Zinc in PDB 6jnl: REF6 ZNF2-4-NAC004 Complex

The structure of REF6 ZNF2-4-NAC004 Complex, PDB code: 6jnl 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 / 2.15
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.160, 89.160, 72.603, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.9

The structure of REF6 ZNF2-4-NAC004 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

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

Zinc binding site 1 out of 3 in the REF6 ZNF2-4-NAC004 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1401 b:75.3 occ:1.00 NE2 A:HIS1290 2.1 48.6 1.0 NE2 A:HIS1286 2.3 92.2 1.0 SG A:CYS1273 2.4 82.3 1.0 SG A:CYS1268 2.4 79.4 1.0 CE1 A:HIS1290 2.5 53.2 1.0 CD2 A:HIS1286 3.0 81.4 1.0 CB A:CYS1268 3.0 74.3 1.0 CB A:CYS1273 3.2 89.4 1.0 CD2 A:HIS1290 3.4 61.2 1.0 CE1 A:HIS1286 3.4 73.3 1.0 ND1 A:HIS1290 3.8 55.6 1.0 CG A:HIS1286 4.2 82.3 1.0 CG A:HIS1290 4.2 54.2 1.0 ND1 A:HIS1286 4.3 73.2 1.0 CA A:CYS1268 4.5 88.3 1.0 CA A:CYS1273 4.6 90.9 1.0 NE2 A:GLN1287 4.8 76.7 1.0 N A:GLY1274 4.8 94.0 1.0 CB A:ILE1270 4.9 85.2 1.0 CZ A:PHE1277 5.0 82.4 1.0

Zinc binding site 2 out of 3 in the REF6 ZNF2-4-NAC004 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1402 b:72.4 occ:1.00 NE2 A:HIS1346 2.2 82.2 1.0 ND1 A:HIS1352 2.2 0.7 1.0 SG A:CYS1328 2.3 68.6 1.0 SG A:CYS1333 2.3 72.9 1.0 CE1 A:HIS1346 2.9 71.9 1.0 CE1 A:HIS1352 3.0 82.8 1.0 CB A:CYS1333 3.1 80.2 1.0 CG A:HIS1352 3.2 90.3 1.0 CB A:CYS1328 3.2 71.8 1.0 CD2 A:HIS1346 3.4 78.0 1.0 CB A:HIS1352 3.6 81.8 1.0 NE2 A:HIS1352 4.0 79.9 1.0 ND1 A:HIS1346 4.1 70.7 1.0 CD2 A:HIS1352 4.2 86.3 1.0 CB A:GLU1330 4.2 90.7 1.0 CG A:HIS1346 4.3 76.6 1.0 OG1 A:THR1350 4.4 79.0 1.0 CA A:CYS1328 4.5 64.1 1.0 CA A:CYS1333 4.6 82.0 1.0 CB A:GLN1335 4.9 68.1 1.0

Zinc binding site 3 out of 3 in the REF6 ZNF2-4-NAC004 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1403 b:53.1 occ:1.00 NE2 A:HIS1316 2.0 50.4 1.0 NE2 A:HIS1320 2.1 51.6 1.0 SG A:CYS1298 2.2 50.6 1.0 SG A:CYS1303 2.3 61.6 1.0 CD2 A:HIS1320 2.8 52.1 1.0 CE1 A:HIS1316 3.0 42.1 1.0 CD2 A:HIS1316 3.1 49.2 1.0 CB A:CYS1298 3.1 56.4 1.0 CB A:CYS1303 3.2 69.6 1.0 CE1 A:HIS1320 3.2 52.6 1.0 ND1 A:HIS1316 4.1 45.8 1.0 CG A:HIS1320 4.1 52.7 1.0 CG A:HIS1316 4.2 48.3 1.0 ND1 A:HIS1320 4.2 62.2 1.0 CB A:TRP1300 4.2 56.2 1.0 CB A:MET1305 4.4 69.7 1.0 CA A:CYS1298 4.6 50.2 1.0 CA A:CYS1303 4.6 69.1 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