Zinc in PDB 6lqf: Crystal Structure of Arabidopsis ARID5 Arid-Phd Cassette in Complex with H3K4ME3 Peptide and Dna

The structure of Crystal Structure of Arabidopsis ARID5 Arid-Phd Cassette in Complex with H3K4ME3 Peptide and Dna, PDB code: 6lqf was solved by R.Liu, J.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.04 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.173, 59.428, 92.958, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.2

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis ARID5 Arid-Phd Cassette in Complex with H3K4ME3 Peptide and Dna (pdb code 6lqf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis ARID5 Arid-Phd Cassette in Complex with H3K4ME3 Peptide and Dna, PDB code: 6lqf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Arabidopsis ARID5 Arid-Phd Cassette in Complex with H3K4ME3 Peptide and Dna


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 ARID5 Arid-Phd Cassette in Complex with H3K4ME3 Peptide and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:23.8 occ:1.00 NE2 A:HIS669 2.0 22.0 1.0 ND1 A:HIS557 2.1 26.4 1.0 OD2 A:ASP575 2.1 22.6 1.0 SG A:CYS559 2.2 25.8 1.0 CG A:ASP575 2.9 22.1 1.0 CB A:CYS559 2.9 50.4 1.0 OD1 A:ASP575 3.0 25.4 1.0 CE1 A:HIS669 3.0 23.9 1.0 CE1 A:HIS557 3.0 28.8 1.0 CG A:HIS557 3.0 32.5 1.0 CD2 A:HIS669 3.0 24.3 1.0 CB A:HIS557 3.4 30.4 1.0 OH A:TYR665 4.0 18.8 1.0 NE2 A:HIS557 4.1 31.1 1.0 ND1 A:HIS669 4.1 20.6 1.0 CD2 A:HIS557 4.2 32.3 1.0 CG A:HIS669 4.2 20.9 1.0 CE2 A:TYR665 4.2 17.3 1.0 CB A:ASP575 4.2 20.1 1.0 CZ A:TYR665 4.4 17.5 1.0 CA A:CYS559 4.5 55.8 1.0 CB A:ARG561 4.5 28.3 1.0 CA A:HIS557 4.7 37.1 1.0 C A:HIS557 4.9 45.3 1.0 O A:ASP575 4.9 20.1 1.0 N A:CYS559 5.0 60.5 1.0 O A:HIS557 5.0 51.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Arabidopsis ARID5 Arid-Phd Cassette in Complex with H3K4ME3 Peptide and Dna


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 ARID5 Arid-Phd Cassette in Complex with H3K4ME3 Peptide and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:22.1 occ:1.00 SG A:CYS727 2.3 24.7 1.0 SG A:CYS724 2.3 23.1 1.0 SG A:CYS691 2.3 19.2 1.0 SG A:CYS694 2.4 24.0 1.0 CB A:CYS727 3.3 24.0 1.0 CB A:CYS691 3.3 18.7 1.0 CB A:CYS694 3.3 20.9 1.0 CB A:CYS724 3.4 21.5 1.0 N A:CYS694 3.7 21.3 1.0 N A:CYS724 4.0 20.0 1.0 CA A:CYS694 4.1 23.0 1.0 N A:CYS727 4.2 26.4 1.0 CA A:CYS724 4.3 21.3 1.0 CA A:CYS727 4.3 26.9 1.0 CB A:SER693 4.4 19.9 1.0 CA A:CYS691 4.7 17.4 1.0 C A:SER693 4.7 22.7 1.0 OG A:SER693 4.8 27.3 1.0 C A:CYS724 4.8 24.7 1.0 O A:CYS724 4.8 22.7 1.0 CD2 A:LEU678 4.9 25.3 1.0 C A:CYS694 4.9 24.1 1.0 CA A:SER693 5.0 18.4 1.0 N A:SER693 5.0 18.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Arabidopsis ARID5 Arid-Phd Cassette in Complex with H3K4ME3 Peptide and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Arabidopsis ARID5 Arid-Phd Cassette in Complex with H3K4ME3 Peptide and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:22.4 occ:1.00 ND1 A:HIS699 2.1 21.9 1.0 SG A:CYS702 2.3 24.1 1.0 SG A:CYS677 2.4 21.8 1.0 SG A:CYS680 2.4 26.5 1.0 CB A:CYS677 3.0 24.5 1.0 CE1 A:HIS699 3.0 29.5 1.0 CG A:HIS699 3.1 22.1 1.0 CB A:CYS680 3.3 26.3 1.0 CB A:CYS702 3.3 26.8 1.0 CB A:HIS699 3.4 19.0 1.0 N A:CYS680 3.8 23.8 1.0 O A:HOH995 3.9 45.1 1.0 CA A:CYS680 4.1 23.2 1.0 N A:HIS699 4.1 19.7 1.0 NE2 A:HIS699 4.2 26.9 1.0 CD2 A:HIS699 4.2 22.3 1.0 CA A:HIS699 4.4 20.1 1.0 CA A:CYS677 4.5 21.0 1.0 CB A:ILE679 4.7 23.2 1.0 CA A:CYS702 4.7 23.8 1.0 C A:CYS680 4.9 26.0 1.0 C A:ILE679 4.9 25.4 1.0 N A:ARG681 5.0 23.2 1.0

L.M.Tan, R.Liu, B.W.Gu, C.J.Zhang, J.Luo, J.Guo, Y.Wang, L.Chen, X.Du, S.Li, C.R.Shao, Y.N.Su, X.W.Cai, R.N.Lin, L.Li, S.Chen, J.Du, X.J.He. Dual Recognition of H3K4ME3 and Dna By the Iswi Component ARID5 Regulates the Floral Transition in Arabidopsis. Plant Cell 2020.
ISSN: ESSN 1532-298X
PubMed: 32358072
DOI: 10.1105/TPC.19.00944