Atomistry » Nickel » PDB 2pr0-2w3u » 2q8c
Atomistry »
  Nickel »
    PDB 2pr0-2w3u »
      2q8c »

Nickel in PDB 2q8c: Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate

Protein crystallography data

The structure of Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate, PDB code: 2q8c 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) 28.90 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.887, 149.121, 57.056, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23.6

Other elements in 2q8c:

The structure of Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate (pdb code 2q8c). 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 JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate, PDB code: 2q8c:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2q8c

Go back to Nickel Binding Sites List in 2q8c
Nickel binding site 1 out of 2 in the Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate


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 JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:29.7
occ:1.00
O2 A:AKG503 1.5 39.6 1.0
O A:HOH609 1.9 39.9 1.0
NE2 A:HIS276 2.0 37.0 1.0
OE1 A:GLU190 2.1 39.2 1.0
NE2 A:HIS188 2.1 37.7 1.0
C1 A:AKG503 2.4 42.5 1.0
O5 A:AKG503 2.5 37.0 1.0
C2 A:AKG503 2.9 37.5 1.0
CE1 A:HIS276 2.9 36.8 1.0
CE1 A:HIS188 3.0 39.3 1.0
CD2 A:HIS276 3.1 35.4 1.0
CD A:GLU190 3.1 39.7 1.0
CD2 A:HIS188 3.2 38.8 1.0
OE2 A:GLU190 3.5 38.4 1.0
O1 A:AKG503 3.6 40.2 1.0
O A:HOH540 4.0 51.7 1.0
ND1 A:HIS276 4.1 37.1 1.0
ND1 A:HIS188 4.1 40.9 1.0
CG A:HIS276 4.2 36.4 1.0
CG A:HIS188 4.3 38.3 1.0
OG A:SER196 4.3 41.0 1.0
O A:HOH550 4.4 40.6 1.0
C3 A:AKG503 4.4 39.5 1.0
CG A:GLU190 4.5 36.2 1.0
CM3 F:M3L9 4.7 51.2 1.0
CG2 A:THR270 4.9 37.5 1.0
CB A:SER196 4.9 37.7 1.0
OG1 A:THR270 4.9 38.2 1.0

Nickel binding site 2 out of 2 in 2q8c

Go back to Nickel Binding Sites List in 2q8c
Nickel binding site 2 out of 2 in the Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate


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 JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:30.1
occ:1.00
O2 B:AKG504 1.8 40.2 1.0
NE2 B:HIS276 2.1 39.8 1.0
O B:HOH600 2.1 48.3 1.0
NE2 B:HIS188 2.1 35.8 1.0
OE1 B:GLU190 2.2 39.1 1.0
O5 B:AKG504 2.4 32.2 1.0
C1 B:AKG504 2.7 40.5 1.0
C2 B:AKG504 2.9 36.8 1.0
CE1 B:HIS188 3.0 38.4 1.0
CE1 B:HIS276 3.0 38.0 1.0
CD2 B:HIS276 3.1 37.6 1.0
CD2 B:HIS188 3.2 37.8 1.0
CD B:GLU190 3.2 39.0 1.0
OE2 B:GLU190 3.5 39.1 1.0
O1 B:AKG504 3.9 43.9 1.0
ND1 B:HIS276 4.1 38.0 1.0
ND1 B:HIS188 4.1 36.9 1.0
CG B:HIS276 4.2 36.1 1.0
CG B:HIS188 4.2 36.4 1.0
OG B:SER196 4.3 40.0 1.0
C3 B:AKG504 4.5 37.9 1.0
CG B:GLU190 4.5 36.8 1.0
O B:HOH579 4.6 46.4 1.0
CM3 G:M3L9 4.6 49.0 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 06:17:57 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy