Chemical elements
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      2p3f
      2p3z
      2p66
      2p67
      2p6m
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      2p75
      2p76
      2p77
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Sodium in the structure of Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus (pdb 2p76)






The binding sites of Sodium atom in the structure of Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus (pdb code 2p76). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2p76 structure was solved by A.A.FEDOROV, E.V.FEDOROV, J.M.SAUDER, S.K.BURLEY, S.C.ALMO, NEW YORK SGXRESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)25.0-2.6
Space groupP3121
a (A)115.164
b (A)115.164
c (A)451.335
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)24.9
Rfree (%)26.5


Sodium Binding Sites:

Sodium binding site 1 out of 8 in 2p76


Sodium binding site 1 out of 8 in 2p76
Click to enlarge
stereopicture of Sodium binding site 1 out of 8 in 2p76
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2p76. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His59, A: Glu87, A: Asp89, A: His102, A: Glu169, A: Gln206, A: Gol501,

conact list:


AtomAtomDistance (A)
NaNE2 A:His594.15
NaCD2 A:His594.49
NaOE1 A:Glu873.86
NaOE2 A:Glu872.65
NaCD A:Glu873.63
NaCG A:Glu874.99
NaCB A:Asp894.70
NaOD2 A:Asp893.17
NaOD1 A:Asp892.56
NaCG A:Asp893.23
NaND1 A:His1024.47
NaCE1 A:His1024.58
NaOE1 A:Glu1692.52
NaCB A:Glu1694.44
NaOE2 A:Glu1693.89
NaCD A:Glu1693.43
NaCG A:Glu1694.53
NaNE2 A:Gln2064.57
NaOE1 A:Gln2064.65
NaCD A:Gln2064.78
NaO2 A:Gol5012.86
NaC1 A:Gol5013.60
NaO1 A:Gol5012.63
NaC3 A:Gol5013.55
NaO3 A:Gol5013.87
NaC2 A:Gol5013.51

interactive model:


Sodium binding site 2 out of 8 in 2p76


Sodium binding site 2 out of 8 in 2p76
Click to enlarge
stereopicture of Sodium binding site 2 out of 8 in 2p76
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2p76. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: His59, B: Arg60, B: Glu87, B: Asp89, B: His102, B: Glu169, B: Gln206, B: Gol501,

conact list:


AtomAtomDistance (A)
NaNE2 B:His593.88
NaCD2 B:His594.26
NaNE B:Arg604.87
NaOE1 B:Glu873.78
NaOE2 B:Glu872.77
NaCD B:Glu873.65
NaCB B:Asp894.64
NaOD2 B:Asp892.96
NaOD1 B:Asp892.62
NaCG B:Asp893.15
NaND1 B:His1024.20
NaCE1 B:His1024.34
NaOE1 B:Glu1692.83
NaCB B:Glu1694.74
NaOE2 B:Glu1694.12
NaCD B:Glu1693.72
NaCG B:Glu1694.85
NaNE2 B:Gln2064.84
NaOE1 B:Gln2064.97
NaO2 B:Gol5012.94
NaC1 B:Gol5013.70
NaO1 B:Gol5012.94
NaC3 B:Gol5013.43
NaO3 B:Gol5013.06
NaC2 B:Gol5013.49

interactive model:


Sodium binding site 3 out of 8 in 2p76


Sodium binding site 3 out of 8 in 2p76
Click to enlarge
stereopicture of Sodium binding site 3 out of 8 in 2p76
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2p76. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: C: His59, C: Glu87, C: Asp89, C: His102, C: Glu169, C: Gln206, C: Gol501,

conact list:


AtomAtomDistance (A)
NaNE2 C:His594.03
NaCD2 C:His594.35
NaOE1 C:Glu873.74
NaOE2 C:Glu872.56
NaCD C:Glu873.51
NaCG C:Glu874.88
NaCB C:Asp894.74
NaOD2 C:Asp893.16
NaOD1 C:Asp892.62
NaCG C:Asp893.26
NaND1 C:His1024.50
NaCE1 C:His1024.62
NaOE1 C:Glu1692.62
NaCB C:Glu1694.50
NaOE2 C:Glu1694.05
NaCD C:Glu1693.55
NaCG C:Glu1694.63
NaNE2 C:Gln2064.58
NaOE1 C:Gln2064.68
NaCD C:Gln2064.81
NaO2 C:Gol5012.83
NaC1 C:Gol5013.52
NaO1 C:Gol5012.79
NaC3 C:Gol5014.04
NaO3 C:Gol5013.63
NaC2 C:Gol5013.61

interactive model:


Sodium binding site 4 out of 8 in 2p76


Sodium binding site 4 out of 8 in 2p76
Click to enlarge
stereopicture of Sodium binding site 4 out of 8 in 2p76
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2p76. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: D: His59, D: Arg60, D: Glu87, D: Asp89, D: His102, D: Glu169, D: Gln206, D: Gol501,

conact list:


AtomAtomDistance (A)
NaNE2 D:His593.91
NaCD2 D:His594.23
NaNE D:Arg604.97
NaOE1 D:Glu873.61
NaOE2 D:Glu872.54
NaCD D:Glu873.44
NaCG D:Glu874.83
NaCB D:Asp894.66
NaOD2 D:Asp893.01
NaOD1 D:Asp892.58
NaCG D:Asp893.16
NaND1 D:His1024.40
NaCE1 D:His1024.57
NaOE1 D:Glu1692.83
NaCB D:Glu1694.64
NaOE2 D:Glu1694.25
NaCD D:Glu1693.75
NaCG D:Glu1694.81
NaNE2 D:Gln2064.63
NaOE1 D:Gln2064.77
NaCD D:Gln2064.90
NaO2 D:Gol5012.93
NaC1 D:Gol5013.62
NaO1 D:Gol5012.64
NaC3 D:Gol5013.90
NaO3 D:Gol5013.74
NaC2 D:Gol5013.64

interactive model:


