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Calcium in PDB 7f9a: Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97

Enzymatic activity of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97

All present enzymatic activity of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97:
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 L97, PDB code: 7f9a 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) 59.93 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.74, 105.92, 145.38, 90, 90, 90
R / Rfree (%) 19.5 / 24.2

Other elements in 7f9a:

The structure of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 3 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 L97 (pdb code 7f9a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97, PDB code: 7f9a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7f9a

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Calcium binding site 1 out of 10 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97


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 L97 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1903

b:63.3
occ:0.77
 OE2 A:GLU1450 2.3 74.5 1.0
O A:HOH2112 2.4 59.7 1.0
OE1 A:GLU1450 2.5 61.5 1.0
O A:HOH2104 2.5 67.5 1.0
O A:HOH2094 2.5 66.3 1.0
CD A:GLU1450 2.7 66.3 1.0
CG A:GLU1450 4.2 62.9 1.0
OD1 A:ASN1500 4.5 62.6 1.0
ND2 A:ASN1500 4.8 50.9 1.0
CG A:ASN1500 4.9 62.1 1.0

Calcium binding site 2 out of 10 in 7f9a

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Calcium binding site 2 out of 10 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97


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 L97 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1904

b:71.8
occ:0.90
 O A:HOH2043 2.2 68.2 1.0
O A:ASP1096 2.5 51.6 1.0
O A:HOH2014 2.5 60.6 1.0
OE2 A:GLU1100 2.6 79.8 1.0
OE1 A:GLU1100 2.9 79.3 1.0
CD A:GLU1100 3.1 76.5 1.0
OD1 A:ASP1096 3.4 69.4 1.0
C A:ASP1096 3.6 53.2 1.0
CG A:ASP1096 3.9 62.7 1.0
O A:HOH2129 4.3 73.0 1.0
OD2 A:ASP1096 4.3 67.7 1.0
O A:HOH2019 4.3 64.1 1.0
CA A:PHE1097 4.4 51.6 1.0
O A:HOH2062 4.4 58.1 1.0
N A:PHE1097 4.4 49.6 1.0
CA A:ASP1096 4.4 54.5 1.0
CG A:GLU1100 4.6 66.5 1.0
CB A:ASP1096 4.7 58.1 1.0
OE2 A:GLU1154 4.8 74.3 1.0
C A:PHE1097 5.0 55.7 1.0

Calcium binding site 3 out of 10 in 7f9a

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Calcium binding site 3 out of 10 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97


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 L97 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1905

b:86.6
occ:1.00
 OD1 A:ASP1096 2.9 69.4 1.0
CG A:ASP1096 3.7 62.7 1.0
OD2 A:ASP1096 4.4 67.7 1.0
CB A:ASP1096 4.5 58.1 1.0
CA A:ASP1096 4.8 54.5 1.0
O A:HOH2062 4.9 58.1 1.0

Calcium binding site 4 out of 10 in 7f9a

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Calcium binding site 4 out of 10 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97


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 L97 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1906

b:82.5
occ:0.85
 SG A:CYS1301 2.7 69.5 1.0
O A:PRO1051 3.9 43.0 1.0
CB A:PRO1051 4.0 40.8 1.0
O B:HOH2059 4.1 47.7 1.0
CB A:CYS1301 4.1 47.6 1.0
C A:PRO1051 4.1 51.9 1.0
CE3 A:TRP1052 4.1 51.6 1.0
CB A:ALA1055 4.3 42.9 1.0
N A:TRP1052 4.4 47.1 1.0
CZ3 A:TRP1052 4.5 61.8 1.0
CA A:TRP1052 4.6 39.9 1.0
CD B:GLU1074 4.6 74.4 1.0
CA A:PRO1051 4.6 45.8 1.0
CG B:GLU1074 4.7 54.4 1.0
OE2 B:GLU1074 4.8 79.1 1.0
OE1 B:GLU1074 4.8 77.0 1.0

Calcium binding site 5 out of 10 in 7f9a

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Calcium binding site 5 out of 10 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97


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 L97 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1907

b:97.2
occ:1.00
 O A:HOH2105 2.3 63.7 1.0
OE1 A:GLU1214 2.5 83.3 1.0
CD A:GLU1214 3.7 76.4 1.0
OE1 A:GLN1237 4.3 72.5 1.0
OE2 A:GLU1214 4.4 78.0 1.0
O A:HOH2025 4.4 70.0 1.0
O A:HOH2098 4.5 58.5 1.0
NZ A:LYS1477 4.5 78.0 1.0
CG A:GLU1214 4.8 62.8 1.0
CB A:GLU1214 4.9 46.4 1.0
O A:GLU1214 5.0 49.4 1.0

