Zinc in PDB 6ax3: Complex Structure of JMJD5 and Symmetric Dimethyl-Arginine (Sdma)

All present enzymatic activity of Complex Structure of JMJD5 and Symmetric Dimethyl-Arginine (Sdma):
1.14.11.27;

The structure of Complex Structure of JMJD5 and Symmetric Dimethyl-Arginine (Sdma), PDB code: 6ax3 was solved by S.Lee, H.Liu, Y.Wang, S.Dai, G.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.64 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.456, 64.706, 77.155, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.9

The binding sites of Zinc atom in the Complex Structure of JMJD5 and Symmetric Dimethyl-Arginine (Sdma) (pdb code 6ax3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Complex Structure of JMJD5 and Symmetric Dimethyl-Arginine (Sdma), PDB code: 6ax3:

Zinc binding site 1 out of 1 in the Complex Structure of JMJD5 and Symmetric Dimethyl-Arginine (Sdma)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex Structure of JMJD5 and Symmetric Dimethyl-Arginine (Sdma) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:30.8 occ:1.00 NE2 A:HIS321 1.9 29.0 1.0 OD2 A:ASP323 2.1 27.8 1.0 O2 A:AKG502 2.2 34.5 1.0 NE2 A:HIS400 2.3 22.5 1.0 O5 A:AKG502 2.3 34.5 1.0 CE1 A:HIS321 2.5 27.6 1.0 O A:2MR501 2.7 31.8 1.0 C1 A:AKG502 2.8 33.7 1.0 C2 A:AKG502 2.9 39.2 1.0 CG A:ASP323 3.1 27.0 1.0 CE1 A:HIS400 3.2 24.4 1.0 CD2 A:HIS321 3.2 25.6 1.0 CD2 A:HIS400 3.2 21.1 1.0 OD1 A:ASP323 3.4 25.5 1.0 O A:HOH621 3.6 23.6 1.0 ND1 A:HIS321 3.7 22.6 1.0 C A:2MR501 3.9 44.5 1.0 O1 A:AKG502 4.0 44.2 1.0 CG A:2MR501 4.0 41.1 1.0 CG A:HIS321 4.1 26.9 1.0 CB A:2MR501 4.2 38.3 1.0 CD A:2MR501 4.3 33.5 1.0 ND1 A:HIS400 4.3 20.5 0.9 CG A:HIS400 4.4 23.7 1.0 CB A:ASP323 4.4 27.4 1.0 C3 A:AKG502 4.4 36.2 1.0 CZ2 A:TRP414 4.6 27.8 0.7 CA A:2MR501 4.7 40.8 1.0 OXT A:2MR501 4.8 50.6 1.0 ND2 A:ASN327 4.8 21.1 1.0

H.Liu, C.Wang, S.Lee, F.Ning, Y.Wang, Q.Zhang, Z.Chen, J.Zang, J.Nix, S.Dai, P.Marrack, J.Hagman, J.Kappler, G.Zhang. Specific Recognition of Arginine Methylated Histone Tails By JMJD5 and JMJD7. Sci Rep V. 8 3275 2018.
ISSN: ESSN 2045-2322
PubMed: 29459673
DOI: 10.1038/S41598-018-21432-8