Atomistry » Vanadium » PDB 4zi4-6py9 » 6edh
Atomistry »
  Vanadium »
    PDB 4zi4-6py9 »
      6edh »

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: Fri Oct 11 20:04:16 2024

Last articles

Cl in 5SGZ
Cl in 5SGY
Cl in 5SGR
Cl in 5SGB
Cl in 5SGG
Cl in 5SFP
Cl in 5SFG
Cl in 5SF7
Cl in 5SG4
Cl in 5SEZ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy