Zinc in PDB 6l6l: Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements
Protein crystallography data
The structure of Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements, PDB code: 6l6l
was solved by
L.Jiang,
Y.Chen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.23 /
2.78
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
42.405,
64.315,
60.776,
90.00,
96.84,
90.00
|
R / Rfree (%)
|
21.6 /
25.2
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements
(pdb code 6l6l). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements, PDB code: 6l6l:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6l6l
Go back to
Zinc Binding Sites List in 6l6l
Zinc binding site 1 out
of 4 in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:30.4
occ:1.00
|
SG
|
A:CYS283
|
2.3
|
39.6
|
1.0
|
SG
|
A:CYS266
|
2.3
|
33.9
|
1.0
|
SG
|
A:CYS280
|
2.4
|
33.5
|
1.0
|
SG
|
A:CYS263
|
2.6
|
37.3
|
1.0
|
CB
|
A:CYS283
|
3.1
|
30.3
|
1.0
|
CB
|
A:CYS266
|
3.4
|
33.3
|
1.0
|
CB
|
A:CYS280
|
3.5
|
34.7
|
1.0
|
CB
|
A:CYS263
|
3.6
|
45.0
|
1.0
|
N
|
A:CYS280
|
3.8
|
33.6
|
1.0
|
N
|
A:CYS266
|
3.8
|
44.9
|
1.0
|
N
|
A:CYS283
|
3.8
|
30.9
|
1.0
|
NH1
|
A:ARG312
|
4.0
|
41.7
|
1.0
|
CA
|
A:CYS283
|
4.1
|
30.0
|
1.0
|
CA
|
A:CYS280
|
4.1
|
34.3
|
1.0
|
CA
|
A:CYS266
|
4.2
|
33.6
|
1.0
|
CB
|
A:VAL265
|
4.4
|
35.5
|
1.0
|
O
|
A:CYS280
|
4.6
|
39.0
|
1.0
|
CG1
|
A:VAL265
|
4.6
|
32.2
|
1.0
|
CB
|
A:ASP268
|
4.6
|
36.9
|
1.0
|
C
|
A:CYS280
|
4.7
|
37.4
|
1.0
|
C
|
A:VAL265
|
4.7
|
45.5
|
1.0
|
NH2
|
A:ARG319
|
4.8
|
22.4
|
1.0
|
C
|
A:CYS266
|
4.9
|
38.9
|
1.0
|
C
|
A:THR279
|
4.9
|
34.9
|
1.0
|
CA
|
A:VAL265
|
4.9
|
31.6
|
1.0
|
C
|
A:GLY282
|
4.9
|
30.9
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6l6l
Go back to
Zinc Binding Sites List in 6l6l
Zinc binding site 2 out
of 4 in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:34.2
occ:1.00
|
SG
|
A:CYS305
|
2.3
|
25.8
|
1.0
|
SG
|
A:CYS315
|
2.3
|
30.6
|
1.0
|
SG
|
A:CYS318
|
2.4
|
41.4
|
1.0
|
SG
|
A:CYS299
|
2.4
|
26.9
|
1.0
|
CB
|
A:CYS305
|
3.3
|
25.6
|
1.0
|
CB
|
A:CYS299
|
3.4
|
25.3
|
1.0
|
CB
|
A:CYS315
|
3.4
|
27.5
|
1.0
|
CB
|
A:CYS318
|
3.4
|
38.1
|
1.0
|
N
|
A:CYS305
|
3.8
|
26.0
|
1.0
|
CA
|
A:CYS299
|
4.1
|
28.7
|
1.0
|
CA
|
A:LYS303
|
4.2
|
30.6
|
1.0
|
N
|
A:CYS318
|
4.2
|
45.2
|
1.0
|
CA
|
A:CYS305
|
4.2
|
29.0
|
1.0
|
N
|
A:ASN304
|
4.3
|
27.1
|
1.0
|
CA
|
A:CYS318
|
4.4
|
38.1
|
1.0
|
N
|
A:LYS303
|
4.4
|
41.7
|
1.0
|
O
|
A:HOH504
|
4.4
|
5.7
|
1.0
|
C
|
A:LYS303
|
4.6
|
33.4
|
1.0
|
CB
|
A:ALA301
|
4.6
|
25.3
|
1.0
|
CA
