Sodium in the structure of Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein (pdb 4gdu)

The binding sites of Sodium atom in the structure of Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein (pdb code 4gdu). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 4gdu structure was solved by J.NOMME, A.LAVIE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)30.0-2.1
Space groupP65
a (A)59.220
b (A)59.220
c (A)298.500
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)16.6
Rfree (%)22.2

Sodium Binding Sites:

Sodium binding site 1 out of 2 in 4gdu


Sodium binding site 1 out of 2 in 4gdu
Click to enlarge
stereopicture of Sodium binding site 1 out of 2 in 4gdu
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 4gdu. 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: Leu55, A: Glu56, A: Asp57, A: Asp58, A: Pro59, A: Glu60, A: Phe61, A: Asn62, A: Ala63, A: Gly64, A: Cys65, A: Gly66,

conact list:


AtomAtomDistance (A)
NaO A:Leu552.44
NaC A:Leu553.51
NaCA A:Leu554.82
NaO A:Glu562.91
NaN A:Glu563.97
NaCB A:Glu564.97
NaC A:Glu563.38
NaCA A:Glu563.57
NaN A:Asp574.36
NaC A:Asp574.57
NaO A:Asp582.28
NaN A:Asp583.98
NaCB A:Asp584.75
NaC A:Asp583.28
NaCA A:Asp584.16
NaN A:Pro594.10
NaC A:Pro594.44
NaCA A:Pro594.19
NaN A:Glu604.53
NaC A:Glu604.99
NaO A:Phe612.62
NaN A:Phe613.84
NaCB A:Phe614.06
NaC A:Phe613.58
NaCA A:Phe614.01
NaN A:Asn624.70
NaO A:Ala632.35
NaN A:Ala633.95
NaC A:Ala633.52
NaCB A:Ala634.75
NaCA A:Ala634.32
NaO A:Gly644.91
NaN A:Gly644.48
NaC A:Gly644.31
NaCA A:Gly644.61
NaO A:Cys652.33
NaN A:Cys653.92
NaCB A:Cys654.65
NaC A:Cys653.49
NaCA A:Cys654.21
NaN A:Gly664.53
NaCA A:Gly664.73

interactive model:


Sodium binding site 2 out of 2 in 4gdu


Sodium binding site 2 out of 2 in 4gdu
Click to enlarge
stereopicture of Sodium binding site 2 out of 2 in 4gdu
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 4gdu. 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: Leu55, B: Glu56, B: Asp57, B: Asp58, B: Pro59, B: Glu60, B: Phe61, B: Asn62, B: Ala63, B: Gly64, B: Cys65, B: Gly66, B: Ser67,

conact list:


AtomAtomDistance (A)
NaO B:Leu552.80
NaC B:Leu553.86
NaO B:Glu562.79
NaN B:Glu564.26
NaC B:Glu563.37
NaCA B:Glu563.70
NaO B:Asp574.99
NaN B:Asp574.30
NaC B:Asp574.52
NaCA B:Asp574.87
NaO B:Asp582.56
NaN B:Asp584.24
NaC B:Asp583.49
NaCA B:Asp584.46
NaO B:Pro594.52
NaN B:Pro594.20
NaC B:Pro594.34
NaCA B:Pro594.13
NaN B:Glu604.89
NaO B:Phe612.54
NaN B:Phe614.02
NaCB B:Phe614.17
NaC B:Phe613.57
NaCA B:Phe614.09
NaN B:Asn624.68
NaC B:Asn624.93
NaO B:Ala632.48
NaN B:Ala633.95
NaC B:Ala633.58
NaCB B:Ala634.66
NaCA B:Ala634.30
NaO B:Gly644.96
NaN B:Gly644.56
NaC B:Gly644.40
NaCA B:Gly644.76
NaO B:Cys652.24
NaN B:Cys653.98
NaCB B:Cys654.89
NaC B:Cys653.32
NaCA B:Cys654.24
NaN B:Gly664.15
NaC B:Gly664.55
NaCA B:Gly664.14
NaN B:Ser674.90

interactive model:




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