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Calcium in PDB 7f9c: 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: 7f9c was solved by N.Malhotra, Y.Manickam, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.29 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.59, 91.66, 83.38, 90, 110.28, 90
R / Rfree (%) 18.8 / 25.3

Other elements in 7f9c:

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) 4 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 7f9c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L96, PDB code: 7f9c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 7f9c

Go back to Calcium Binding Sites List in 7f9c
Calcium binding site 1 out of 7 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:84.9
occ:1.00
 O A:HOH2015 2.3 58.5 1.0
OE1 A:GLN1378 3.1 78.4 1.0
O A:SER1376 3.4 64.8 1.0
OG A:SER1376 3.4 65.4 1.0
CD A:GLN1378 4.1 75.0 1.0
C A:SER1376 4.5 68.1 1.0
CB A:SER1376 4.7 60.7 1.0
CG A:GLN1378 4.9 62.9 1.0
CB A:GLN1378 4.9 55.1 1.0
NE2 A:GLN1378 4.9 72.6 1.0

Calcium binding site 2 out of 7 in 7f9c

Go back to Calcium Binding Sites List in 7f9c
Calcium binding site 2 out of 7 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:Ca1906

b:56.6
occ:0.73
 O A:HOH2087 2.4 63.8 1.0
O A:HOH2003 2.6 63.1 1.0
O A:ASP1096 2.6 51.2 1.0
OE2 A:GLU1100 2.7 79.5 1.0
OD2 A:ASP1096 3.2 83.3 1.0
CD A:GLU1100 3.6 73.4 1.0
C A:ASP1096 3.6 46.6 1.0
CG A:ASP1096 3.8 74.6 1.0
OE1 A:GLU1100 3.9 81.5 1.0
OD1 A:ASP1096 4.2 79.9 1.0
CA A:ASP1096 4.4 43.6 1.0
N A:PHE1097 4.6 46.6 1.0
CA A:PHE1097 4.6 47.4 1.0
CB A:ASP1096 4.7 58.8 1.0

Calcium binding site 3 out of 7 in 7f9c

Go back to Calcium Binding Sites List in 7f9c
Calcium binding site 3 out of 7 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:Ca1907

b:77.2
occ:0.74
 OD2 A:ASP1026 2.4 88.0 1.0
CG A:ASP1026 3.2 80.1 1.0
OD1 A:ASP1026 3.3 89.0 1.0
OD1 A:ASN1023 4.2 71.7 1.0
ND2 A:ASN1023 4.4 87.9 1.0
CG A:ASN1023 4.5 80.3 1.0
CB A:ASP1026 4.7 62.3 1.0

Calcium binding site 4 out of 7 in 7f9c

Go back to Calcium Binding Sites List in 7f9c
Calcium binding site 4 out of 7 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:78.3
occ:1.00
 OE2 B:GLU1100 2.6 71.9 1.0
O B:ASP1096 2.7 60.8 1.0
O B:HOH2067 2.9 68.1 1.0
O B:HOH2070 2.9 65.6 1.0
OD1 B:ASP1096 3.0 95.3 1.0
CD B:GLU1100 3.4 83.4 1.0
OE1 B:GLU1100 3.4 82.5 1.0
C B:ASP1096 3.9 62.3 1.0
CG B:ASP1096 4.1 87.5 1.0
CA B:ASP1096 4.6 55.8 1.0
CG B:GLU1100 4.7 80.7 1.0
OD2 B:ASP1096 4.8 92.8 1.0
N B:PHE1097 4.9 60.4 1.0
CB B:ASP1096 4.9 70.7 1.0
CA B:PHE1097 5.0 53.7 1.0

Calcium binding site 5 out of 7 in 7f9c

Go back to Calcium Binding Sites List in 7f9c
Calcium binding site 5 out of 7 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 5 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:Ca1904

b:93.1
occ:1.00
 O B:HOH2008 2.4 53.2 1.0
O B:HOH2059 2.6 56.2 1.0
OD2 B:ASP1220 3.2 95.9 1.0
OD1 B:ASP1220 3.2 75.5 1.0
CG B:ASP1220 3.5 80.0 1.0
CB B:ASP1220 4.8 65.5 1.0
O B:ASP1220 4.8 56.0 1.0

Calcium binding site 6 out of 7 in 7f9c

Go back to Calcium Binding Sites List in 7f9c
Calcium binding site 6 out of 7 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 6 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:Ca1906

b:67.6
occ:0.55
 CA B:CA1906 0.0 67.6 0.6
CA B:CA1906 2.1 72.3 0.5
O B:GLY1263 2.5 83.4 1.0
C B:GLY1263 3.5 78.2 1.0
CA B:GLY1263 3.9 77.4 1.0
N B:GLU1264 4.7 74.8 1.0
O B:HOH2018 5.0 72.0 1.0

Calcium binding site 7 out of 7 in 7f9c

Go back to Calcium Binding Sites List in 7f9c
Calcium binding site 7 out of 7 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 7 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:Ca1906

b:72.3
occ:0.45
 CA B:CA1906 0.0 72.3 0.5
CA B:CA1906 2.1 67.6 0.6
O B:GLY1263 3.2 83.4 1.0
O B:HOH2018 3.6 72.0 1.0
C B:GLY1263 4.0 78.2 1.0
CA B:GLY1263 4.2 77.4 1.0
NZ B:LYS1265 4.5 71.7 1.0
CE B:LYS1265 4.6 78.1 1.0
CG B:LYS1265 4.7 66.5 1.0

Reference:

N.Malhotra, Y.Manickam, A.Sharma. Hsprs with Atp Binding Pocket Inhibitor To Be Published.
Page generated: Tue Apr 4 18:08:38 2023

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