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Nickel in PDB 2w2i: Crystal Structure of the Human 2-Oxoglutarate Oxygenase LOC390245

Protein crystallography data

The structure of Crystal Structure of the Human 2-Oxoglutarate Oxygenase LOC390245, PDB code: 2w2i was solved by W.W.Yue, S.Ng, N.Shafqat, E.Ugochukwu, M.Mcdonough, A.C.W.Pike, P.Filippakopoulos, F.Von Delft, C.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, C.Schofield, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 111.80 / 2.1
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 90.904, 111.009, 224.199, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.6

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Human 2-Oxoglutarate Oxygenase LOC390245 (pdb code 2w2i). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of the Human 2-Oxoglutarate Oxygenase LOC390245, PDB code: 2w2i:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 2w2i

Go back to Nickel Binding Sites List in 2w2i
Nickel binding site 1 out of 3 in the Crystal Structure of the Human 2-Oxoglutarate Oxygenase LOC390245


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 the Human 2-Oxoglutarate Oxygenase LOC390245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni601

b:26.9
occ:1.00
O A:HOH2114 1.9 6.8 1.0
NE2 A:HIS189 2.0 2.0 1.0
O22 A:PD2602 2.1 32.2 1.0
N1 A:PD2602 2.2 21.5 1.0
NE2 A:HIS277 2.2 14.8 1.0
OE2 A:GLU191 2.2 12.4 1.0
C21 A:PD2602 2.8 24.3 1.0
CE1 A:HIS189 2.9 8.6 1.0
C2 A:PD2602 2.9 21.6 1.0
CE1 A:HIS277 3.0 13.3 1.0
CD2 A:HIS189 3.1 10.0 1.0
C6 A:PD2602 3.2 27.1 1.0
CD A:GLU191 3.2 10.9 1.0
CD2 A:HIS277 3.3 8.1 1.0
O A:HOH2089 3.6 32.7 1.0
O A:HOH2112 3.6 18.0 1.0
OE1 A:GLU191 3.7 5.6 1.0
O21 A:PD2602 4.0 36.5 1.0
ND1 A:HIS189 4.0 2.4 1.0
CG A:HIS189 4.2 4.6 1.0
ND1 A:HIS277 4.2 15.9 1.0
O A:HOH2111 4.2 28.1 1.0
C3 A:PD2602 4.3 27.1 1.0
CG A:HIS277 4.4 8.9 1.0
OG A:SER197 4.4 14.5 1.0
C5 A:PD2602 4.4 26.6 1.0
CG A:GLU191 4.5 5.6 1.0
C4 A:PD2602 4.9 22.2 1.0
O A:HOH2080 4.9 15.5 1.0

Nickel binding site 2 out of 3 in 2w2i

Go back to Nickel Binding Sites List in 2w2i
Nickel binding site 2 out of 3 in the Crystal Structure of the Human 2-Oxoglutarate Oxygenase LOC390245


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Human 2-Oxoglutarate Oxygenase LOC390245 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni401

b:30.4
occ:1.00
O B:HOH2078 1.9 4.5 1.0
NE2 B:HIS189 2.0 2.0 1.0
O22 B:PD2402 2.2 36.6 1.0
N1 B:PD2402 2.2 25.5 1.0
OE2 B:GLU191 2.2 13.1 1.0
NE2 B:HIS277 2.2 14.8 1.0
C21 B:PD2402 2.8 32.8 1.0
CE1 B:HIS189 2.8 8.7 1.0
C2 B:PD2402 2.9 29.6 1.0
CE1 B:HIS277 3.1 13.1 1.0
CD2 B:HIS189 3.1 9.9 1.0
C6 B:PD2402 3.2 33.1 1.0
CD B:GLU191 3.2 11.3 1.0
CD2 B:HIS277 3.3 8.4 1.0
O B:HOH2080 3.5 30.0 1.0
OE1 B:GLU191 3.7 5.6 1.0
O B:HOH2120 3.7 9.3 1.0
O21 B:PD2402 4.0 41.2 1.0
ND1 B:HIS189 4.0 2.0 1.0
CG B:HIS189 4.1 5.2 1.0
ND1 B:HIS277 4.2 16.1 1.0
O B:HOH2119 4.3 22.6 1.0
C3 B:PD2402 4.3 27.7 1.0
CG B:HIS277 4.4 9.0 1.0
CG B:GLU191 4.5 5.6 1.0
C5 B:PD2402 4.5 28.6 1.0
OG B:SER197 4.5 14.6 1.0
C4 B:PD2402 4.9 28.1 1.0

Nickel binding site 3 out of 3 in 2w2i

Go back to Nickel Binding Sites List in 2w2i
Nickel binding site 3 out of 3 in the Crystal Structure of the Human 2-Oxoglutarate Oxygenase LOC390245


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Human 2-Oxoglutarate Oxygenase LOC390245 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni501

b:35.7
occ:1.00
O C:HOH2066 1.9 2.0 1.0
NE2 C:HIS189 1.9 2.0 1.0
N1 C:PD2502 2.2 30.8 1.0
OE2 C:GLU191 2.2 12.0 1.0
NE2 C:HIS277 2.2 15.1 1.0
O22 C:PD2502 2.3 40.9 1.0
C21 C:PD2502 2.8 30.3 1.0
CE1 C:HIS189 2.8 8.2 1.0
C2 C:PD2502 2.9 34.1 1.0
CD2 C:HIS189 3.0 10.1 1.0
CE1 C:HIS277 3.1 13.1 1.0
CD C:GLU191 3.2 10.9 1.0
C6 C:PD2502 3.2 45.9 1.0
CD2 C:HIS277 3.3 8.1 1.0
OE1 C:GLU191 3.7 5.0 1.0
O C:HOH2070 3.8 31.2 1.0
O C:HOH2103 3.9 7.2 1.0
O C:HOH2104 4.0 25.1 1.0
O21 C:PD2502 4.0 38.9 1.0
ND1 C:HIS189 4.0 2.2 1.0
CG C:HIS189 4.1 4.9 1.0
ND1 C:HIS277 4.2 16.4 1.0
C3 C:PD2502 4.3 34.1 1.0
CG C:HIS277 4.4 8.4 1.0
CG C:GLU191 4.4 5.7 1.0
OG C:SER197 4.5 14.1 1.0
C5 C:PD2502 4.5 46.6 1.0
C4 C:PD2502 4.9 40.8 1.0

Reference:

L.Hillringhaus, W.W.Yue, N.R.Rose, S.S.Ng, C.Gileadi, C.Loenarz, S.H.Bello, J.E.Bray, C.J.Schofield, U.Oppermann. Structural and Evolutionary Basis For the Dual Substrate Selectivity of Human KDM4 Histone Demethylase Family. J.Biol.Chem. V. 286 41616 2011.
ISSN: ISSN 0021-9258
PubMed: 21914792
DOI: 10.1074/JBC.M111.283689
Page generated: Fri Sep 25 08:15:48 2020
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