Zinc in PDB 6jnm: REF6 ZNF2-4-NAC004-MC3 Complex

The structure of REF6 ZNF2-4-NAC004-MC3 Complex, PDB code: 6jnm was solved by Q.Q.Yao, B.X.Wu, J.B.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.05
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	88.516, 88.516, 72.330, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.8

The binding sites of Zinc atom in the REF6 ZNF2-4-NAC004-MC3 Complex (pdb code 6jnm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the REF6 ZNF2-4-NAC004-MC3 Complex, PDB code: 6jnm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the REF6 ZNF2-4-NAC004-MC3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of REF6 ZNF2-4-NAC004-MC3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1401 b:31.4 occ:1.00 SG A:CYS1273 1.8 47.7 1.0 NE2 A:HIS1290 1.8 18.8 1.0 SG A:CYS1268 2.0 40.9 1.0 NE2 A:HIS1286 2.0 25.2 1.0 CD2 A:HIS1290 2.8 23.0 1.0 CE1 A:HIS1290 2.9 21.8 1.0 CD2 A:HIS1286 3.0 26.6 1.0 CE1 A:HIS1286 3.1 24.1 1.0 CB A:CYS1273 3.2 38.9 1.0 CB A:CYS1268 3.3 36.5 1.0 O A:HOH1517 3.4 65.1 1.0 CG A:HIS1290 4.0 23.6 1.0 ND1 A:HIS1290 4.0 21.1 1.0 CG A:HIS1286 4.1 26.3 1.0 ND1 A:HIS1286 4.2 23.3 1.0 CB A:ILE1270 4.6 34.4 1.0 OE1 A:GLN1287 4.6 26.4 1.0 CA A:CYS1268 4.7 39.0 1.0 CA A:CYS1273 4.7 35.8 1.0 NE2 A:GLN1287 5.0 23.7 1.0 CZ A:PHE1277 5.0 33.1 1.0

Zinc binding site 2 out of 6 in the REF6 ZNF2-4-NAC004-MC3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of REF6 ZNF2-4-NAC004-MC3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1402 b:18.3 occ:1.00 NE2 A:HIS1320 2.0 18.7 1.0 NE2 A:HIS1316 2.1 16.5 1.0 SG A:CYS1303 2.2 19.9 1.0 SG A:CYS1298 2.3 16.5 1.0 CD2 A:HIS1320 2.9 17.3 1.0 CB A:CYS1303 3.1 25.5 1.0 CD2 A:HIS1316 3.1 15.3 1.0 CE1 A:HIS1320 3.1 18.9 1.0 CE1 A:HIS1316 3.2 15.8 1.0 CB A:CYS1298 3.2 19.1 1.0 CG A:HIS1320 4.1 17.1 1.0 ND1 A:HIS1320 4.1 17.8 1.0 CB A:TRP1300 4.2 20.6 1.0 CG A:HIS1316 4.2 15.2 1.0 ND1 A:HIS1316 4.2 16.9 1.0 CB A:MET1305 4.3 28.9 1.0 CA A:CYS1303 4.5 25.6 1.0 CA A:CYS1298 4.6 21.5 1.0

Zinc binding site 3 out of 6 in the REF6 ZNF2-4-NAC004-MC3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of REF6 ZNF2-4-NAC004-MC3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1403 b:32.0 occ:1.00 SG A:CYS1333 1.8 41.3 1.0 SG A:CYS1328 1.9 34.5 1.0 NE2 A:HIS1346 2.0 37.9 1.0 ND1 A:HIS1352 2.3 47.5 1.0 CE1 A:HIS1346 2.9 36.5 1.0 CD2 A:HIS1346 3.0 30.9 1.0 CB A:CYS1333 3.1 42.9 1.0 CG A:HIS1352 3.2 42.0 1.0 CB A:CYS1328 3.3 31.7 1.0 CE1 A:HIS1352 3.3 41.2 1.0 CB A:HIS1352 3.4 33.5 1.0 ND1 A:HIS1346 4.0 35.0 1.0 CG A:HIS1346 4.1 33.5 1.0 CB A:GLU1330 4.2 42.0 1.0 CD2 A:HIS1352 4.3 40.8 1.0 NE2 A:HIS1352 4.3 46.0 1.0 OG1 A:THR1350 4.4 31.9 1.0 CA A:CYS1333 4.5 38.4 1.0 CA A:CYS1328 4.6 28.2 1.0 CA A:HIS1352 4.9 32.6 1.0 CB A:GLN1335 5.0 31.5 1.0

