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Nickel in PDB 3sw8: Strep Peptide Deformylase with A Time Dependent Dichlorobenzamide- Reverse Hydroxamic Acid

Enzymatic activity of Strep Peptide Deformylase with A Time Dependent Dichlorobenzamide- Reverse Hydroxamic Acid

All present enzymatic activity of Strep Peptide Deformylase with A Time Dependent Dichlorobenzamide- Reverse Hydroxamic Acid:
3.5.1.88;

Protein crystallography data

The structure of Strep Peptide Deformylase with A Time Dependent Dichlorobenzamide- Reverse Hydroxamic Acid, PDB code: 3sw8 was solved by N.Campobasso, K.J.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.12 / 1.70
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 50.015, 50.015, 91.605, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.3

Other elements in 3sw8:

The structure of Strep Peptide Deformylase with A Time Dependent Dichlorobenzamide- Reverse Hydroxamic Acid also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Strep Peptide Deformylase with A Time Dependent Dichlorobenzamide- Reverse Hydroxamic Acid (pdb code 3sw8). 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 Dichlorobenzamide- Reverse Hydroxamic Acid, PDB code: 3sw8:

Nickel binding site 1 out of 1 in 3sw8

Go back to Nickel Binding Sites List in 3sw8
Nickel binding site 1 out of 1 in the Strep Peptide Deformylase with A Time Dependent Dichlorobenzamide- Reverse Hydroxamic Acid


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 Dichlorobenzamide- Reverse Hydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ni204

b:24.6
occ:1.00
 O13 P:5LI205 2.2 17.5 1.0
NE2 P:HIS177 2.2 17.0 1.0
O15 P:5LI205 2.3 23.1 1.0
NE2 P:HIS173 2.3 19.3 1.0
SG P:CYS130 2.5 22.3 1.0
C7 P:5LI205 2.8 19.4 1.0
N12 P:5LI205 2.9 21.2 1.0
CE1 P:HIS177 3.2 15.4 1.0
CD2 P:HIS173 3.2 18.4 1.0
CD2 P:HIS177 3.2 14.2 1.0
CE1 P:HIS173 3.4 20.7 1.0
NE2 P:GLN77 3.4 17.7 1.0
CB P:CYS130 3.6 19.8 1.0
O P:HOH244 3.8 20.9 1.0
CA P:CYS130 3.9 20.4 1.0
CD P:GLN77 3.9 14.9 1.0
OE1 P:GLN77 4.1 14.8 1.0
C10 P:5LI205 4.3 23.9 1.0
ND1 P:HIS177 4.3 17.8 1.0
CG P:HIS177 4.3 14.3 1.0
N P:LEU131 4.4 19.0 1.0
CG P:HIS173 4.4 16.2 1.0
ND1 P:HIS173 4.5 18.0 1.0
OE1 P:GLU174 4.5 15.4 1.0
C P:CYS130 4.6 21.5 1.0
C9 P:5LI205 4.7 27.2 1.0
N11 P:5LI205 4.7 22.5 1.0
O P:HOH215 4.8 16.1 1.0
OE2 P:GLU174 4.8 20.3 1.0
O P:GLY129 4.8 22.7 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: Wed Dec 16 01:27:50 2020

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