|
A:CYS315
|
4.8
|
25.5
|
1.0
|
C
|
A:CYS299
|
4.9
|
26.5
|
1.0
|
N
|
A:LEU300
|
4.9
|
22.1
|
1.0
|
C
|
A:ASN304
|
4.9
|
26.8
|
1.0
|
N
|
A:ALA301
|
5.0
|
31.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6l6l
Go back to
Zinc Binding Sites List in 6l6l
Zinc binding site 3 out
of 4 in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:31.6
occ:1.00
|
SG
|
B:CYS283
|
2.4
|
55.6
|
1.0
|
SG
|
B:CYS266
|
2.6
|
36.0
|
1.0
|
SG
|
B:CYS280
|
2.7
|
42.4
|
1.0
|
SG
|
B:CYS263
|
2.9
|
48.4
|
1.0
|
CB
|
B:CYS283
|
3.2
|
25.3
|
1.0
|
CB
|
B:CYS263
|
3.5
|
36.9
|
1.0
|
CB
|
B:CYS280
|
3.7
|
34.6
|
1.0
|
CB
|
B:CYS266
|
3.8
|
37.3
|
1.0
|
N
|
B:CYS266
|
4.0
|
38.8
|
1.0
|
N
|
B:CYS280
|
4.0
|
34.7
|
1.0
|
N
|
B:CYS283
|
4.0
|
27.7
|
1.0
|
CA
|
B:CYS283
|
4.2
|
26.4
|
1.0
|
CA
|
B:CYS280
|
4.4
|
34.7
|
1.0
|
CB
|
B:VAL265
|
4.4
|
39.2
|
1.0
|
CA
|
B:CYS266
|
4.4
|
38.6
|
1.0
|
NH1
|
B:ARG312
|
4.4
|
32.7
|
1.0
|
CG1
|
B:VAL265
|
4.6
|
39.0
|
1.0
|
C
|
B:VAL265
|
4.8
|
39.9
|
1.0
|
CB
|
B:ASP268
|
4.9
|
35.1
|
1.0
|
O
|
B:CYS280
|
4.9
|
32.3
|
1.0
|
C
|
B:CYS280
|
4.9
|
33.3
|
1.0
|
NH2
|
B:ARG319
|
5.0
|
24.6
|
1.0
|
CA
|
B:VAL265
|
5.0
|
40.2
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6l6l
Go back to
Zinc Binding Sites List in 6l6l
Zinc binding site 4 out
of 4 in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:28.1
occ:1.00
|
SG
|
B:CYS315
|
2.3
|
27.6
|
1.0
|
SG
|
B:CYS299
|
2.3
|
49.4
|
1.0
|
SG
|
B:CYS305
|
2.3
|
38.9
|
1.0
|
SG
|
B:CYS318
|
2.4
|
32.1
|
1.0
|
CB
|
B:CYS299
|
3.2
|
43.3
|
1.0
|
CB
|
B:CYS305
|
3.3
|
38.3
|
1.0
|
CB
|
B:CYS318
|
3.4
|
30.2
|
1.0
|
CB
|
B:CYS315
|
3.4
|
29.4
|
1.0
|
N
|
B:CYS305
|
3.9
|
42.6
|
1.0
|
CA
|
B:CYS299
|
4.0
|
38.3
|
1.0
|
N
|
B:CYS318
|
4.1
|
26.3
|
1.0
|
CA
|
B:CYS305
|
4.2
|
42.0
|
1.0
|
CA
|
B:LYS303
|
4.3
|
41.3
|
1.0
|
CA
|
B:CYS318
|
4.3
|
30.2
|
1.0
|
N
|
B:ASN304
|
4.4
|
56.4
|
1.0
|
N
|
B:LYS303
|
4.5
|
51.1
|
1.0
|
C
|
B:LYS303
|
4.6
|
42.6
|
1.0
|
CB
|
B:ALA301
|
4.7
|
44.4
|
1.0
|
CD2
|
B:TYR317
|
4.7
|
28.8
|
1.0
|
C
|
B:CYS299
|
4.8
|
39.0
|
1.0
|
CA
|
B:CYS315
|
4.8
|
29.0
|
1.0
|
N
|
B:ALA301
|
4.8
|
46.8
|
1.0
|
N
|
B:LEU300
|
4.9
|
39.7
|
1.0
|
C
|
B:ASN304
|
5.0
|
45.2
|
1.0
|
|
Reference:
L.Jiang,
S.Dai,
J.Li,
X.Liang,
L.Qu,
X.Chen,
M.Guo,
Z.Chen,
L.Chen,
H.Wei,
Y.Chen.
Structural Basis of Binding of Homodimers of the Nuclear Receptor NR4A2 to Selective Nur-Responsive Dna Elements. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31723028
DOI: 10.1074/JBC.RA119.010730
Page generated: Tue Oct 29 02:24:24 2024
|