Nickel in PDB 3u4s: Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine

The structure of Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine, PDB code: 3u4s was solved by J.Ma, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.28 / 2.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.819, 150.060, 55.917, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.2

The structure of Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine (pdb code 3u4s). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine, PDB code: 3u4s:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:30.6 occ:1.00 OE2 A:GLU190 2.1 24.6 1.0 NE2 A:HIS276 2.2 20.4 1.0 NE2 A:HIS188 2.2 23.5 1.0 OAX A:08P503 2.2 30.9 1.0 OAW A:08P503 2.2 29.6 1.0 O A:HOH719 2.3 31.5 1.0 CAR A:08P503 2.8 31.9 1.0 CAS A:08P503 2.9 31.4 1.0 CE1 A:HIS188 3.0 24.8 1.0 CE1 A:HIS276 3.0 22.1 1.0 CD A:GLU190 3.1 25.7 1.0 CD2 A:HIS276 3.2 20.2 1.0 CD2 A:HIS188 3.2 25.8 1.0 OE1 A:GLU190 3.4 27.8 1.0 HM13 C:M3L9 3.9 39.3 1.0 OAY A:08P503 4.1 30.4 1.0 ND1 A:HIS188 4.1 23.8 1.0 N A:08P503 4.2 36.0 1.0 ND1 A:HIS276 4.2 22.4 1.0 OG A:SER196 4.2 35.8 1.0 CG A:HIS188 4.3 23.9 1.0 CG A:HIS276 4.3 22.9 1.0 CG A:GLU190 4.4 23.0 1.0 HA A:08P503 4.6 42.0 1.0 O A:HOH650 4.6 36.9 1.0 S A:08P503 4.6 78.7 1.0 HM31 C:M3L9 4.8 36.4 1.0 H A:08P503 4.8 43.2 1.0 CM1 C:M3L9 4.8 32.7 1.0 CG2 A:THR270 4.9 30.1 1.0 CB A:SER196 4.9 28.9 1.0 CA A:08P503 4.9 35.0 1.0 HE3 C:M3L9 5.0 40.5 1.0

Nickel binding site 2 out of 2 in the Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:29.4 occ:1.00 OAX B:08P503 1.9 24.6 1.0 NE2 B:HIS188 2.1 23.2 1.0 NE2 B:HIS276 2.1 25.6 1.0 OE2 B:GLU190 2.2 28.9 1.0 OAW B:08P503 2.2 28.2 1.0 O B:HOH752 2.3 33.5 1.0 CAS B:08P503 2.7 31.2 1.0 CAR B:08P503 2.8 31.1 1.0 CE1 B:HIS188 2.8 28.2 1.0 CE1 B:HIS276 3.0 26.8 1.0 CD2 B:HIS276 3.1 20.3 1.0 CD B:GLU190 3.2 30.4 1.0 CD2 B:HIS188 3.2 29.2 1.0 OE1 B:GLU190 3.5 34.3 1.0 HM12 D:M3L9 3.8 49.6 1.0 OAY B:08P503 3.9 31.1 1.0 ND1 B:HIS188 4.0 25.6 1.0 ND1 B:HIS276 4.1 26.2 1.0 N B:08P503 4.1 35.5 1.0 CG B:HIS188 4.2 27.5 1.0 CG B:HIS276 4.2 25.2 1.0 OG B:SER196 4.3 38.0 1.0 O B:HOH670 4.4 36.0 1.0 S B:08P503 4.4 55.0 1.0 CG B:GLU190 4.5 30.5 1.0 HA B:08P503 4.6 41.5 1.0 HM32 D:M3L9 4.6 50.7 1.0 H B:08P503 4.7 42.5 1.0 CM1 D:M3L9 4.8 41.3 1.0 CA B:08P503 4.9 34.6 1.0 CB B:SER196 4.9 32.0 1.0 HM13 D:M3L9 5.0 49.6 1.0

E.C.Woon, A.Tumber, A.Kawamura, L.Hillringhaus, W.Ge, N.R.Rose, J.H.Ma, M.C.Chan, L.J.Walport, K.H.Che, S.S.Ng, B.D.Marsden, U.Oppermann, M.A.Mcdonough, C.J.Schofield. Linking of 2-Oxoglutarate and Substrate Binding Sites Enables Potent and Highly Selective Inhibition of Jmjc Histone Demethylases. Angew.Chem.Int.Ed.Engl. V. 51 1631 2012.
ISSN: ISSN 1433-7851
PubMed: 22241642
DOI: 10.1002/ANIE.201107833