Calcium binding site 6 out of 10 in 7f9a

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Calcium binding site 6 out of 10 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97


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 L97 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1908

b:104.7
occ:1.00
 OD1 A:ASP1466 2.7 90.2 1.0
CG A:ASP1466 3.7 86.9 1.0
O A:LEU1467 3.7 76.9 1.0
OD2 A:ASP1466 3.9 95.3 1.0
C A:LEU1467 4.3 78.0 1.0
CA A:GLU1468 4.7 69.4 1.0
N A:GLU1468 4.7 76.9 1.0
C A:ASP1466 5.0 71.5 1.0

Calcium binding site 7 out of 10 in 7f9a

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Calcium binding site 7 out of 10 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97


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 L97 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1911

b:79.8
occ:0.95
 OE2 A:GLU1074 2.7 91.1 1.0
SG B:CYS1301 3.1 76.9 1.0
CE3 B:TRP1052 3.8 46.6 1.0
CD A:GLU1074 3.8 75.9 1.0
O B:PRO1051 3.9 37.5 1.0
CB B:PRO1051 4.1 40.2 1.0
C B:PRO1051 4.1 46.2 1.0
CZ3 B:TRP1052 4.2 54.8 1.0
CB B:CYS1301 4.3 57.3 1.0
CB B:ALA1055 4.3 46.1 1.0
N B:TRP1052 4.4 43.8 1.0
CA B:TRP1052 4.5 40.7 1.0
OE1 A:GLU1074 4.6 66.3 1.0
CA B:PRO1051 4.7 40.9 1.0
CG A:GLU1074 4.8 48.6 1.0
CD2 B:TRP1052 5.0 47.8 1.0

Calcium binding site 8 out of 10 in 7f9a

Go back to Calcium Binding Sites List in 7f9a
Calcium binding site 8 out of 10 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97


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 L97 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1903

b:96.8
occ:1.00
 O B:HOH2079 2.5 83.3 1.0
O B:ASP1096 2.5 54.0 1.0
O B:HOH2052 2.6 63.8 1.0
O B:HOH2002 2.7 68.5 1.0
OE2 B:GLU1100 2.9 81.5 1.0
OD1 B:ASP1096 3.1 76.4 1.0
OE1 B:GLU1100 3.5 78.4 1.0
CD B:GLU1100 3.5 77.6 1.0
C B:ASP1096 3.6 65.5 1.0
CG B:ASP1096 3.8 73.0 1.0
OD2 B:ASP1096 4.2 77.2 1.0
CA B:ASP1096 4.2 60.8 1.0
CB B:ASP1096 4.6 65.1 1.0
N B:PHE1097 4.7 62.6 1.0
CA B:PHE1097 4.8 64.0 1.0
CG B:GLU1100 5.0 75.0 1.0

Calcium binding site 9 out of 10 in 7f9a

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Calcium binding site 9 out of 10 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97


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 L97 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1904

b:112.8
occ:1.00
 OE1 B:GLU1264 2.6 93.9 1.0
CA B:CA1905 3.5 110.3 1.0
CD B:GLU1264 3.6 91.2 1.0
O B:LYS1265 3.7 65.0 1.0
OE2 B:GLU1264 3.7 94.6 1.0
C B:LYS1265 5.0 70.4 1.0
CG B:GLU1264 5.0 81.0 1.0

Calcium binding site 10 out of 10 in 7f9a

Go back to Calcium Binding Sites List in 7f9a
Calcium binding site 10 out of 10 in the Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Homo Sapiens Prolyl-Trna Synthetase (Hsprs) in Complex with L-Proline and Compound L97 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1905

b:110.3
occ:1.00
 OE2 B:GLU1264 2.4 94.6 1.0
CD B:GLU1264 3.4 91.2 1.0
CA B:CA1904 3.5 112.8 1.0
OE1 B:GLU1264 3.7 93.9 1.0
CG B:GLU1264 4.7 81.0 1.0

Reference:

N.Malhotra, Y.Manickam, A.Sharma. Hsprs with Atp Binding Pocket Inhibitor To Be Published.
Page generated: Fri Jul 19 00:39:52 2024

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