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Calcium in PDB 7f98: 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: 7f98 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) 59.94 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.72, 106.11, 145.29, 90, 90, 90
R / Rfree (%) 19 / 23.5

Other elements in 7f98:

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

Zinc (Zn) 2 atoms
Chlorine (Cl) 1 atom

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 7f98). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L95, PDB code: 7f98:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7f98

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Calcium binding site 1 out of 9 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:90.7
occ:1.00
 O A:HOH2019 2.3 53.9 1.0
O A:ASP1096 2.7 47.9 1.0
OE1 A:GLU1100 2.8 93.2 1.0
OE2 A:GLU1100 3.1 83.2 1.0
CD A:GLU1100 3.3 81.1 1.0
OD1 A:ASP1096 3.4 56.0 1.0
O A:HOH2029 3.5 53.9 1.0
C A:ASP1096 3.8 54.9 1.0
CG A:ASP1096 4.0 51.4 1.0
OE2 A:GLU1154 4.3 73.6 1.0
OD2 A:ASP1096 4.4 54.3 1.0
O A:HOH2072 4.5 47.5 1.0
CA A:PHE1097 4.6 49.2 1.0
CA A:ASP1096 4.7 51.6 1.0
N A:PHE1097 4.7 54.1 1.0
CG A:GLU1100 4.8 63.7 1.0
CB A:ASP1096 4.9 46.7 1.0

Calcium binding site 2 out of 9 in 7f98

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Calcium binding site 2 out of 9 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:89.7
occ:1.00
 OD2 A:ASP1220 2.4 79.1 1.0
OD1 A:ASP1220 3.1 83.2 1.0
CG A:ASP1220 3.1 71.9 1.0
O A:HOH2049 4.4 59.0 1.0
CB A:ASP1220 4.5 57.1 1.0
O A:HOH2004 4.9 73.5 1.0

Calcium binding site 3 out of 9 in 7f98

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Calcium binding site 3 out of 9 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
A:Ca1905

b:98.1
occ:1.00
 O A:HOH2099 2.6 67.0 1.0
OD2 A:ASP1466 2.6 81.5 1.0
O A:LEU1467 3.1 62.0 1.0
CG A:ASP1466 3.4 80.6 1.0
OD1 A:ASP1466 3.7 82.0 1.0
C A:LEU1467 4.0 60.5 1.0
N A:GLU1468 4.6 60.4 1.0
CA A:GLU1468 4.7 60.4 1.0
C A:ASP1466 4.7 59.5 1.0
CB A:ASP1466 4.7 68.2 1.0
N A:LEU1467 4.8 53.9 1.0
O A:ASP1466 4.8 58.9 1.0

Calcium binding site 4 out of 9 in 7f98

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Calcium binding site 4 out of 9 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
A:Ca1906

b:86.4
occ:1.00
 SG A:CYS1301 2.6 67.1 1.0
CB A:CYS1301 4.0 43.1 1.0
O A:PRO1051 4.1 35.4 1.0
O B:HOH2035 4.2 40.6 1.0
CB A:ALA1055 4.2 37.5 1.0
CB A:PRO1051 4.3 35.6 1.0
C A:PRO1051 4.4 44.6 1.0
CE3 A:TRP1052 4.4 39.9 1.0
CG B:GLU1074 4.6 50.3 1.0
CD B:GLU1074 4.7 70.8 1.0
OE1 B:GLU1074 4.7 74.5 1.0
CZ3 A:TRP1052 4.7 48.0 1.0
N A:TRP1052 4.7 41.7 1.0
CA A:TRP1052 4.8 35.3 1.0
CA A:PRO1051 4.9 40.0 1.0

Calcium binding site 5 out of 9 in 7f98

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Calcium binding site 5 out of 9 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
A:Ca1907

b:109.1
occ:1.00
 OE1 A:GLU1264 2.9 85.1 1.0
OE2 A:GLU1264 3.3 77.1 1.0
CD A:GLU1264 3.5 82.2 1.0
CG A:GLU1264 4.9 83.8 1.0

