Nickel in PDB 4hon: Crystal Structure of Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate

The structure of Crystal Structure of Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate, PDB code: 4hon was solved by S.Krishnan, R.C.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.93 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.202, 79.675, 175.938, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.4

The structure of Crystal Structure of Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate (pdb code 4hon). 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 Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate, PDB code: 4hon:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human JMJD2D/KDM4D in Complex with An 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 Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:13.5 occ:1.00 O2 A:AKG401 2.1 15.0 1.0 O A:HOH507 2.1 19.5 1.0 NE2 A:HIS280 2.1 9.0 1.0 OE1 A:GLU194 2.1 11.6 1.0 NE2 A:HIS192 2.1 15.1 1.0 O5 A:AKG401 2.2 14.8 1.0 C1 A:AKG401 2.8 15.5 1.0 C2 A:AKG401 2.9 13.3 1.0 CE1 A:HIS280 2.9 9.4 1.0 CE1 A:HIS192 3.0 13.3 1.0 CD A:GLU194 3.1 12.1 1.0 CD2 A:HIS280 3.2 9.1 1.0 CD2 A:HIS192 3.2 13.6 1.0 OE2 A:GLU194 3.5 12.2 1.0 O1 A:AKG401 4.1 15.0 1.0 OG A:SER200 4.1 15.0 1.0 ND1 A:HIS280 4.1 9.6 1.0 ND1 A:HIS192 4.2 10.7 1.0 CG A:HIS280 4.2 9.4 1.0 CG A:HIS192 4.3 13.5 1.0 C3 A:AKG401 4.3 15.5 1.0 C2 A:PDO415 4.3 33.0 1.0 CG A:GLU194 4.4 11.4 1.0 C1 A:PDO415 4.4 36.7 1.0 O1 A:PDO415 4.5 33.3 1.0 CM1 F:M3L9 4.5 18.2 1.0 CB A:SER200 4.7 13.8 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human JMJD2D/KDM4D in Complex with An 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 Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:14.2 occ:1.00 O B:HOH508 2.0 19.6 1.0 OE1 B:GLU194 2.1 12.0 1.0 NE2 B:HIS280 2.1 11.6 1.0 NE2 B:HIS192 2.1 12.7 1.0 O2 B:AKG401 2.2 15.4 1.0 O5 B:AKG401 2.2 13.8 1.0 C2 B:AKG401 2.9 18.1 1.0 C1 B:AKG401 2.9 18.4 1.0 CE1 B:HIS192 3.0 14.6 1.0 CE1 B:HIS280 3.0 11.6 1.0 CD B:GLU194 3.1 15.1 1.0 CD2 B:HIS280 3.1 11.1 1.0 CD2 B:HIS192 3.2 13.8 1.0 OE2 B:GLU194 3.5 14.1 1.0 O1 B:AKG401 4.1 17.7 1.0 ND1 B:HIS192 4.1 12.1 1.0 OG B:SER200 4.2 13.8 1.0 ND1 B:HIS280 4.2 12.9 1.0 CG B:HIS280 4.2 12.1 1.0 CG B:HIS192 4.3 12.7 1.0 C3 B:AKG401 4.4 19.3 1.0 CG B:GLU194 4.4 12.6 1.0 O B:HOH649 4.5 29.2 1.0 CM1 G:M3L9 4.5 20.4 1.0 CB B:SER200 4.8 13.0 1.0

S.Krishnan, R.C.Trievel. Structural and Functional Analysis of JMJD2D Reveals Molecular Basis For Site-Specific Demethylation Among JMJD2 Demethylases. Structure V. 21 98 2013.
ISSN: ISSN 0969-2126
PubMed: 23219879
DOI: 10.1016/J.STR.2012.10.018