.9 1.0
O A:LYS1265 4.3 47.8 1.0
CG A:GLU1264 4.5 54.1 1.0
O A:HOH2180 4.6 50.6 1.0

Calcium binding site 4 out of 4 in 7f99

Go back to Calcium Binding Sites List in 7f99
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:Ca1903

b:77.5
occ:0.99
 O B:HOH2135 2.5 38.8 0.3
O B:HOH2043 2.6 47.0 0.6
O B:ASP1096 2.7 39.5 1.0
OE2 B:GLU1100 2.7 77.8 1.0
OE1 B:GLU1100 3.4 77.5 1.0
CD B:GLU1100 3.5 73.0 1.0
C B:ASP1096 3.9 41.7 1.0
O B:HOH2135 3.9 34.2 0.7
OD2 B:ASP1096 4.1 69.9 1.0
CG B:ASP1096 4.3 65.5 1.0
OD1 B:ASP1096 4.5 77.5 1.0
CA B:ASP1096 4.6 40.2 1.0
CA B:PHE1097 4.8 40.5 1.0
N B:PHE1097 4.8 39.6 1.0
O B:HOH2050 4.9 42.2 1.0
CG B:GLU1100 4.9 49.5 1.0

Reference:

N.Malhotra, Y.Manickam, A.Sharma. Hsprs with Atp Binding Pocket Inhibitor To Be Published.
Page generated: Wed Jul 9 22:01:33 2025

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