Calcium binding site 6 out of 9 in 7f98

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Calcium binding site 6 out of 9 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
A:Ca1908

b:89.8
occ:1.00
 OE2 A:GLU1074 2.7 89.3 1.0
SG B:CYS1301 3.7 68.5 1.0
CD A:GLU1074 3.9 73.5 1.0
CE3 B:TRP1052 4.0 39.8 1.0
O B:PRO1051 4.1 34.9 1.0
CB B:PRO1051 4.3 34.8 1.0
CZ3 B:TRP1052 4.3 48.4 1.0
C B:PRO1051 4.3 36.9 1.0
O B:HOH2053 4.4 43.0 1.0
CB B:ALA1055 4.5 35.0 1.0
O B:HOH2054 4.5 51.8 1.0
CB B:CYS1301 4.5 49.6 1.0
N B:TRP1052 4.6 39.2 1.0
OE1 A:GLU1074 4.7 76.1 1.0
CG A:GLU1074 4.7 49.2 1.0
CA B:TRP1052 4.7 35.9 1.0
CA B:PRO1051 4.9 38.5 1.0

Calcium binding site 7 out of 9 in 7f98

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Calcium binding site 7 out of 9 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 7 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:58.5
occ:1.00
 O B:HOH2128 2.3 55.8 1.0
OE1 B:GLN1378 2.4 53.2 1.0
O B:SER1376 2.5 55.3 1.0
O B:HOH2091 2.5 53.3 1.0
O B:HOH2117 2.7 59.5 1.0
CB B:SER1376 3.5 56.6 1.0
C B:SER1376 3.5 56.8 1.0
CD B:GLN1378 3.6 52.5 1.0
CA B:SER1376 3.9 59.7 1.0
CG B:GLN1378 4.3 51.4 1.0
CB B:GLN1378 4.5 50.9 1.0
NE2 B:GLN1378 4.6 58.6 1.0
O B:CYS1377 4.6 52.7 1.0
OG B:SER1376 4.7 56.5 1.0
N B:CYS1377 4.7 56.3 1.0
C B:CYS1377 4.8 60.1 1.0
O B:HOH2115 5.0 56.4 1.0

Calcium binding site 8 out of 9 in 7f98

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Calcium binding site 8 out of 9 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 8 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:101.4
occ:1.00
 O B:HOH2079 2.3 67.9 1.0
O B:ASP1096 2.5 50.1 1.0
O B:HOH2081 2.7 83.3 1.0
O B:HOH2025 3.0 63.5 1.0
OE2 B:GLU1100 3.5 75.2 1.0
OE1 B:GLU1100 3.6 58.9 1.0
OD2 B:ASP1096 3.6 81.4 1.0
C B:ASP1096 3.7 60.6 1.0
CG B:ASP1096 3.9 76.3 1.0
CD B:GLU1100 4.0 63.9 1.0
OD1 B:ASP1096 4.1 84.9 1.0
CA B:ASP1096 4.2 57.3 1.0
O B:HOH2068 4.6 52.5 1.0
CB B:ASP1096 4.7 60.4 1.0
N B:PHE1097 4.8 57.7 1.0
CD B:PRO1099 4.9 52.8 1.0
CA B:PHE1097 4.9 51.5 1.0

Calcium binding site 9 out of 9 in 7f98

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Calcium binding site 9 out of 9 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 9 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:101.6
occ:1.00
 OE1 B:GLU1264 2.9 88.2 1.0
OE2 B:GLU1264 2.9 81.1 1.0
CD B:GLU1264 3.3 84.3 1.0
CG B:GLU1264 4.8 75.7 1.0

Reference:

N.Malhotra, Y.Manickam, A.Sharma. Hsprs with Atp Binding Pocket Inhibitor To Be Published.
Page generated: Wed Jul 9 22:00:42 2025

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