Zinc in PDB 6jnm: REF6 ZNF2-4-NAC004-MC3 Complex
Protein crystallography data
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
|
Zinc Binding Sites:
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 6jnm
Go back to
Zinc Binding Sites List in 6jnm
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 6jnm
Go back to
Zinc Binding Sites List in 6jnm
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 6jnm
Go back to
Zinc Binding Sites List in 6jnm
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 6jnm
Go back to
Zinc Binding Sites List in 6jnm
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 6jnm
Go back to
Zinc Binding Sites List in 6jnm
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 6jnm
Go back to
Zinc Binding Sites List in 6jnm
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
|
|
Reference:
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
Page generated: Tue Oct 29 01:16:17 2024
|