Sodium binding site 5 out of 8 in 2p76


Sodium binding site 5 out of 8 in 2p76
Click to enlarge
stereopicture of Sodium binding site 5 out of 8 in 2p76
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 2p76. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: His59, E: Glu87, E: Asp89, E: His102, E: Glu169, E: Gln206, E: Gol501,

conact list:


AtomAtomDistance (A)
NaNE2 E:His594.09
NaCD2 E:His594.41
NaOE1 E:Glu873.72
NaOE2 E:Glu872.61
NaCD E:Glu873.54
NaCG E:Glu874.94
NaCB E:Asp894.56
NaOD2 E:Asp892.98
NaOD1 E:Asp892.48
NaCG E:Asp893.08
NaND1 E:His1024.36
NaCE1 E:His1024.51
NaOE1 E:Glu1692.73
NaCB E:Glu1694.51
NaOE2 E:Glu1694.05
NaCD E:Glu1693.59
NaCG E:Glu1694.66
NaNE2 E:Gln2064.64
NaOE1 E:Gln2064.80
NaCD E:Gln2064.90
NaO2 E:Gol5012.91
NaC1 E:Gol5013.56
NaO1 E:Gol5012.86
NaC3 E:Gol5014.24
NaO3 E:Gol5013.61
NaC2 E:Gol5013.70

interactive model:


Sodium binding site 6 out of 8 in 2p76


Sodium binding site 6 out of 8 in 2p76
Click to enlarge
stereopicture of Sodium binding site 6 out of 8 in 2p76
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 2p76. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: F: His59, F: Glu87, F: Asp89, F: His102, F: Glu169, F: Gln206, F: Gol501,

conact list:


AtomAtomDistance (A)
NaNE2 F:His594.09
NaCD2 F:His594.39
NaOE1 F:Glu873.74
NaOE2 F:Glu872.57
NaCD F:Glu873.52
NaCG F:Glu874.89
NaCB F:Asp894.67
NaOD2 F:Asp893.10
NaOD1 F:Asp892.57
NaCG F:Asp893.20
NaND1 F:His1024.49
NaCE1 F:His1024.62
NaOE1 F:Glu1692.62
NaCB F:Glu1694.46
NaOE2 F:Glu1694.02
NaCD F:Glu1693.53
NaCG F:Glu1694.60
NaNE2 F:Gln2064.55
NaOE1 F:Gln2064.63
NaCD F:Gln2064.78
NaO2 F:Gol5012.76
NaC1 F:Gol5013.66
NaO1 F:Gol5012.78
NaC3 F:Gol5013.64
NaO3 F:Gol5013.92
NaC2 F:Gol5013.50

interactive model:


Sodium binding site 7 out of 8 in 2p76


Sodium binding site 7 out of 8 in 2p76
Click to enlarge
stereopicture of Sodium binding site 7 out of 8 in 2p76
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 2p76. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: G: His59, G: Glu87, G: Asp89, G: His102, G: Glu169, G: Gln206, G: Gol501,

conact list:


AtomAtomDistance (A)
NaNE2 G:His594.14
NaCD2 G:His594.47
NaOE1 G:Glu873.76
NaOE2 G:Glu872.64
NaCD G:Glu873.58
NaCG G:Glu874.97
NaCB G:Asp894.54
NaOD2 G:Asp892.97
NaOD1 G:Asp892.44
NaCG G:Asp893.06
NaND1 G:His1024.36
NaCE1 G:His1024.51
NaOE1 G:Glu1692.64
NaCB G:Glu1694.44
NaOE2 G:Glu1693.99
NaCD G:Glu1693.51
NaCG G:Glu1694.58
NaNE2 G:Gln2064.64
NaOE1 G:Gln2064.82
NaCD G:Gln2064.90
NaO2 G:Gol5012.85
NaC1 G:Gol5013.75
NaO1 G:Gol5012.70
NaC3 G:Gol5014.09
NaO3 G:Gol5014.62
NaC2 G:Gol5013.71

interactive model:


Sodium binding site 8 out of 8 in 2p76


Sodium binding site 8 out of 8 in 2p76
Click to enlarge
stereopicture of Sodium binding site 8 out of 8 in 2p76
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 2p76. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: H: His59, H: Glu87, H: Asp89, H: His102, H: Glu169, H: Gln206, H: Gol501,

conact list:


AtomAtomDistance (A)
NaNE2 H:His593.92
NaCD2 H:His594.24
NaOE1 H:Glu873.71
NaOE2 H:Glu872.55
NaCD H:Glu873.49
NaCG H:Glu874.86
NaCB H:Asp894.76
NaOD2 H:Asp893.13
NaOD1 H:Asp892.68
NaCG H:Asp893.27
NaND1 H:His1024.46
NaCE1 H:His1024.58
NaOE1 H:Glu1692.76
NaCB H:Glu1694.64
NaOE2 H:Glu1694.17
NaCD H:Glu1693.69
NaCG H:Glu1694.78
NaNE2 H:Gln2064.62
NaOE1 H:Gln2064.67
NaCD H:Gln2064.85
NaO2 H:Gol5012.90
NaC1 H:Gol5013.73
NaO1 H:Gol5012.87
NaC3 H:Gol5013.49
NaO3 H:Gol5014.47
NaC2 H:Gol5013.52

interactive model:




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