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Nickel in PDB 2q8d: Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate

Protein crystallography data

The structure of Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate, PDB code: 2q8d 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) 37.80 / 2.29
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.857, 148.642, 57.346, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.1

Other elements in 2q8d:

The structure of Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate (pdb code 2q8d). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate, PDB code: 2q8d:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2q8d

Go back to Nickel Binding Sites List in 2q8d
Nickel binding site 1 out of 2 in the Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate


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 JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:39.3
occ:1.00
NE2 A:HIS276 2.2 34.0 1.0
OE1 A:GLU190 2.2 42.2 1.0
NE2 A:HIS188 2.3 35.4 1.0
O1 A:SIN503 2.3 24.5 0.5
O2 A:SIN503 2.7 25.9 0.5
C1 A:SIN503 2.8 26.7 0.5
CD2 A:HIS276 3.1 31.0 1.0
CE1 A:HIS188 3.2 33.8 1.0
CD A:GLU190 3.2 38.5 1.0
CE1 A:HIS276 3.2 33.2 1.0
CD2 A:HIS188 3.4 33.9 1.0
OE2 A:GLU190 3.4 37.9 1.0
O A:HOH574 4.1 52.0 1.0
OG A:SER196 4.2 36.1 1.0
CG A:HIS276 4.3 32.9 1.0
C2 A:SIN503 4.3 28.4 0.5
ND1 A:HIS188 4.3 34.0 1.0
ND1 A:HIS276 4.3 34.6 1.0
CG A:HIS188 4.4 32.9 1.0
CG A:GLU190 4.6 36.9 1.0
CB A:SER196 4.8 33.3 1.0
CG2 A:THR270 4.9 32.1 1.0
C3 A:SIN503 4.9 28.5 0.5
OG1 A:THR270 4.9 32.6 1.0

Nickel binding site 2 out of 2 in 2q8d

Go back to Nickel Binding Sites List in 2q8d
Nickel binding site 2 out of 2 in the Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate


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 JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:40.8
occ:1.00
NE2 B:HIS188 2.2 34.5 1.0
OE1 B:GLU190 2.3 37.0 1.0
O1 B:SIN504 2.3 31.8 1.0
NE2 B:HIS276 2.3 32.4 1.0
O2 B:SIN504 2.7 33.7 1.0
C1 B:SIN504 2.8 33.2 1.0
CE1 B:HIS188 3.1 35.9 1.0
CD2 B:HIS276 3.2 31.9 1.0
CD B:GLU190 3.3 35.3 1.0
CE1 B:HIS276 3.3 33.0 1.0
CD2 B:HIS188 3.3 34.9 1.0
OE2 B:GLU190 3.6 35.8 1.0
ND1 B:HIS188 4.2 37.1 1.0
C2 B:SIN504 4.3 35.6 1.0
OG B:SER196 4.3 35.1 1.0
CG B:HIS188 4.4 33.2 1.0
CG B:HIS276 4.4 32.1 1.0
ND1 B:HIS276 4.4 34.5 1.0
CG B:GLU190 4.6 33.4 1.0
C3 B:SIN504 4.9 35.3 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: Wed Dec 16 01:19:17 2020

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