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Calcium in PDB 7f9b: Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95

Enzymatic activity of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95

All present enzymatic activity of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95:
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 L95, PDB code: 7f9b 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) 45.48 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.73, 90.96, 83.49, 90, 110.03, 90
R / Rfree (%) 18.9 / 23.6

Other elements in 7f9b:

The structure of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 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 L95 (pdb code 7f9b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95, PDB code: 7f9b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7f9b

Go back to Calcium Binding Sites List in 7f9b
Calcium binding site 1 out of 6 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95


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 L95 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1903

b:71.1
occ:0.95
 O A:HOH2058 2.2 60.8 1.0
OE1 A:GLU1100 2.4 85.6 1.0
O A:ASP1096 2.6 54.0 1.0
CD A:GLU1100 3.3 74.1 1.0
OD1 A:ASP1096 3.4 79.0 1.0
OE2 A:GLU1100 3.6 77.2 1.0
C A:ASP1096 3.8 49.8 1.0
CG A:ASP1096 4.4 71.5 1.0
OE2 A:GLU1154 4.5 74.9 1.0
CA A:PHE1097 4.6 51.4 1.0
CG A:GLU1100 4.6 55.5 1.0
N A:PHE1097 4.7 52.0 1.0
CA A:ASP1096 4.7 49.4 1.0

Calcium binding site 2 out of 6 in 7f9b

Go back to Calcium Binding Sites List in 7f9b
Calcium binding site 2 out of 6 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95


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 L95 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1904

b:76.7
occ:0.92
 OD1 A:ASN1356 2.6 91.5 1.0
CG A:ASN1356 3.2 80.7 1.0
ND2 A:ASN1356 3.3 82.0 1.0
O A:HOH2025 4.1 58.1 1.0
CB A:PHE1355 4.1 52.1 1.0
O A:GLY1352 4.2 71.6 1.0
OE1 A:GLU1359 4.3 78.2 1.0
N A:ASN1356 4.3 61.7 1.0
CB A:ASN1356 4.5 67.4 1.0
CA A:ASN1356 4.6 60.2 1.0
CD A:GLU1359 4.8 76.2 1.0
C A:PHE1355 4.9 51.9 1.0
OE2 A:GLU1359 4.9 77.9 1.0
CD2 A:PHE1355 4.9 51.3 1.0

Calcium binding site 3 out of 6 in 7f9b

Go back to Calcium Binding Sites List in 7f9b
Calcium binding site 3 out of 6 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95


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 L95 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1903

b:63.5
occ:0.85
 O B:HOH2054 2.3 57.2 1.0
O B:HOH2120 2.5 47.6 1.0
O B:ASP1096 2.6 47.9 1.0
OE2 B:GLU1100 2.7 72.7 1.0
OE1 B:GLU1100 3.2 69.5 1.0
CD B:GLU1100 3.4 68.9 1.0
C B:ASP1096 3.8 53.3 1.0
OD1 B:ASP1096 4.4 68.0 1.0
CG B:ASP1096 4.6 63.9 1.0
CA B:ASP1096 4.6 51.6 1.0
OE2 B:GLU1154 4.6 66.7 1.0
CA B:PHE1097 4.6 48.8 1.0
N B:PHE1097 4.7 48.4 1.0
CG B:GLU1100 4.9 50.5 1.0
OD2 B:ASP1096 4.9 58.8 1.0
CB B:ASP1096 5.0 53.0 1.0

Calcium binding site 4 out of 6 in 7f9b

Go back to Calcium Binding Sites List in 7f9b
Calcium binding site 4 out of 6 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95


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 L95 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1904

b:42.0
occ:0.45
 CA B:CA1904 0.0 42.0 0.5
O B:HOH2125 2.4 52.5 1.0
CA B:CA1904 2.5 63.5 0.6
OD1 B:ASP1220 2.5 59.5 1.0
O B:ASP1220 2.5 41.3 1.0
C B:ASP1220 3.4 42.3 1.0
O B:HOH2122 3.6 45.8 1.0
CG B:ASP1220 3.7 51.4 1.0
NZ B:LYS1215 3.8 53.7 1.0
CA B:ASP1220 4.0 41.8 1.0
N B:TYR1221 4.4 34.6 1.0
OE1 B:GLU1212 4.4 82.4 1.0
CB B:ASP1220 4.5 44.5 1.0
O B:HOH2012 4.5 49.3 1.0
CB B:TYR1221 4.6 39.2 1.0
O B:HOH2128 4.6 49.5 1.0
O B:HOH2133 4.6 53.4 1.0
OD2 B:ASP1220 4.6 58.4 1.0
CA B:TYR1221 4.8 36.9 1.0
CD1 B:TYR1221 5.0 34.8 1.0

Calcium binding site 5 out of 6 in 7f9b

Go back to Calcium Binding Sites List in 7f9b
Calcium binding site 5 out of 6 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95


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 L95 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1904

b:63.5
occ:0.55
 CA B:CA1904 0.0 63.5 0.6
O B:HOH2012 2.4 49.3 1.0
OD1 B:ASP1220 2.4 59.5 1.0
CA B:CA1904 2.5 42.0 0.5
O B:HOH2133 2.7 53.4 1.0
CG B:ASP1220 3.4 51.4 1.0
O B:HOH2125 3.7 52.5 1.0
OD2 B:ASP1220 3.7 58.4 1.0
O B:ASP1220 4.5 41.3 1.0
CB B:ASP1220 4.8 44.5 1.0
C B:ASP1220 4.9 42.3 1.0
CD1 B:TYR1221 5.0 34.8 1.0

Calcium binding site 6 out of 6 in 7f9b

Go back to Calcium Binding Sites List in 7f9b
Calcium binding site 6 out of 6 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95


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 L95 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1905

b:76.0
occ:0.92
 O B:GLY1263 2.5 77.0 1.0
C B:GLY1263 3.6 73.4 1.0
CA B:GLY1263 3.9 67.0 1.0
OE1 B:GLU1257 4.3 87.2 1.0
N B:GLU1264 4.7 74.4 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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