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Nickel in PDB 3ms5: Crystal Structure of Human Gamma-Butyrobetaine,2-Oxoglutarate Dioxygenase 1 (BBOX1)

Enzymatic activity of Crystal Structure of Human Gamma-Butyrobetaine,2-Oxoglutarate Dioxygenase 1 (BBOX1)

All present enzymatic activity of Crystal Structure of Human Gamma-Butyrobetaine,2-Oxoglutarate Dioxygenase 1 (BBOX1):
1.14.11.1;

Protein crystallography data

The structure of Crystal Structure of Human Gamma-Butyrobetaine,2-Oxoglutarate Dioxygenase 1 (BBOX1), PDB code: 3ms5 was solved by T.Krojer, G.Kochan, M.A.Mcdonough, F.Von Delft, I.K.H.Leung, L.Henry, T.D.W.Claridge, E.Pilka, E.Ugochukwu, J.Muniz, P.Filippakopoulos, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.Edwards, K.L.Kavanagh, C.J.Schofield, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.45 / 1.82
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 107.366, 107.366, 205.054, 90.00, 90.00, 120.00
R / Rfree (%) 14.7 / 18.3

Other elements in 3ms5:

The structure of Crystal Structure of Human Gamma-Butyrobetaine,2-Oxoglutarate Dioxygenase 1 (BBOX1) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Human Gamma-Butyrobetaine,2-Oxoglutarate Dioxygenase 1 (BBOX1) (pdb code 3ms5). 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 Crystal Structure of Human Gamma-Butyrobetaine,2-Oxoglutarate Dioxygenase 1 (BBOX1), PDB code: 3ms5:

Nickel binding site 1 out of 1 in 3ms5

Go back to Nickel Binding Sites List in 3ms5
Nickel binding site 1 out of 1 in the Crystal Structure of Human Gamma-Butyrobetaine,2-Oxoglutarate Dioxygenase 1 (BBOX1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human Gamma-Butyrobetaine,2-Oxoglutarate Dioxygenase 1 (BBOX1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni388

b:15.6
occ:1.00
 O2 A:OGA390 2.0 17.1 1.0
NE2 A:HIS347 2.1 13.0 1.0
O2' A:OGA390 2.1 17.3 1.0
NE2 A:HIS202 2.1 12.6 1.0
O A:HOH800 2.1 16.8 1.0
OD1 A:ASP204 2.1 15.7 1.0
C1 A:OGA390 2.7 16.4 1.0
C2 A:OGA390 2.7 16.8 1.0
CD2 A:HIS347 3.0 15.0 1.0
CE1 A:HIS202 3.0 15.1 1.0
CE1 A:HIS347 3.1 13.6 1.0
CD2 A:HIS202 3.1 13.7 1.0
CG A:ASP204 3.1 14.4 1.0
OD2 A:ASP204 3.4 14.4 1.0
O1 A:OGA390 3.9 16.8 1.0
N1 A:OGA390 4.0 16.8 1.0
ND1 A:HIS347 4.1 13.6 1.0
ND1 A:HIS202 4.2 14.6 1.0
CG A:HIS347 4.2 13.1 1.0
CG A:HIS202 4.2 13.2 1.0
O1 A:EDO393 4.2 17.4 1.0
NE2 A:GLN215 4.3 17.7 1.0
OE1 A:GLN215 4.3 20.8 1.0
CB A:ASP204 4.5 14.1 1.0
C1 A:EDO393 4.6 16.2 1.0
C3 A:REE391 4.7 17.0 1.0
CD A:GLN215 4.7 19.0 1.0
C4 A:OGA390 4.8 15.8 1.0
C2 A:REE391 4.8 16.1 1.0
CA A:ASP204 4.9 14.7 1.0
CD1 A:LEU199 5.0 16.2 1.0

Reference:

I.K.Leung, T.J.Krojer, G.T.Kochan, L.Henry, F.Von Delft, T.D.Claridge, U.Oppermann, M.A.Mcdonough, C.J.Schofield. Structural and Mechanistic Studies on Gamma-Butyrobetaine Hydroxylase. Chem. Biol. V. 17 1316 2010.
ISSN: ISSN 1879-1301
PubMed: 21168767
DOI: 10.1016/J.CHEMBIOL.2010.09.016
Page generated: Wed Oct 9 17:32:41 2024

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