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Nickel in PDB 3e3u: Crystal Structure of Mycobacterium Tuberculosis Peptide Deformylase in Complex with Inhibitor

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Peptide Deformylase in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Peptide Deformylase in Complex with Inhibitor:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Peptide Deformylase in Complex with Inhibitor, PDB code: 3e3u was solved by W.Meng, M.Xu, S.Pan, J.Koehn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.32 / 1.56
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.870, 54.765, 40.215, 90.00, 94.39, 90.00
R / Rfree (%) 17.1 / 20.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Mycobacterium Tuberculosis Peptide Deformylase in Complex with Inhibitor (pdb code 3e3u). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Mycobacterium Tuberculosis Peptide Deformylase in Complex with Inhibitor, PDB code: 3e3u:

Nickel binding site 1 out of 1 in 3e3u

Go back to Nickel Binding Sites List in 3e3u
Nickel binding site 1 out of 1 in the Crystal Structure of Mycobacterium Tuberculosis Peptide Deformylase in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Peptide Deformylase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni200

b:13.2
occ:1.00
O35 A:NVC201 2.0 13.0 1.0
NE2 A:HIS148 2.0 13.4 1.0
NE2 A:HIS152 2.1 15.2 1.0
O39 A:NVC201 2.4 13.3 1.0
SG A:CYS106 2.4 12.6 1.0
N34 A:NVC201 2.8 12.3 1.0
C37 A:NVC201 3.0 13.0 1.0
CE1 A:HIS152 3.0 10.7 1.0
CE1 A:HIS148 3.0 9.6 1.0
CD2 A:HIS148 3.0 9.7 1.0
CD2 A:HIS152 3.1 9.9 1.0
NE2 A:GLN56 3.2 13.7 1.0
CB A:CYS106 3.5 12.1 1.0
O A:HOH219 3.7 15.4 1.0
CD A:GLN56 3.8 12.6 1.0
CA A:CYS106 3.8 11.6 1.0
OE1 A:GLN56 4.0 12.4 1.0
ND1 A:HIS148 4.1 13.9 1.0
N A:LEU107 4.1 11.7 1.0
ND1 A:HIS152 4.1 15.6 1.0
C31 A:NVC201 4.1 12.9 1.0
CG A:HIS148 4.2 10.4 1.0
CG A:HIS152 4.2 12.8 1.0
C A:CYS106 4.4 11.2 1.0
C29 A:NVC201 4.5 11.4 1.0
OE1 A:GLU149 4.7 11.8 1.0
C40 A:NVC201 4.7 12.3 1.0
CG A:GLN56 4.8 10.6 1.0
N A:SER108 4.8 11.6 1.0
O A:GLY105 4.9 12.1 1.0
O A:HOH213 4.9 12.7 1.0

Reference:

A.Pichota, J.Duraiswamy, Z.Yin, T.H.Keller, J.Alam, S.Liung, G.Lee, M.Ding, G.Wang, W.L.Chan, M.Schreiber, I.Ma, D.Beer, X.Ngew, K.Mukherjee, M.Nanjundappa, J.W.Teo, P.Thayalan, A.Yap, T.Dick, W.Meng, M.Xu, J.Koehn, S.H.Pan, K.Clark, X.Xie, C.Shoen, M.Cynamon. Peptide Deformylase Inhibitors of Mycobacterium Tuberculosis: Synthesis, Structural Investigations, and Biological Results. Bioorg.Med.Chem.Lett. V. 18 6568 2008.
ISSN: ISSN 0960-894X
PubMed: 19008098
DOI: 10.1016/J.BMCL.2008.10.040
Page generated: Fri Sep 25 08:21:27 2020
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