Zinc in PDB 4v2v: JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa

The structure of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa, PDB code: 4v2v was solved by R.Chowdhury, S.K.Madden, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.589 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.020, 149.910, 57.380, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.08

The structure of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa (pdb code 4v2v). 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 (25-29) Ark(ME3)Sa, PDB code: 4v2v:
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 (25-29) Ark(ME3)Sa


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 (25-29) Ark(ME3)Sa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1358 b:31.0 occ:1.00 SG A:CYS306 2.3 35.8 1.0 SG A:CYS234 2.3 29.2 1.0 SG A:CYS308 2.4 32.2 1.0 NE2 A:HIS240 2.4 32.3 1.0 CB A:CYS234 3.2 44.5 1.0 CD2 A:HIS240 3.2 32.6 1.0 CB A:CYS306 3.3 39.1 1.0 CE1 A:HIS240 3.5 33.7 1.0 CB A:CYS308 3.5 55.5 1.0 N A:CYS308 3.7 60.3 1.0 CA A:CYS306 4.0 41.5 1.0 CA A:CYS308 4.1 56.0 1.0 N A:SER307 4.1 62.9 1.0 C A:CYS306 4.3 51.7 1.0 N A:ARG309 4.4 50.7 1.0 CG A:HIS240 4.4 30.7 1.0 C A:CYS308 4.5 52.6 1.0 ND1 A:HIS240 4.5 33.6 1.0 O A:HOH2170 4.5 39.5 1.0 CA A:CYS234 4.6 44.8 1.0 O A:HOH2208 4.6 46.0 1.0 CG A:ARG309 4.7 52.2 1.0 CB A:ARG309 4.7 50.7 1.0 C A:SER307 4.8 70.6 1.0 CA A:PHE237 4.8 28.0 1.0 CD A:ARG309 4.9 51.7 1.0 O A:ALA236 4.9 26.3 1.0

Zinc binding site 2 out of 2 in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa


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 (25-29) Ark(ME3)Sa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1357 b:34.0 occ:1.00 SG B:CYS306 2.2 37.8 1.0 NE2 B:HIS240 2.2 38.0 1.0 SG B:CYS234 2.3 35.5 1.0 SG B:CYS308 2.4 42.9 1.0 CB B:CYS234 3.2 47.9 1.0 CD2 B:HIS240 3.2 35.8 1.0 CE1 B:HIS240 3.2 38.9 1.0 CB B:CYS306 3.4 41.8 1.0 CB B:CYS308 3.6 59.1 1.0 N B:CYS308 3.6 62.2 1.0 CA B:CYS306 4.0 44.2 1.0 CA B:CYS308 4.1 58.5 1.0 N B:SER307 4.2 65.1 1.0 ND1 B:HIS240 4.3 37.1 1.0 C B:CYS306 4.3 54.3 1.0 CG B:HIS240 4.3 34.4 1.0 N B:ARG309 4.3 54.0 1.0 O B:HOH2189 4.5 36.8 1.0 C B:CYS308 4.6 56.4 1.0 CG B:ARG309 4.6 52.6 1.0 CA B:CYS234 4.6 49.1 1.0 C B:SER307 4.7 71.8 1.0 CA B:PHE237 4.7 32.6 1.0 CD B:ARG309 4.8 50.8 1.0 CB B:ARG309 4.9 53.0 1.0 CA B:SER307 5.0 73.2 1.0 N B:PHE237 5.0 28.8 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.