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Nickel in PDB 3svj: Strep Peptide Deformylase with A Time Dependent Thiazolidine Amide

Enzymatic activity of Strep Peptide Deformylase with A Time Dependent Thiazolidine Amide

All present enzymatic activity of Strep Peptide Deformylase with A Time Dependent Thiazolidine Amide:
3.5.1.88;

Protein crystallography data

The structure of Strep Peptide Deformylase with A Time Dependent Thiazolidine Amide, PDB code: 3svj was solved by N.Campobasso, P.Ward, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.07 / 1.55
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 50.385, 50.385, 92.472, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.8

Other elements in 3svj:

The structure of Strep Peptide Deformylase with A Time Dependent Thiazolidine Amide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Strep Peptide Deformylase with A Time Dependent Thiazolidine Amide (pdb code 3svj). 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 Strep Peptide Deformylase with A Time Dependent Thiazolidine Amide, PDB code: 3svj:

Nickel binding site 1 out of 1 in 3svj

Go back to Nickel Binding Sites List in 3svj
Nickel binding site 1 out of 1 in the Strep Peptide Deformylase with A Time Dependent Thiazolidine Amide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Strep Peptide Deformylase with A Time Dependent Thiazolidine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ni208

b:50.7
occ:1.00
 NE2 P:HIS173 2.1 25.3 1.0
NE2 P:HIS177 2.2 24.2 1.0
O P:HOH291 2.3 30.7 1.0
SG P:OCS130 2.6 34.8 1.0
O P:HOH295 2.9 45.9 1.0
CD2 P:HIS173 3.0 30.1 1.0
CE1 P:HIS177 3.1 30.2 1.0
CD2 P:HIS177 3.2 24.5 1.0
CE1 P:HIS173 3.2 28.6 1.0
OD1 P:OCS130 3.5 35.7 1.0
OD2 P:OCS130 3.5 36.1 1.0
NE2 P:GLN77 3.6 25.2 1.0
CB P:OCS130 3.7 28.5 1.0
O P:HOH266 3.9 29.6 1.0
CD P:GLN77 4.0 25.0 1.0
OE1 P:GLN77 4.0 24.3 1.0
CA P:OCS130 4.2 27.0 1.0
CG P:HIS173 4.2 24.5 1.0
OE2 P:GLU174 4.2 27.9 1.0
ND1 P:HIS177 4.3 26.5 1.0
ND1 P:HIS173 4.3 26.9 1.0
CG P:HIS177 4.3 25.0 1.0
N P:LEU131 4.6 31.6 1.0
OE1 P:GLU174 4.7 28.9 1.0
O P:HOH260 4.7 27.9 1.0
CD P:GLU174 4.8 28.0 1.0
O P:GLY129 4.9 32.2 1.0
C P:OCS130 4.9 31.8 1.0

Reference:

R.Totoritis, C.Duraiswami, A.N.Taylor, J.J.Kerrigan, N.Campobasso, K.J.Smith, P.Ward, B.W.King, M.Murrayz-Thompson, A.D.Jones, G.S.Van Aller, K.M.Aubart, M.Zalacain, S.H.Thrall, T.D.Meek, B.Schwartz. Understanding the Origins of Time-Dependent Inhibition By Polypeptide Deformylase Inhibitors. Biochemistry V. 50 6642 2011.
ISSN: ISSN 0006-2960
PubMed: 21711014
DOI: 10.1021/BI200655G
Page generated: Mon Aug 18 18:58:47 2025

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