Zinc in PDB 6jnn: REF6 ZNF2-4-NAC004-MC1 Complex

The structure of REF6 ZNF2-4-NAC004-MC1 Complex, PDB code: 6jnn 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 / 2.60
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	70.969, 70.969, 141.076, 90.00, 90.00, 120.00
R / Rfree (%)	25.1 / 26.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the REF6 ZNF2-4-NAC004-MC1 Complex (pdb code 6jnn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the REF6 ZNF2-4-NAC004-MC1 Complex, PDB code: 6jnn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the REF6 ZNF2-4-NAC004-MC1 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-MC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1401 b:21.8 occ:1.00 NE2 A:HIS1316 2.0 38.7 1.0 SG A:CYS1303 2.1 39.5 1.0 SG A:CYS1298 2.1 25.8 1.0 NE2 A:HIS1320 2.2 18.4 1.0 CE1 A:HIS1316 2.8 37.4 1.0 CE1 A:HIS1320 2.9 18.6 1.0 CD2 A:HIS1316 3.1 33.0 1.0 CB A:CYS1303 3.2 37.1 1.0 CB A:CYS1298 3.2 27.2 1.0 CD2 A:HIS1320 3.4 19.3 1.0 ND1 A:HIS1316 4.0 33.7 1.0 CB A:MET1305 4.1 33.0 1.0 ND1 A:HIS1320 4.1 19.5 1.0 CG A:HIS1316 4.2 33.6 1.0 CB A:TRP1300 4.3 32.4 1.0 CG A:HIS1320 4.4 20.1 1.0 CA A:CYS1298 4.6 23.1 1.0 CA A:CYS1303 4.6 36.1 1.0 C A:CYS1303 5.0 33.6 1.0 N A:MET1305 5.0 28.7 1.0 CG A:MET1305 5.0 37.2 1.0

Zinc binding site 2 out of 12 in the REF6 ZNF2-4-NAC004-MC1 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-MC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1402 b:63.0 occ:1.00 ND1 A:HIS1352 2.1 70.9 1.0 SG A:CYS1328 2.2 51.0 1.0 SG A:CYS1333 2.2 90.2 1.0 CE1 A:HIS1346 2.6 58.5 1.0 CE1 A:HIS1352 2.8 71.0 1.0 CB A:CYS1333 3.0 88.3 1.0 NE2 A:HIS1346 3.2 59.6 1.0 CG A:HIS1352 3.3 71.6 1.0 CB A:CYS1328 3.4 50.1 1.0 ND1 A:HIS1346 3.8 54.4 1.0 CB A:HIS1352 3.9 71.3 1.0 NE2 A:HIS1352 4.0 74.6 1.0 NE2 A:GLN1335 4.0 64.8 1.0 CB A:GLU1330 4.3 68.4 1.0 CD2 A:HIS1352 4.3 72.6 1.0 CA A:CYS1333 4.4 88.7 1.0 OG1 A:THR1350 4.5 64.9 1.0 CD2 A:HIS1346 4.5 56.5 1.0 CA A:CYS1328 4.7 47.6 1.0 CG A:HIS1346 4.8 54.4 1.0 CG A:GLU1330 4.9 67.0 1.0 N A:GLY1334 5.0 78.4 1.0

Zinc binding site 3 out of 12 in the REF6 ZNF2-4-NAC004-MC1 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-MC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1403 b:34.0 occ:1.00 SG A:CYS1268 2.1 35.2 1.0 NE2 A:HIS1286 2.1 19.4 1.0 SG A:CYS1273 2.1 23.4 1.0 NE2 A:HIS1290 2.4 24.0 1.0 CB A:CYS1268 2.9 40.0 1.0 CD2 A:HIS1286 3.0 21.4 1.0 CE1 A:HIS1286 3.2 22.0 1.0 CE1 A:HIS1290 3.2 27.7 1.0 CD2 A:HIS1290 3.5 25.4 1.0 O A:CYS1273 3.7 37.2 1.0 CB A:CYS1273 3.9 30.5 1.0 CG A:HIS1286 4.2 22.6 1.0 ND1 A:HIS1286 4.2 23.2 1.0 CB A:ILE1270 4.3 42.6 1.0 ND1 A:HIS1290 4.4 29.1 1.0 CA A:CYS1268 4.4 44.7 1.0 C A:CYS1273 4.5 32.1 1.0 CG A:HIS1290 4.6 28.5 1.0 CG1 A:ILE1270 4.6 40.1 1.0 OE1 A:GLN1287 4.7 57.0 1.0 NE2 A:GLN1287 4.8 54.4 1.0 CA A:CYS1273 4.8 30.7 1.0 CZ A:PHE1277 4.9 21.7 1.0 N A:ILE1270 5.0 45.5 1.0 C A:CYS1268 5.0 45.8 1.0 CE2 A:PHE1277 5.0 20.4 1.0

