Chemical elements
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    PDB 1d11-1ej2
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    PDB 1gb6-1goh
    PDB 1gq2-1ikp
    PDB 1ikq-1jz1
    PDB 1jz2-1kvs
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    PDB 1kvt-1me8
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    PDB 4ecn-4g8t
    PDB 4gdt-8icw
    PDB 8icx-9icy

Sodium in the structure of Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene (pdb 1k2x)






The binding sites of Sodium atom in the structure of Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene (pdb code 1k2x). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 1k2x structure was solved by D.BOREK, M.JASKOLSKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)19.5-1.6
Space groupP212121
a (A)50.296
b (A)77.624
c (A)148.152
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)16.3
Rfree (%)19.8


Sodium Binding Sites:

Sodium binding site 1 out of 2 in 1k2x


Sodium binding site 1 out of 2 in 1k2x
Click to enlarge
stereopicture of Sodium binding site 1 out of 2 in 1k2x
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1k2x. 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: Leu60, A: Glu61, A: Glu62, A: Cme63, A: Pro64, A: Phe66, A: Asn67, A: Ala68, A: Gly69, A: Ile70, A: Gly71,

conact list:


AtomAtomDistance (A)
NaO A:Leu602.77
NaC A:Leu603.82
NaO A:Glu612.47
NaN A:Glu614.18
NaCB A:Glu614.92
NaC A:Glu613.20
NaCA A:Glu613.59
NaO A:Glu624.78
NaN A:Glu624.24
NaC A:Glu624.24
NaCA A:Glu624.77
NaO A:Cme632.56
NaN A:Cme633.98
NaCB A:Cme634.58
NaC A:Cme633.14
NaCA A:Cme634.11
NaN A:Pro644.21
NaC A:Pro644.59
NaCA A:Pro644.23
NaO A:Phe662.58
NaN A:Phe664.18
NaCB A:Phe664.31
NaC A:Phe663.65
NaCA A:Phe664.23
NaN A:Asn674.73
NaC A:Asn675.00
NaO A:Ala682.33
NaN A:Ala684.00
NaC A:Ala683.53
NaCB A:Ala684.67
NaCA A:Ala684.34
NaO A:Gly694.63
NaN A:Gly694.51
NaC A:Gly694.18
NaCA A:Gly694.58
NaO A:Ile702.29
NaN A:Ile703.93
NaCB A:Ile704.54
NaC A:Ile703.42
NaCA A:Ile704.17
NaN A:Gly714.41
NaC A:Gly714.95
NaCA A:Gly714.56

interactive model:


Sodium binding site 2 out of 2 in 1k2x


Sodium binding site 2 out of 2 in 1k2x
Click to enlarge
stereopicture of Sodium binding site 2 out of 2 in 1k2x
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1k2x. 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: Leu60, C: Glu61, C: Glu62, C: Cme63, C: Pro64, C: Phe66, C: Asn67, C: Ala68, C: Gly69, C: Ile70, C: Gly71,

conact list:


AtomAtomDistance (A)
NaO C:Leu602.80
NaC C:Leu603.85
NaO C:Glu612.39
NaN C:Glu614.21
NaCB C:Glu614.93
NaC C:Glu613.16
NaCA C:Glu613.59
NaO C:Glu624.70
NaN C:Glu624.22
NaC C:Glu624.22
NaCA C:Glu624.73
NaO C:Cme632.52
NaN C:Cme633.82
NaCB C:Cme634.77
NaC C:Cme633.53
NaCA C:Cme634.19
NaO C:Pro644.92
NaN C:Pro644.22
NaC C:Pro644.59
NaCA C:Pro644.28
NaO C:Phe662.58
NaN C:Phe664.18
NaCB C:Phe664.32
NaC C:Phe663.64
NaCA C:Phe664.22
NaN C:Asn674.74
NaO C:Ala682.27
NaN C:Ala683.98
NaC C:Ala683.48
NaCB C:Ala684.64
NaCA C:Ala684.29
NaO C:Gly694.56
NaN C:Gly694.45
NaC C:Gly694.13
NaCA C:Gly694.54
NaO C:Ile702.32
NaN C:Ile703.91
NaCB C:Ile704.64
NaC C:Ile703.47
NaCA C:Ile704.22
NaN C:Gly714.46
NaC C:Gly714.95
NaCA C:Gly714.59

interactive model:




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