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Nickel in PDB 2q8e: Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase

Protein crystallography data

The structure of Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase, PDB code: 2q8e was solved by J.-F.Couture, E.Collazo, P.Ortiz-Tello, J.S.Brunzelle, R.C.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.97 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.294, 148.964, 56.810, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 26

Other elements in 2q8e:

The structure of Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase (pdb code 2q8e). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase, PDB code: 2q8e:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2q8e

Go back to Nickel Binding Sites List in 2q8e
Nickel binding site 1 out of 2 in the Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:37.8
occ:1.00
O A:HOH563 1.5 34.0 1.0
NE2 A:HIS276 1.9 40.4 1.0
O2 A:OGA503 2.0 49.5 1.0
OE1 A:GLU190 2.1 47.7 1.0
NE2 A:HIS188 2.1 39.5 1.0
O2' A:OGA503 2.3 46.6 1.0
CE1 A:HIS188 2.8 44.9 1.0
CE1 A:HIS276 2.8 41.9 1.0
C1 A:OGA503 2.9 54.7 1.0
C2 A:OGA503 3.0 53.0 1.0
CD2 A:HIS276 3.0 38.3 1.0
CD A:GLU190 3.2 46.1 1.0
CD2 A:HIS188 3.3 45.6 1.0
OE2 A:GLU190 3.6 44.9 1.0
ND1 A:HIS276 4.0 43.5 1.0
ND1 A:HIS188 4.0 44.7 1.0
O1 A:OGA503 4.1 53.9 1.0
CG A:HIS276 4.1 40.3 1.0
OG A:SER196 4.1 40.6 0.5
CG A:HIS188 4.3 44.0 1.0
N1 A:OGA503 4.3 56.2 1.0
OG A:SER196 4.4 38.4 0.5
CG A:GLU190 4.5 38.9 1.0
O A:HOH580 4.6 58.3 1.0
CB A:SER196 4.7 40.0 1.0
CM3 F:M3L36 4.8 62.9 1.0
CG2 A:THR270 4.8 43.0 1.0
OG1 A:THR270 4.9 43.2 1.0
C4 A:OGA503 5.0 53.7 1.0

Nickel binding site 2 out of 2 in 2q8e

Go back to Nickel Binding Sites List in 2q8e
Nickel binding site 2 out of 2 in the Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:41.2
occ:1.00
O2 B:OGA504 1.8 48.2 1.0
NE2 B:HIS188 2.1 43.7 1.0
NE2 B:HIS276 2.1 45.5 1.0
OE1 B:GLU190 2.2 48.2 1.0
O2' B:OGA504 2.3 40.9 1.0
C1 B:OGA504 2.7 52.0 1.0
CE1 B:HIS188 2.9 44.0 1.0
C2 B:OGA504 2.9 47.9 1.0
CE1 B:HIS276 3.0 45.1 1.0
CD2 B:HIS188 3.2 44.0 1.0
CD B:GLU190 3.2 46.6 1.0
CD2 B:HIS276 3.2 44.3 1.0
OE2 B:GLU190 3.5 44.9 1.0
O1 B:OGA504 3.9 54.1 1.0
ND1 B:HIS188 4.1 42.6 1.0
ND1 B:HIS276 4.1 44.5 1.0
CG B:HIS188 4.2 43.6 1.0
OG B:SER196 4.2 50.5 1.0
N1 B:OGA504 4.3 52.5 1.0
CG B:HIS276 4.3 42.3 1.0
CG B:GLU190 4.5 43.0 1.0
O B:HOH580 4.6 60.3 1.0
CM3 G:M3L36 4.6 61.2 1.0
CG2 B:THR270 4.9 44.5 1.0
OG1 B:THR270 5.0 46.6 1.0

Reference:

J.F.Couture, E.Collazo, P.A.Ortiz-Tello, J.S.Brunzelle, R.C.Trievel. Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase. Nat.Struct.Mol.Biol. V. 14 689 2007.
ISSN: ISSN 1545-9993
PubMed: 17589523
DOI: 10.1038/NSMB1273
Page generated: Thu Oct 29 06:18:00 2020
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