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Sodium in the structure of Crystal Structure Analysis of Leut Complexed With L-Leucine, Sodium, and Imipramine (pdb 2q72)






The binding sites of Sodium atom in the structure of Crystal Structure Analysis of Leut Complexed With L-Leucine, Sodium, and Imipramine (pdb code 2q72). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2q72 structure was solved by S.K.SINGH, A.YAMASHITA, E.GOUAUX, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)27.4-1.7
Space groupC121
a (A)88.000
b (A)86.640
c (A)81.130
alpha (°)90.00
beta (°)95.76
gamma (°)90.00
Rfactor (%)20.3
Rfree (%)21.9


Sodium Binding Sites:

Sodium binding site 1 out of 2 in 2q72


Sodium binding site 1 out of 2 in 2q72
Click to enlarge
stereopicture of Sodium binding site 1 out of 2 in 2q72
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2q72. 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: Gly20, A: Asn21, A: Ala22, A: Val23, A: Gly24, A: Phe350, A: Ala351, A: Gly352, A: Leu353, A: Thr354, A: Ser355,

conact list:


AtomAtomDistance (A)
NaO A:Gly202.23
NaC A:Gly203.37
NaCA A:Gly204.00
NaO A:Asn214.30
NaN A:Asn214.48
NaC A:Asn214.57
NaCA A:Asn214.81
NaC A:Ala224.87
NaO A:Val232.21
NaN A:Val234.45
NaCB A:Val234.89
NaC A:Val233.22
NaCA A:Val234.34
NaN A:Gly243.85
NaCA A:Gly243.66
NaO A:Phe3504.39
NaO A:Ala3512.28
NaC A:Ala3513.39
NaCB A:Ala3514.83
NaCA A:Ala3513.97
NaO A:Gly3524.56
NaN A:Gly3524.52
NaC A:Gly3524.68
NaCA A:Gly3524.82
NaC A:Leu3534.98
NaO A:Thr3543.96
NaN A:Thr3543.99
NaCB A:Thr3543.26
NaCG2 A:Thr3544.61
NaOG1 A:Thr3542.28
NaC A:Thr3543.28
NaCA A:Thr3543.67
NaN A:Ser3552.91
NaCB A:Ser3553.26
NaOG A:Ser3552.35
NaC A:Ser3554.96
NaCA A:Ser3553.48

interactive model:


Sodium binding site 2 out of 2 in 2q72


Sodium binding site 2 out of 2 in 2q72
Click to enlarge
stereopicture of Sodium binding site 2 out of 2 in 2q72
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2q72. 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: Ala22, A: Val23, A: Gly24, A: Gly26, A: Asn27, A: Phe253, A: Thr254, A: Leu255, A: Asn286, A: Glu290, A: Leu601,

conact list:


AtomAtomDistance (A)
NaO A:Ala222.19
NaC A:Ala223.13
NaCB A:Ala224.44
NaCA A:Ala224.12
NaN A:Val233.83
NaC A:Val234.37
NaCA A:Val233.81
NaN A:Gly243.93
NaC A:Gly264.83
NaCA A:Gly264.92
NaN A:Asn274.36
NaCB A:Asn274.56
NaND2 A:Asn273.59
NaOD1 A:Asn272.31
NaCG A:Asn273.24
NaCA A:Asn274.86
NaO A:Phe2534.72
NaO A:Thr2542.29
NaN A:Thr2544.59
NaCB A:Thr2543.41
NaCG2 A:Thr2544.46
NaOG1 A:Thr2542.46
NaC A:Thr2543.09
NaCA A:Thr2543.21
NaN A:Leu2554.37
NaCA A:Leu2554.98
NaCB A:Asn2864.80
NaND2 A:Asn2863.60
NaOD1 A:Asn2862.55
NaCG A:Asn2863.41
NaOE2 A:Glu2904.28
NaO A:Leu6014.55
NaN A:Leu6013.57
NaC A:Leu6013.58
NaCA A:Leu6014.14
NaOXT A:Leu6012.57

interactive model:




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