Zinc in PDB 4v2w: JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35)

The structure of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35), PDB code: 4v2w was solved by R.Chowdhury, D.Zafred, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.072 / 1.81
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.711, 149.740, 57.508, 90.00, 90.00, 90.00
R / Rfree (%)	17.24 / 20.82

The structure of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35) also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35) (pdb code 4v2w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35), PDB code: 4v2w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:37.3 occ:1.00 SG A:CYS306 2.2 40.7 1.0 NE2 A:HIS240 2.2 34.6 1.0 SG A:CYS234 2.3 37.3 1.0 SG A:CYS308 2.3 48.0 1.0 H A:CYS308 2.8 77.7 1.0 HB2 A:CYS234 3.0 51.9 1.0 CB A:CYS234 3.2 43.2 1.0 CD2 A:HIS240 3.2 36.0 1.0 CE1 A:HIS240 3.2 39.6 1.0 HD2 A:HIS240 3.3 43.2 1.0 HB2 A:CYS306 3.3 44.2 1.0 CB A:CYS306 3.3 36.9 1.0 HB3 A:CYS234 3.4 51.9 1.0 HE1 A:HIS240 3.4 47.6 1.0 CB A:CYS308 3.6 66.8 1.0 HB3 A:CYS308 3.6 80.1 1.0 N A:CYS308 3.6 64.7 1.0 HA A:CYS306 3.6 49.5 1.0 H A:SER307 3.8 66.6 1.0 HA A:PHE237 3.8 37.8 1.0 H A:ARG309 3.9 85.2 1.0 HG3 A:ARG309 3.9 83.3 1.0 CA A:CYS306 3.9 41.3 1.0 HB2 A:ARG309 4.1 84.2 1.0 CA A:CYS308 4.1 66.4 1.0 N A:SER307 4.1 55.5 1.0 HB3 A:CYS306 4.2 44.2 1.0 N A:ARG309 4.2 71.0 1.0 HD2 A:ARG309 4.3 78.7 1.0 C A:CYS306 4.3 49.1 1.0 ND1 A:HIS240 4.3 37.4 1.0 CG A:HIS240 4.3 35.2 1.0 HB2 A:CYS308 4.4 80.1 1.0 C A:CYS308 4.5 68.7 1.0 CG A:ARG309 4.6 69.4 1.0 CA A:CYS234 4.6 47.5 1.0 O A:HOH2222 4.6 48.3 1.0 C A:SER307 4.7 66.8 1.0 CB A:ARG309 4.7 70.2 1.0 O A:HOH2221 4.7 45.9 1.0 CA A:PHE237 4.7 31.5 1.0 HE A:ARG309 4.8 78.5 1.0 HA A:CYS234 4.8 57.0 1.0 CD A:ARG309 4.8 65.6 1.0 O A:ALA236 4.8 30.8 1.0 CA A:SER307 5.0 66.1 1.0 HA A:CYS308 5.0 79.6 1.0 N A:PHE237 5.0 31.6 1.0

Zinc binding site 2 out of 2 in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:33.3 occ:1.00 NE2 B:HIS240 2.1 30.2 1.0 SG B:CYS306 2.2 36.2 1.0 SG B:CYS234 2.3 33.5 1.0 SG B:CYS308 2.4 37.4 1.0 H B:CYS308 2.9 64.9 1.0 HB2 B:CYS234 3.0 50.0 1.0 CE1 B:HIS240 3.1 31.9 1.0 CD2 B:HIS240 3.1 31.3 1.0 CB B:CYS234 3.2 41.7 1.0 HE1 B:HIS240 3.2 38.3 1.0 HD2 B:HIS240 3.3 37.6 1.0 HB2 B:CYS306 3.3 38.9 1.0 CB B:CYS306 3.3 32.4 1.0 HB3 B:CYS308 3.5 64.7 1.0 CB B:CYS308 3.5 53.9 1.0 HA B:CYS306 3.6 40.1 1.0 HB3 B:CYS234 3.6 50.0 1.0 N B:CYS308 3.6 54.1 1.0 H B:SER307 3.7 53.7 1.0 CA B:CYS306 3.9 33.5 1.0 HA B:PHE237 4.0 31.8 1.0 HB2 B:ARG309 4.0 76.4 1.0 CA B:CYS308 4.0 55.4 1.0 N B:SER307 4.0 44.8 1.0 HD2 B:ARG309 4.1 75.3 1.0 HB3 B:CYS306 4.1 38.9 1.0 ND1 B:HIS240 4.2 30.2 1.0 H B:ARG309 4.2 70.4 1.0 CG B:HIS240 4.2 30.5 1.0 C B:CYS306 4.2 41.7 1.0 HB2 B:CYS308 4.3 64.7 1.0 HG3 B:ARG309 4.4 78.3 1.0 N B:ARG309 4.4 58.6 1.0 C B:CYS308 4.5 57.6 1.0 HA B:CYS234 4.5 54.0 1.0 CA B:CYS234 4.5 45.0 1.0 O B:HOH2176 4.6 41.1 1.0 O B:ALA236 4.6 27.8 1.0 H B:ALA236 4.6 49.4 1.0 CD B:ARG309 4.7 62.8 1.0 C B:SER307 4.8 54.4 1.0 CB B:ARG309 4.8 63.7 1.0 O B:HOH2218 4.8 48.4 1.0 CG B:ARG309 4.8 65.3 1.0 HE B:ARG309 4.8 78.2 1.0 CA B:PHE237 4.9 26.5 1.0 HA B:CYS308 4.9 66.4 1.0 CA B:SER307 5.0 51.6 1.0 NE B:ARG309 5.0 65.2 1.0

S.T.Williams, L.J.Walport, R.J.Hopkinson, S.K.Madden, R.Chowdhury, C.J.Schofield, A.Kawamura. Studies on the Catalytic Domains of Multiple Jmjc Oxygenases Using Peptide Substrates To Be Published.