Zinc binding site 4 out of 12 in the REF6 ZNF2-4-NAC004-MC1 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-MC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1401 b:28.3 occ:1.00 NE2 B:HIS1286 2.0 19.1 1.0 NE2 B:HIS1290 2.2 37.5 1.0 SG B:CYS1268 2.3 35.6 1.0 SG B:CYS1273 2.5 29.3 1.0 CE1 B:HIS1290 2.9 41.4 1.0 CD2 B:HIS1286 3.0 18.4 1.0 CE1 B:HIS1286 3.1 19.6 1.0 CB B:CYS1268 3.2 39.8 1.0 CD2 B:HIS1290 3.3 38.3 1.0 CB B:CYS1273 3.6 31.4 1.0 ND1 B:HIS1290 4.1 42.0 1.0 ND1 B:HIS1286 4.2 18.3 1.0 CG B:HIS1286 4.2 17.6 1.0 CG B:HIS1290 4.4 38.2 1.0 CD1 B:ILE1270 4.4 42.7 1.0 CA B:CYS1268 4.7 36.2 1.0 CB B:ILE1270 4.7 39.1 1.0 CA B:CYS1273 5.0 28.9 1.0 NE2 B:GLN1287 5.0 19.1 1.0

Zinc binding site 5 out of 12 in the REF6 ZNF2-4-NAC004-MC1 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-MC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1402 b:31.8 occ:1.00 NE2 B:HIS1320 1.8 22.5 1.0 SG B:CYS1298 2.0 21.6 1.0 NE2 B:HIS1316 2.2 15.1 1.0 SG B:CYS1303 2.3 29.9 1.0 CE1 B:HIS1320 2.5 23.2 1.0 CB B:CYS1303 3.0 37.0 1.0 CD2 B:HIS1320 3.0 23.2 1.0 CE1 B:HIS1316 3.0 15.7 1.0 CB B:CYS1298 3.3 23.3 1.0 CD2 B:HIS1316 3.3 16.3 1.0 ND1 B:HIS1320 3.7 24.6 1.0 CB B:TRP1300 3.9 26.8 1.0 CG B:HIS1320 4.0 24.3 1.0 ND1 B:HIS1316 4.2 17.6 1.0 CG B:HIS1316 4.4 17.7 1.0 CA B:CYS1303 4.5 40.1 1.0 CA B:CYS1298 4.6 22.1 1.0 CB B:MET1305 4.6 37.1 1.0 N B:TRP1300 4.8 25.2 1.0 CG B:TRP1300 4.9 25.6 1.0 CA B:TRP1300 4.9 27.8 1.0

Zinc binding site 6 out of 12 in the REF6 ZNF2-4-NAC004-MC1 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-MC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1403 b:81.4 occ:1.00 ND1 B:HIS1352 1.9 76.3 1.0 SG B:CYS1328 2.2 74.2 1.0 NE2 B:HIS1346 2.3 70.5 1.0 SG B:CYS1333 2.7 75.2 1.0 CG B:HIS1352 2.8 83.4 1.0 CE1 B:HIS1352 2.9 78.2 1.0 CB B:HIS1352 3.1 85.8 1.0 CE1 B:HIS1346 3.1 71.0 1.0 CD2 B:HIS1346 3.4 68.5 1.0 CB B:CYS1333 3.4 78.4 1.0 CB B:CYS1328 3.6 68.7 1.0 CB B:GLU1330 3.9 81.3 1.0 CD2 B:HIS1352 4.0 87.6 1.0 NE2 B:HIS1352 4.0 83.4 1.0 ND1 B:HIS1346 4.3 71.8 1.0 CG2 B:THR1350 4.3 66.5 1.0 CG B:HIS1346 4.4 66.5 1.0 NE2 B:GLN1335 4.4 58.7 1.0 CG B:GLU1330 4.6 90.2 1.0 CA B:HIS1352 4.6 82.4 1.0 CA B:CYS1328 4.8 72.1 1.0 CA B:CYS1333 4.9 77.0 1.0 N B:GLU1330 5.0 70.5 1.0

Zinc binding site 7 out of 12 in the REF6 ZNF2-4-NAC004-MC1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of REF6 ZNF2-4-NAC004-MC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn1401 b:30.4 occ:1.00 NE2 N:HIS1316 2.0 21.8 1.0 SG N:CYS1298 2.1 39.5 1.0 NE2 N:HIS1320 2.3 57.7 1.0 SG N:CYS1303 2.3 36.1 1.0 CE1 N:HIS1316 2.5 24.8 1.0 CE1 N:HIS1320 3.1 50.3 1.0 CB N:CYS1303 3.2 32.5 1.0 CB N:CYS1298 3.3 37.1 1.0 CD2 N:HIS1316 3.3 23.3 1.0 CD2 N:HIS1320 3.3 52.2 1.0 ND1 N:HIS1316 3.8 23.3 1.0 CB N:TRP1300 4.1 22.7 1.0 CG N:HIS1316 4.2 23.1 1.0 ND1 N:HIS1320 4.2 49.9 1.0 CG N:HIS1320 4.4 48.8 1.0 CB N:MET1305 4.6 55.6 1.0 CA N:CYS1298 4.7 31.8 1.0 CA N:CYS1303 4.7 33.5 1.0 N N:TRP1300 4.9 22.0 1.0

