Zinc in PDB 5yko: Crystal Structure of Arabidopsis Thaliana JMJ14 Catalytic Domain in Complex with Nog and H3K4ME3 Peptide

The structure of Crystal Structure of Arabidopsis Thaliana JMJ14 Catalytic Domain in Complex with Nog and H3K4ME3 Peptide, PDB code: 5yko was solved by Z.Yang, J.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.34 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.639, 100.113, 109.405, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.4

The structure of Crystal Structure of Arabidopsis Thaliana JMJ14 Catalytic Domain in Complex with Nog and H3K4ME3 Peptide also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana JMJ14 Catalytic Domain in Complex with Nog and H3K4ME3 Peptide (pdb code 5yko). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana JMJ14 Catalytic Domain in Complex with Nog and H3K4ME3 Peptide, PDB code: 5yko:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Arabidopsis Thaliana JMJ14 Catalytic Domain in Complex with Nog and H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Arabidopsis Thaliana JMJ14 Catalytic Domain in Complex with Nog and H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:45.2 occ:1.00 SG A:CYS519 2.3 40.8 1.0 CB A:CYS522 2.4 41.6 1.0 SG A:CYS542 2.4 39.8 1.0 SG A:CYS522 2.4 94.2 1.0 ND1 A:HIS545 2.8 43.1 1.0 CB A:CYS519 3.1 39.1 1.0 N A:CYS522 3.3 50.8 1.0 CA A:CYS522 3.4 47.8 1.0 CB A:CYS542 3.5 40.0 1.0 CG A:HIS545 3.6 51.7 1.0 CB A:HIS545 3.7 45.4 1.0 CE1 A:HIS545 3.7 45.1 1.0 N A:CYS542 4.0 43.4 1.0 CA A:CYS542 4.4 42.1 1.0 CB A:TYR524 4.4 35.9 1.0 C A:LEU521 4.4 48.2 1.0 OG A:SER429 4.5 39.0 1.0 C A:CYS522 4.5 45.1 1.0 CA A:CYS519 4.6 43.9 1.0 CB A:LEU521 4.7 48.9 1.0 CD2 A:HIS545 4.7 58.1 1.0 N A:PHE523 4.8 46.4 1.0 NE2 A:HIS545 4.8 58.4 1.0 N A:HIS545 4.8 41.1 1.0 CA A:HIS545 4.9 44.2 1.0 N A:TYR524 4.9 39.4 1.0 CA A:LEU521 4.9 49.0 1.0 N A:LEU521 5.0 47.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Arabidopsis Thaliana JMJ14 Catalytic Domain in Complex with Nog and H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Arabidopsis Thaliana JMJ14 Catalytic Domain in Complex with Nog and H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:69.6 occ:1.00 SG A:CYS535 2.4 1.0 1.0 SG A:CYS550 2.5 0.5 1.0 CB A:CYS550 2.5 67.9 1.0 SG A:CYS533 2.5 75.3 1.0 CB A:CYS533 3.0 51.6 1.0 CB A:CYS552 3.4 70.3 1.0 CB A:CYS535 3.4 56.9 1.0 SG A:CYS552 3.5 86.8 1.0 CA A:CYS550 4.0 67.5 1.0 N A:CYS535 4.3 58.2 1.0 N A:CYS552 4.3 72.5 1.0 CD A:ARG557 4.4 56.4 1.0 CA A:CYS533 4.4 49.0 1.0 CA A:CYS552 4.5 74.4 1.0 CA A:CYS535 4.5 58.8 1.0 N A:SER551 4.6 79.0 1.0 NH2 A:ARG557 4.6 72.5 1.0 C A:CYS550 4.7 73.5 1.0 N A:CYS550 4.8 64.6 1.0 NE A:ARG557 4.8 58.9 1.0 N A:LYS534 4.9 51.8 1.0 C A:CYS533 4.9 52.7 1.0 CZ A:ARG557 5.0 63.8 1.0

Z.Yang, Q.Qiu, W.Chen, B.Jia, X.Chen, H.Hu, K.He, X.Deng, S.Li, W.A.Tao, X.Cao, J.Du. Structure of the Arabidopsis JMJ14-H3K4ME3 Complex Provides Insight Into the Substrate Specificity of KDM5 Subfamily Histone Demethylases. Plant Cell V. 30 167 2018.
ISSN: ESSN 1532-298X
PubMed: 29233856
DOI: 10.1105/TPC.17.00666