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Vanadium in PDB 6edh: Taurine:2OG Dioxygenase (Taud) Bound to the Vanadyl Ion, Taurine, and Succinate

Enzymatic activity of Taurine:2OG Dioxygenase (Taud) Bound to the Vanadyl Ion, Taurine, and Succinate

All present enzymatic activity of Taurine:2OG Dioxygenase (Taud) Bound to the Vanadyl Ion, Taurine, and Succinate:
1.14.11.17;

Protein crystallography data

The structure of Taurine:2OG Dioxygenase (Taud) Bound to the Vanadyl Ion, Taurine, and Succinate, PDB code: 6edh was solved by K.M.Davis, M.Altmyer, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.35 / 1.73
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.410, 54.199, 87.385, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.5

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Taurine:2OG Dioxygenase (Taud) Bound to the Vanadyl Ion, Taurine, and Succinate (pdb code 6edh). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Taurine:2OG Dioxygenase (Taud) Bound to the Vanadyl Ion, Taurine, and Succinate, PDB code: 6edh:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 6edh

Go back to Vanadium Binding Sites List in 6edh
Vanadium binding site 1 out of 2 in the Taurine:2OG Dioxygenase (Taud) Bound to the Vanadyl Ion, Taurine, and Succinate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Taurine:2OG Dioxygenase (Taud) Bound to the Vanadyl Ion, Taurine, and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V302

b:26.8
occ:1.00
V1 A:VVO302 0.0 26.8 1.0
O1 A:VVO302 1.8 28.9 1.0
O A:HOH436 2.0 29.9 1.0
NE2 A:HIS255 2.1 24.6 1.0
O A:HOH485 2.1 33.4 1.0
NE2 A:HIS99 2.2 26.0 1.0
OD1 A:ASP101 2.2 25.5 1.0
CE1 A:HIS255 3.0 23.8 1.0
CE1 A:HIS99 3.1 27.2 1.0
CD2 A:HIS255 3.1 24.6 1.0
CG A:ASP101 3.1 30.2 1.0
CD2 A:HIS99 3.2 24.6 1.0
OD2 A:ASP101 3.4 31.7 1.0
OD1 A:ASN95 4.0 52.5 1.0
O A:HOH429 4.1 42.5 1.0
ND1 A:HIS255 4.2 23.0 1.0
O A:HOH534 4.2 42.0 1.0
ND1 A:HIS99 4.2 23.3 1.0
CG A:HIS255 4.2 22.2 1.0
CG A:HIS99 4.3 23.2 1.0
CG A:ASN95 4.3 51.6 1.0
CB A:ASP101 4.5 24.3 1.0
ND2 A:ASN95 4.7 52.8 1.0
O A:HOH538 4.8 46.1 1.0
NH1 A:ARG270 4.8 58.1 1.0
CA A:ASP101 4.9 23.0 1.0
O A:HOH515 4.9 28.0 1.0
CB A:ASN95 4.9 41.5 1.0

Vanadium binding site 2 out of 2 in 6edh

Go back to Vanadium Binding Sites List in 6edh
Vanadium binding site 2 out of 2 in the Taurine:2OG Dioxygenase (Taud) Bound to the Vanadyl Ion, Taurine, and Succinate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Taurine:2OG Dioxygenase (Taud) Bound to the Vanadyl Ion, Taurine, and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V302

b:23.0
occ:1.00
V1 B:VVO302 0.0 23.0 1.0
O1 B:VVO302 1.9 36.8 1.0
OD1 B:ASP101 2.1 22.1 1.0
NE2 B:HIS255 2.1 23.3 1.0
NE2 B:HIS99 2.1 21.9 1.0
O4 B:SIN301 2.1 39.4 1.0
O3 B:SIN301 2.2 29.8 1.0
C4 B:SIN301 2.5 37.4 1.0
CG B:ASP101 3.0 22.4 1.0
CD2 B:HIS99 3.0 23.0 1.0
CE1 B:HIS255 3.0 22.1 1.0
CD2 B:HIS255 3.1 21.0 1.0
CE1 B:HIS99 3.1 23.3 1.0
OD2 B:ASP101 3.2 26.5 1.0
NH1 B:ARG270 3.7 25.3 1.0
OD1 B:ASN95 3.9 30.9 1.0
C3 B:SIN301 4.0 36.5 1.0
ND1 B:HIS255 4.1 22.8 1.0
CG B:HIS99 4.2 19.2 1.0
CG B:HIS255 4.2 20.1 1.0
ND1 B:HIS99 4.2 21.3 1.0
CB B:ASP101 4.4 22.6 1.0
C2 B:TAU303 4.4 31.1 1.0
CG B:ASN95 4.6 37.1 1.0
CA B:ASP101 4.8 23.1 1.0
C2 B:SIN301 4.8 33.1 1.0
CZ B:ARG270 4.9 27.4 1.0
O3 B:TAU303 4.9 28.3 1.0
CZ2 B:TRP248 5.0 26.3 1.0
N B:ASP101 5.0 20.2 1.0

Reference:

K.M.Davis, M.Altmyer, R.J.Martinie, I.Schaperdoth, C.Krebs, J.M.Bollinger Jr., A.K.Boal. Structure of A Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-Glutarate-Dependent Dioxygenase, Taud. Biochemistry V. 58 4218 2019.
ISSN: ISSN 0006-2960
PubMed: 31503454
DOI: 10.1021/ACS.BIOCHEM.9B00598
Page generated: Wed Dec 16 02:31:44 2020

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