Zinc binding site 4 out of 6 in the REF6 ZNF2-4-NAC004-MC3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of REF6 ZNF2-4-NAC004-MC3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1401 b:31.5 occ:1.00 SG B:CYS1273 1.6 62.7 1.0 NE2 B:HIS1290 1.9 18.2 1.0 NE2 B:HIS1286 2.0 24.7 1.0 SG B:CYS1268 2.2 32.0 1.0 CD2 B:HIS1290 2.8 20.4 1.0 CD2 B:HIS1286 2.9 25.6 1.0 CB B:CYS1273 3.0 40.6 1.0 CE1 B:HIS1290 3.0 22.0 1.0 CE1 B:HIS1286 3.0 23.7 1.0 CB B:CYS1268 3.4 36.5 1.0 CG B:HIS1290 4.0 22.2 1.0 ND1 B:HIS1290 4.1 21.4 1.0 CG B:HIS1286 4.1 25.0 1.0 ND1 B:HIS1286 4.1 22.7 1.0 CB B:ILE1270 4.5 36.3 1.0 CA B:CYS1273 4.5 38.7 1.0 OE1 B:GLN1287 4.6 27.8 1.0 CG1 B:ILE1270 4.8 36.4 1.0 CA B:CYS1268 4.8 39.9 1.0 NE2 B:GLN1287 4.9 19.9 1.0

Zinc binding site 5 out of 6 in the REF6 ZNF2-4-NAC004-MC3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of REF6 ZNF2-4-NAC004-MC3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1402 b:18.6 occ:1.00 NE2 B:HIS1320 2.1 14.0 1.0 NE2 B:HIS1316 2.1 12.5 1.0 SG B:CYS1303 2.2 19.7 1.0 SG B:CYS1298 2.2 16.8 1.0 CD2 B:HIS1320 2.9 14.3 1.0 CD2 B:HIS1316 3.0 12.4 1.0 CB B:CYS1303 3.1 24.6 1.0 CE1 B:HIS1316 3.2 13.7 1.0 CB B:CYS1298 3.2 17.5 1.0 CE1 B:HIS1320 3.2 13.4 1.0 CG B:HIS1320 4.1 14.8 1.0 CG B:HIS1316 4.2 12.7 1.0 ND1 B:HIS1320 4.2 13.5 1.0 ND1 B:HIS1316 4.2 14.3 1.0 CB B:TRP1300 4.3 19.1 1.0 CB B:MET1305 4.3 28.6 1.0 CA B:CYS1303 4.5 25.1 1.0 CA B:CYS1298 4.6 19.0 1.0

Zinc binding site 6 out of 6 in the REF6 ZNF2-4-NAC004-MC3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of REF6 ZNF2-4-NAC004-MC3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1403 b:31.0 occ:1.00 SG B:CYS1333 1.8 41.8 1.0 SG B:CYS1328 1.9 32.5 1.0 NE2 B:HIS1346 2.0 38.4 1.0 ND1 B:HIS1352 2.2 41.8 1.0 CE1 B:HIS1346 2.9 36.9 1.0 CD2 B:HIS1346 3.1 30.7 1.0 CB B:CYS1333 3.1 42.5 1.0 CG B:HIS1352 3.1 38.7 1.0 CE1 B:HIS1352 3.2 38.4 1.0 CB B:CYS1328 3.2 32.8 1.0 CB B:HIS1352 3.4 33.3 1.0 ND1 B:HIS1346 4.0 37.5 1.0 CB B:GLU1330 4.1 48.5 1.0 CG B:HIS1346 4.2 34.5 1.0 NE2 B:HIS1352 4.3 41.0 1.0 CD2 B:HIS1352 4.3 39.3 1.0 OG1 B:THR1350 4.3 33.2 1.0 CA B:CYS1333 4.5 38.3 1.0 CA B:CYS1328 4.6 28.7 1.0 CB B:GLN1335 4.9 31.7 1.0 CA B:HIS1352 4.9 33.8 1.0

Q.Qiu, H.Mei, X.Deng, K.He, B.Wu, Q.Yao, J.Zhang, F.Lu, J.Ma, X.Cao. Dna Methylation Repels Targeting of Arabidopsis REF6. Nat Commun V. 10 2063 2019.
ISSN: ESSN 2041-1723
PubMed: 31048693
DOI: 10.1038/S41467-019-10026-1