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Nickel in PDB 3opt: Crystal Structure of the RPH1 Catalytic Core with A-Ketoglutarate

Enzymatic activity of Crystal Structure of the RPH1 Catalytic Core with A-Ketoglutarate

All present enzymatic activity of Crystal Structure of the RPH1 Catalytic Core with A-Ketoglutarate:
1.14.11.27;

Protein crystallography data

The structure of Crystal Structure of the RPH1 Catalytic Core with A-Ketoglutarate, PDB code: 3opt was solved by Y.Chang, J.Wu, X.Tong, J.Zhou, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.74 / 2.20
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 109.415, 109.415, 145.958, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 23.6

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the RPH1 Catalytic Core with A-Ketoglutarate (pdb code 3opt). 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 the RPH1 Catalytic Core with A-Ketoglutarate, PDB code: 3opt:

Nickel binding site 1 out of 1 in 3opt

Go back to Nickel Binding Sites List in 3opt
Nickel binding site 1 out of 1 in the Crystal Structure of the RPH1 Catalytic Core with A-Ketoglutarate


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 RPH1 Catalytic Core with A-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni500

b:17.9
occ:1.00
NE2 A:HIS323 2.4 7.0 1.0
OE1 A:GLU237 2.4 25.7 1.0
NE2 A:HIS235 2.5 12.2 1.0
O5 A:AKG501 2.6 44.4 1.0
O2 A:AKG501 2.6 49.0 1.0
O A:HOH451 2.7 27.0 1.0
C2 A:AKG501 2.9 34.6 1.0
CD A:GLU237 3.1 22.2 1.0
CE1 A:HIS235 3.2 17.8 1.0
C1 A:AKG501 3.2 38.9 1.0
CD2 A:HIS323 3.2 31.5 1.0
OE2 A:GLU237 3.3 24.6 1.0
CE1 A:HIS323 3.4 41.8 1.0
CD2 A:HIS235 3.7 29.7 1.0
C3 A:AKG501 3.9 30.1 1.0
CG A:GLU237 4.3 26.7 1.0
ND1 A:HIS235 4.4 30.0 1.0
OG A:SER243 4.4 17.6 1.0
O1 A:AKG501 4.4 56.2 1.0
CG A:HIS323 4.4 11.7 1.0
ND1 A:HIS323 4.5 22.4 1.0
CG A:HIS235 4.6 35.4 1.0
C4 A:AKG501 4.7 17.4 1.0
CG2 A:THR317 4.9 7.6 1.0
OG1 A:THR317 5.0 43.1 1.0

Reference:

Y.Chang, J.Wu, X.J.Tong, J.Q.Zhou, J.Ding. Crystal Structure of the Catalytic Core of Saccharomyces Cerevesiae Histone Demethylase RPH1: Insights Into the Substrate Specificity and Catalytic Mechanism Biochem.J. V. 433 295 2011.
ISSN: ISSN 0264-6021
PubMed: 21067515
DOI: 10.1042/BJ20101418
Page generated: Fri Sep 25 08:31:24 2020
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