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Cadmium in the structure of Crystal Structure of Peptide Deformylase, XOO1075, From Xanthomonas Oryzae Pv. Oryzae KACC10331 (pdb 3dld)

The binding sites of Cadmium atom in the structure of Crystal Structure of Peptide Deformylase, XOO1075, From Xanthomonas Oryzae Pv. Oryzae KACC10331 (pdb code 3dld). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 3dld structure was solved by H.P.-T.NGO, J.K.KIM, J.H.JUNG, L.W.KANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)36.9-2.6
Space groupP6122
a (A)58.968
b (A)58.968
c (A)266.285
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)19.2
Rfree (%)24

Cadmium Binding Sites:

Cadmium binding site 1 out of 3 in 3dld


Cadmium binding site 1 out of 3 in 3dld
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stereopicture of Cadmium binding site 1 out of 3 in 3dld
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3dld. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Arg116, A: Glu128, A: Arg129, A: Glu130, A: Hoh182, A: Hoh199, A: Hoh210, A: Hoh262,

conact list:


AtomAtomDistance (A)
CdCD A:Arg1164.13
CdNH1 A:Arg1164.96
CdO A:Glu1284.20
CdOE1 A:Glu1282.48
CdOE2 A:Glu1282.90
CdCD A:Glu1283.05
CdC A:Glu1284.68
CdCG A:Glu1284.57
CdN A:Arg1294.95
CdC A:Arg1294.80
CdCA A:Arg1294.77
CdN A:Glu1304.59
CdOE1 A:Glu1302.64
CdOE2 A:Glu1302.49
CdCD A:Glu1302.92
CdCG A:Glu1304.46
CdO A:Hoh1822.40
CdO A:Hoh1994.87
CdO A:Hoh2104.56
CdO A:Hoh2624.37

interactive model:


Cadmium binding site 2 out of 3 in 3dld


Cadmium binding site 2 out of 3 in 3dld
Click to enlarge
stereopicture of Cadmium binding site 2 out of 3 in 3dld
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3dld. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Gln51, A: Gly98, A: Cys99, A: Leu100, A: His141, A: Glu142, A: His145, A: Hoh177, A: Hoh192, A: Hoh234, A: Hoh236,

conact list:


AtomAtomDistance (A)
CdNE2 A:Gln513.61
CdOE1 A:Gln513.78
CdCD A:Gln513.89
CdO A:Gly984.24
CdN A:Cys994.95
CdCB A:Cys993.38
CdSG A:Cys992.40
CdC A:Cys994.74
CdCA A:Cys993.82
CdN A:Leu1004.63
CdNE2 A:His1412.31
CdND1 A:His1414.43
CdCD2 A:His1413.22
CdCE1 A:His1413.33
CdCG A:His1414.41
CdOE1 A:Glu1424.41
CdOE2 A:Glu1424.14
CdCD A:Glu1424.70
CdNE2 A:His1452.35
CdND1 A:His1454.38
CdCD2 A:His1453.41
CdCE1 A:His1453.21
CdCG A:His1454.51
CdO A:Hoh1772.14
CdO A:Hoh1923.85
CdO A:Hoh2344.37
CdO A:Hoh2364.47

interactive model:


Cadmium binding site 3 out of 3 in 3dld


Cadmium binding site 3 out of 3 in 3dld
Click to enlarge
stereopicture of Cadmium binding site 3 out of 3 in 3dld
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3dld. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Tyr114, A: Glu132, A: Hoh232,

conact list:


AtomAtomDistance (A)
CdCE2 A:Tyr1144.34
CdCZ A:Tyr1144.96
CdOH A:Tyr1144.49
CdOE1 A:Glu1322.20
CdOE2 A:Glu1323.89
CdCD A:Glu1323.35
CdCG A:Glu1324.50
CdO A:Hoh2322.66

interactive model:




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