Zinc binding site 8 out of 12 in the REF6 ZNF2-4-NAC004-MC1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of REF6 ZNF2-4-NAC004-MC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn1402 b:70.0 occ:1.00 ND1 N:HIS1352 2.1 78.4 1.0 SG N:CYS1333 2.3 92.1 1.0 CE1 N:HIS1346 2.6 34.0 1.0 SG N:CYS1328 2.7 86.9 1.0 CE1 N:HIS1352 2.8 76.4 1.0 CB N:CYS1328 3.1 76.3 1.0 NE2 N:HIS1346 3.2 31.6 1.0 CG N:HIS1352 3.2 73.7 1.0 CB N:CYS1333 3.3 80.9 1.0 ND1 N:HIS1346 3.7 33.6 1.0 CB N:HIS1352 3.7 70.5 1.0 CB N:GLU1330 3.9 91.1 1.0 NE2 N:HIS1352 4.0 78.4 1.0 NE2 N:GLN1335 4.1 52.3 1.0 CD2 N:HIS1352 4.2 75.3 1.0 CD2 N:HIS1346 4.4 32.8 1.0 OG1 N:THR1350 4.6 34.1 1.0 CA N:CYS1328 4.6 70.5 1.0 CG N:GLU1330 4.6 89.9 1.0 CA N:CYS1333 4.7 87.7 1.0 CG N:HIS1346 4.7 37.2 1.0 N N:GLY1334 4.8 78.2 1.0 CB N:THR1350 4.9 39.8 1.0 CG2 N:THR1350 5.0 42.9 1.0

Zinc binding site 9 out of 12 in the REF6 ZNF2-4-NAC004-MC1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of REF6 ZNF2-4-NAC004-MC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn1403 b:0.7 occ:1.00 SG N:CYS1268 2.6 0.1 1.0 CD1 N:ILE1270 2.7 71.8 1.0 NE2 N:GLN1287 2.8 68.7 1.0 SG N:CYS1273 3.2 72.2 1.0 ND1 N:HIS1286 3.3 83.3 1.0 CE1 N:HIS1286 3.4 84.4 1.0 NE2 N:HIS1290 3.6 0.5 1.0 CD N:GLN1287 3.6 73.7 1.0 CB N:CYS1268 3.7 0.3 1.0 CD2 N:HIS1290 3.7 0.4 1.0 OE1 N:GLN1287 3.8 76.5 1.0 CG1 N:ILE1270 4.1 80.8 1.0 CB N:CYS1273 4.4 85.3 1.0 CG N:HIS1286 4.5 82.7 1.0 NE2 N:HIS1286 4.6 78.3 1.0 CE1 N:HIS1290 4.7 0.8 1.0 O N:HIS1286 4.8 86.3 1.0 CA N:CYS1268 4.9 0.8 1.0 CG N:HIS1290 4.9 1.0 1.0 CG N:GLN1287 4.9 72.4 1.0

Zinc binding site 10 out of 12 in the REF6 ZNF2-4-NAC004-MC1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of REF6 ZNF2-4-NAC004-MC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1401 b:46.2 occ:1.00 SG G:CYS1303 2.0 38.7 1.0 NE2 G:HIS1316 2.4 22.0 1.0 SG G:CYS1298 2.5 54.7 1.0 NE2 G:HIS1320 2.7 36.5 1.0 CE1 G:HIS1316 2.7 22.5 1.0 CE1 G:HIS1320 3.0 38.9 1.0 CB G:CYS1303 3.2 41.7 1.0 CB G:CYS1298 3.3 55.1 1.0 CD2 G:HIS1316 3.7 22.4 1.0 CB G:MET1305 3.9 44.9 1.0 CD2 G:HIS1320 4.0 39.0 1.0 ND1 G:HIS1316 4.0 21.5 1.0 ND1 G:HIS1320 4.3 40.3 1.0 CG G:HIS1316 4.5 23.5 1.0 CA G:CYS1303 4.5 45.7 1.0 CB G:TRP1300 4.6 37.2 1.0 N G:MET1305 4.7 36.4 1.0 CA G:CYS1298 4.8 49.9 1.0 CG G:HIS1320 4.8 39.6 1.0 CA G:MET1305 4.9 41.1 1.0 CG G:MET1305 4.9 52.0 1.0 CZ G:PHE1307 4.9 64.3 1.0 C G:CYS1303 5.0 48.6 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