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Vanadium in PDB 6db2: X-Ray Crystal Structure of Vioc Bound to Vanadyl Ion, L-Homoarginine, and Succinate

Enzymatic activity of X-Ray Crystal Structure of Vioc Bound to Vanadyl Ion, L-Homoarginine, and Succinate

All present enzymatic activity of X-Ray Crystal Structure of Vioc Bound to Vanadyl Ion, L-Homoarginine, and Succinate:
1.14.11.41;

Protein crystallography data

The structure of X-Ray Crystal Structure of Vioc Bound to Vanadyl Ion, L-Homoarginine, and Succinate, PDB code: 6db2 was solved by N.P.Dunham, A.J.Mitchell, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.61 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.025, 66.637, 63.224, 90.00, 109.47, 90.00
R / Rfree (%) 17.5 / 20

Vanadium Binding Sites:

The binding sites of Vanadium atom in the X-Ray Crystal Structure of Vioc Bound to Vanadyl Ion, L-Homoarginine, and Succinate (pdb code 6db2). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total only one binding site of Vanadium was determined in the X-Ray Crystal Structure of Vioc Bound to Vanadyl Ion, L-Homoarginine, and Succinate, PDB code: 6db2:

Vanadium binding site 1 out of 1 in 6db2

Go back to Vanadium Binding Sites List in 6db2
Vanadium binding site 1 out of 1 in the X-Ray Crystal Structure of Vioc Bound to Vanadyl Ion, L-Homoarginine, and Succinate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of X-Ray Crystal Structure of Vioc Bound to Vanadyl Ion, L-Homoarginine, and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V403

b:9.0
occ:1.00
V1 A:VVO403 0.0 9.0 1.0
O1 A:VVO403 1.7 12.7 1.0
OE1 A:GLU170 2.0 9.8 1.0
O4 A:SIN401 2.1 13.8 1.0
NE2 A:HIS316 2.2 8.6 1.0
NE2 A:HIS168 2.2 9.0 1.0
O3 A:SIN401 2.5 16.8 1.0
C4 A:SIN401 2.6 14.8 1.0
CE1 A:HIS316 3.0 8.6 1.0
CD A:GLU170 3.0 9.8 1.0
CE1 A:HIS168 3.2 9.0 1.0
CD2 A:HIS316 3.2 8.5 1.0
CD2 A:HIS168 3.3 9.0 1.0
OE2 A:GLU170 3.4 10.1 1.0
ND1 A:HIS316 4.1 8.5 1.0
C3 A:SIN401 4.1 14.2 1.0
NH1 A:ARG334 4.2 12.5 1.0
CG A:HIS316 4.2 8.4 1.0
ND1 A:HIS168 4.3 8.7 1.0
CG A:HIS168 4.4 8.8 1.0
CG A:GLU170 4.4 9.3 1.0
CB A:HRG402 4.6 14.1 1.0
CB A:GLU170 4.7 9.1 1.0
N A:HRG402 4.8 14.6 1.0
CG' A:HRG402 4.9 13.5 1.0
C2 A:SIN401 4.9 13.5 1.0
CD2 A:LEU165 4.9 9.7 1.0
CG A:HRG402 5.0 13.1 1.0
CA A:GLU170 5.0 8.8 1.0

Reference:

N.P.Dunham, W.C.Chang, A.J.Mitchell, R.J.Martinie, B.Zhang, J.A.Bergman, L.J.Rajakovich, B.Wang, A.Silakov, C.Krebs, A.K.Boal, J.M.Bollinger. Two Distinct Mechanisms For C-C Desaturation By Iron(II)- and 2-(Oxo)Glutarate-Dependent Oxygenases: Importance of Alpha-Heteroatom Assistance. J. Am. Chem. Soc. V. 140 7116 2018.
ISSN: ESSN 1520-5126
PubMed: 29708749
DOI: 10.1021/JACS.8B01933
Page generated: Thu Oct 29 07:05:59 2020

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