Zinc in PDB 6ip4: Crystal Structure of Arabidopsis Thaliana JMJ13 Catalytic Domain in Complex with Nog and An H3K27ME3 Peptide

The structure of Crystal Structure of Arabidopsis Thaliana JMJ13 Catalytic Domain in Complex with Nog and An H3K27ME3 Peptide, PDB code: 6ip4 was solved by H.Hu, J.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.37 / 2.60
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.794, 128.794, 230.642, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 24.7

The structure of Crystal Structure of Arabidopsis Thaliana JMJ13 Catalytic Domain in Complex with Nog and An H3K27ME3 Peptide also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana JMJ13 Catalytic Domain in Complex with Nog and An H3K27ME3 Peptide (pdb code 6ip4). 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 JMJ13 Catalytic Domain in Complex with Nog and An H3K27ME3 Peptide, PDB code: 6ip4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Arabidopsis Thaliana JMJ13 Catalytic Domain in Complex with Nog and An H3K27ME3 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 JMJ13 Catalytic Domain in Complex with Nog and An H3K27ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:72.6 occ:1.00 SG A:CYS500 2.2 67.9 1.0 SG A:CYS522 2.2 63.0 1.0 NE2 A:HIS525 2.3 74.7 1.0 SG A:CYS503 2.6 95.4 1.0 CD2 A:HIS525 2.8 82.8 1.0 CB A:CYS503 3.1 69.1 1.0 CB A:CYS500 3.3 78.7 1.0 CE1 A:HIS525 3.5 87.8 1.0 CB A:CYS522 3.6 61.5 1.0 N A:CYS503 3.7 76.5 1.0 N A:CYS522 3.9 62.6 1.0 CA A:CYS503 4.0 76.7 1.0 CG A:HIS525 4.0 81.0 1.0 CA A:CYS522 4.2 66.2 1.0 ND1 A:HIS525 4.4 87.4 1.0 O A:CYS522 4.6 79.9 1.0 N A:LYS504 4.7 75.5 1.0 C A:CYS522 4.7 75.5 1.0 CB A:ARG524 4.7 63.9 1.0 CB A:LEU502 4.8 71.3 1.0 CA A:CYS500 4.8 71.3 1.0 C A:LEU502 4.9 76.0 1.0 C A:CYS503 4.9 76.2 1.0 N A:ARG505 4.9 67.0 1.0 C A:VAL521 4.9 75.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Arabidopsis Thaliana JMJ13 Catalytic Domain in Complex with Nog and An H3K27ME3 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 JMJ13 Catalytic Domain in Complex with Nog and An H3K27ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:88.3 occ:1.00 ND1 A:HIS519 2.1 0.4 1.0 SG A:CYS534 2.1 0.6 1.0 SG A:CYS516 2.3 92.6 1.0 SG A:CYS514 2.4 81.1 1.0 CE1 A:HIS519 2.7 98.1 1.0 CB A:CYS534 3.0 89.1 1.0 CB A:CYS514 3.3 86.1 1.0 CG A:HIS519 3.3 91.8 1.0 N A:CYS516 3.5 93.5 1.0 CB A:CYS516 3.6 0.6 1.0 N A:HIS519 3.9 72.7 1.0 CB A:HIS519 3.9 72.9 1.0 CA A:CYS516 4.0 97.0 1.0 OG A:SER518 4.0 95.3 1.0 NE2 A:HIS519 4.0 86.8 1.0 N A:SER518 4.1 75.0 1.0 N A:TYR517 4.1 81.0 1.0 N A:GLU515 4.2 87.3 1.0 CD2 A:HIS519 4.3 94.1 1.0 CA A:CYS534 4.3 86.8 1.0 C A:CYS516 4.4 89.4 1.0 N A:CYS534 4.4 94.6 1.0 CA A:HIS519 4.5 71.7 1.0 C A:SER518 4.5 81.6 1.0 C A:GLU515 4.5 99.8 1.0 CA A:CYS514 4.6 82.5 1.0 C A:CYS514 4.7 80.8 1.0 CA A:SER518 4.7 78.9 1.0 CA A:GLU515 4.8 92.0 1.0 CB A:SER518 4.9 87.1 1.0 CD1 A:LEU532 5.0 94.0 1.0 CB A:LEU532 5.0 0.4 1.0

S.Zheng, H.Hu, H.Ren, Z.Yang, Q.Qiu, W.Qi, X.Liu, X.Chen, X.Cui, S.Li, B.Zhou, D.Sun, X.Cao, J.Du. The Arabidopsis H3K27ME3 Demethylase Jumonji 13 Is A Temperature and Photoperiod Dependent Flowering Repressor. Nat Commun V. 10 1303 2019.
ISSN: ESSN 2041-1723
PubMed: 30899015
DOI: 10.1038/S41467-019-09310-X