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Zinc in the structure of Crystal Structure of Human Aspartyl Aminopeptidase (Dnpep), in Complex With Aspartic Acid Hydroxamate (pdb 3l6s)

The binding sites of Zinc atom in the structure of Crystal Structure of Human Aspartyl Aminopeptidase (Dnpep), in Complex With Aspartic Acid Hydroxamate (pdb code 3l6s). This binding sites where shown with 5.0 Angstroms radius around Zinc atom.
The 3l6s structure was solved by A.CHAIKUAD, E.PILKA, M.VOLLMAR, T.KROJER, J.R.C.MUNIZ, F.VONDELFT, C.H.ARROWSMITH, A.M.EDWARDS, J.WEIGELT, C.BOUNTRA, K.L.KAVANAGH, U.OPPERMANN, STRUCTURAL GENOMICS CONSORTIUM(SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)54.7-2.2
Space groupF432
a (A)244.595
b (A)244.595
c (A)244.595
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)15.5
Rfree (%)19.5

Zinc Binding Sites:

Zinc binding site 1 out of 2 in 3l6s


Zinc binding site 1 out of 2 in 3l6s
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stereopicture of Zinc binding site 1 out of 2 in 3l6s
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3l6s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His104, A: Pro108, A: Asp274, A: Glu311, A: Glu312, A: Met449, A: His450, A: Zn487, A: Sd3489, A: Hoh565, A: Hoh642,

conact list:


AtomAtomDistance (A)
ZnNE2 A:His1044.58
ZnCE1 A:His1044.54
ZnCD A:Pro1084.72
ZnCG A:Pro1084.81
ZnCB A:Asp2744.35
ZnOD2 A:Asp2742.02
ZnOD1 A:Asp2743.39
ZnCG A:Asp2743.02
ZnOE1 A:Glu3114.26
ZnOE1 A:Glu3122.03
ZnOE2 A:Glu3122.61
ZnCD A:Glu3122.63
ZnCG A:Glu3124.12
ZnCG A:Met4494.79
ZnSD A:Met4494.61
ZnNE2 A:His4502.14
ZnND1 A:His4504.26
ZnCD2 A:His4503.05
ZnCE1 A:His4503.17
ZnCG A:His4504.22
ZnZN A:Zn4873.39
ZnN A:Sd34894.99
ZnCB A:Sd34894.31
ZnND2 A:Sd34892.97
ZnOD1 A:Sd34892.00
ZnOAD A:Sd34892.20
ZnCG A:Sd34892.83
ZnO A:Hoh5654.87
ZnO A:Hoh6424.99

interactive model:


Zinc binding site 2 out of 2 in 3l6s


Zinc binding site 2 out of 2 in 3l6s
Click to enlarge
stereopicture of Zinc binding site 2 out of 2 in 3l6s
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3l6s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His104, A: Asp274, A: Asn275, A: Glu311, A: Glu312, A: Asp356, A: Met357, A: Zn486, A: Sd3489, A: Hoh502,

conact list:


AtomAtomDistance (A)
ZnNE2 A:His1042.19
ZnND1 A:His1044.24
ZnCD2 A:His1043.26
ZnCE1 A:His1043.07
ZnCG A:His1044.36
ZnCB A:Asp2744.24
ZnOD2 A:Asp2743.27
ZnC A:Asp2744.81
ZnOD1 A:Asp2742.06
ZnCG A:Asp2742.93
ZnCA A:Asp2744.68
ZnN A:Asn2754.95
ZnCB A:Asn2753.92
ZnND2 A:Asn2754.39
ZnOD1 A:Asn2754.68
ZnCG A:Asn2754.18
ZnCA A:Asn2754.88
ZnOE1 A:Glu3113.87
ZnOE2 A:Glu3114.38
ZnCD A:Glu3114.31
ZnOE1 A:Glu3123.69
ZnCD A:Glu3124.57
ZnCB A:Asp3564.17
ZnOD2 A:Asp3562.49
ZnOD1 A:Asp3562.10
ZnCG A:Asp3562.64
ZnCA A:Asp3564.86
ZnN A:Met3574.77
ZnZN A:Zn4863.39
ZnN A:Sd34894.08
ZnCB A:Sd34894.79
ZnND2 A:Sd34892.74
ZnOD1 A:Sd34893.93
ZnOAD A:Sd34892.17
ZnCG A:Sd34893.62
ZnCA A:Sd34894.86
ZnO A:Hoh5024.74

interactive model:




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