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Nickel in PDB 3tqd: Structure of the 3-Deoxy-D-Manno-Octulosonate Cytidylyltransferase (Kdsb) From Coxiella Burnetii

Enzymatic activity of Structure of the 3-Deoxy-D-Manno-Octulosonate Cytidylyltransferase (Kdsb) From Coxiella Burnetii

All present enzymatic activity of Structure of the 3-Deoxy-D-Manno-Octulosonate Cytidylyltransferase (Kdsb) From Coxiella Burnetii:
2.7.7.38;

Protein crystallography data

The structure of Structure of the 3-Deoxy-D-Manno-Octulosonate Cytidylyltransferase (Kdsb) From Coxiella Burnetii, PDB code: 3tqd was solved by M.C.Franklin, J.Cheung, M.Rudolph, M.Cassidy, E.Gary, F.Burshteyn, J.Love, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.62 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.752, 51.616, 78.874, 90.00, 111.92, 90.00
R / Rfree (%) 18.8 / 22.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the 3-Deoxy-D-Manno-Octulosonate Cytidylyltransferase (Kdsb) From Coxiella Burnetii (pdb code 3tqd). 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 Structure of the 3-Deoxy-D-Manno-Octulosonate Cytidylyltransferase (Kdsb) From Coxiella Burnetii, PDB code: 3tqd:

Nickel binding site 1 out of 1 in 3tqd

Go back to Nickel Binding Sites List in 3tqd
Nickel binding site 1 out of 1 in the Structure of the 3-Deoxy-D-Manno-Octulosonate Cytidylyltransferase (Kdsb) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the 3-Deoxy-D-Manno-Octulosonate Cytidylyltransferase (Kdsb) From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni300

b:95.7
occ:1.00
 O A:ASN173 2.2 44.0 1.0
OE1 A:GLN175 2.5 49.2 1.0
O A:HOH294 2.5 17.7 1.0
O A:HOH297 2.5 23.9 1.0
CD A:GLN175 3.4 50.3 1.0
C A:ASN173 3.4 44.4 1.0
NE2 A:GLN175 3.9 49.3 1.0
N A:GLN175 4.0 43.1 1.0
CA A:LEU174 4.3 40.8 1.0
N A:LEU174 4.3 41.9 1.0
CB A:ASN173 4.3 47.0 1.0
CA A:ASN173 4.3 45.8 1.0
C A:LEU174 4.5 42.2 1.0
CB A:GLN175 4.5 45.5 1.0
CG A:GLN175 4.5 48.8 1.0
O A:HOH263 4.8 20.6 1.0
CA A:GLN175 4.9 43.3 1.0

Reference:

M.C.Franklin, J.Cheung, M.J.Rudolph, F.Burshteyn, M.Cassidy, E.Gary, B.Hillerich, Z.K.Yao, P.R.Carlier, M.Totrov, J.D.Love. Structural Genomics For Drug Design Against the Pathogen Coxiella Burnetii. Proteins V. 83 2124 2015.
ISSN: ISSN 0887-3585
PubMed: 26033498
DOI: 10.1002/PROT.24841
Page generated: Mon Aug 18 19:00:30 2025

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