Zinc in PDB 6lc1: Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter
Protein crystallography data
The structure of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter, PDB code: 6lc1
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)
|
29.65 /
3.12
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
36.822,
63.210,
91.762,
109.98,
90.21,
89.54
|
R / Rfree (%)
|
20.9 /
26.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter
(pdb code 6lc1). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter, PDB code: 6lc1:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 6lc1
Go back to
Zinc Binding Sites List in 6lc1
Zinc binding site 1 out
of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter
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 NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn401
b:96.1
occ:1.00
|
SG
|
J:CYS303
|
2.4
|
93.9
|
1.0
|
SG
|
J:CYS319
|
2.4
|
97.8
|
1.0
|
SG
|
J:CYS309
|
2.5
|
94.4
|
1.0
|
SG
|
J:CYS322
|
2.5
|
97.4
|
1.0
|
CB
|
J:CYS303
|
3.2
|
90.5
|
1.0
|
CB
|
J:CYS309
|
3.3
|
98.0
|
1.0
|
CB
|
J:CYS319
|
3.3
|
93.9
|
1.0
|
CB
|
J:CYS322
|
3.6
|
94.9
|
1.0
|
CA
|
J:CYS303
|
4.1
|
90.3
|
1.0
|
CA
|
J:CYS309
|
4.4
|
0.2
|
1.0
|
N
|
J:CYS309
|
4.4
|
0.7
|
1.0
|
N
|
J:CYS322
|
4.5
|
88.9
|
1.0
|
N
|
J:LYS307
|
4.5
|
0.3
|
1.0
|
CA
|
J:LYS307
|
4.5
|
0.6
|
1.0
|
CA
|
J:CYS322
|
4.6
|
91.0
|
1.0
|
N
|
J:ASP308
|
4.7
|
0.8
|
1.0
|
C
|
J:ASP308
|
4.7
|
0.0
|
1.0
|
CB
|
J:ALA305
|
4.7
|
95.0
|
1.0
|
CA
|
J:CYS319
|
4.7
|
87.2
|
1.0
|
C
|
J:LYS307
|
4.7
|
0.3
|
1.0
|
C
|
J:CYS303
|
4.8
|
96.0
|
1.0
|
O
|
J:ASP308
|
4.8
|
0.8
|
1.0
|
N
|
J:ALA305
|
4.9
|
0.8
|
1.0
|
|
Zinc binding site 2 out
of 8 in 6lc1
Go back to
Zinc Binding Sites List in 6lc1
Zinc binding site 2 out
of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter
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 NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn402
b:87.6
occ:1.00
|
SG
|
J:CYS287
|
2.4
|
78.1
|
1.0
|
SG
|
J:CYS267
|
2.4
|
79.8
|
1.0
|
SG
|
J:CYS270
|
2.5
|
94.4
|
1.0
|
SG
|
J:CYS284
|
2.6
|
90.5
|
1.0
|
CB
|
J:CYS284
|
2.9
|
82.5
|
1.0
|
CB
|
J:CYS270
|
3.3
|
91.5
|
1.0
|
CB
|
J:CYS287
|
3.4
|
79.7
|
1.0
|
CB
|
J:CYS267
|
3.7
|
82.2
|
1.0
|
N
|
J:CYS270
|
3.7
|
91.9
|
1.0
|
NH1
|
J:ARG316
|
4.0
|
89.9
|
1.0
|
N
|
J:CYS284
|
4.0
|
85.0
|
1.0
|
CA
|
J:CYS284
|
4.0
|
84.6
|
1.0
|
CA
|
J:CYS270
|
4.1
|
89.5
|
1.0
|
N
|
J:CYS287
|
4.1
|
74.7
|
1.0
|
CA
|
J:CYS287
|
4.4
|
74.5
|
1.0
|
CB
|
J:VAL269
|
4.4
|
83.7
|
1.0
|
N
|
J:GLY271
|
4.7
|
82.0
|
1.0
|
C
|
J:CYS270
|
4.8
|
85.5
|
1.0
|
NH2
|
J:ARG323
|
4.8
|
75.3
|
1.0
|
C
|
J:VAL269
|
4.8
|
86.0
|
1.0
|
CD
|
J:ARG316
|
4.9
|
84.0
|
1.0
|
CB
|
J:ASP272
|
4.9
|
93.0
|
1.0
|
N
|
J:ASP272
|
5.0
|
86.3
|
1.0
|
|
Zinc binding site 3 out
of 8 in 6lc1
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Zinc Binding Sites List in 6lc1
Zinc binding site 3 out
of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter
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 NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:81.1
occ:1.00
|
SG
|
A:CYS270
|
2.4
|
0.5
|
1.0
|
SG
|
A:CYS267
|
2.4
|
88.4
|
1.0
|
SG
|
A:CYS287
|
2.6
|
79.3
|
1.0
|
CB
|
A:CYS284
|
2.7
|
91.2
|
1.0
|
CB
|
A:CYS270
|
3.2
|
0.2
|
1.0
|
N
|
A:CYS270
|
3.6
|
99.8
|
1.0
|
CB
|
A:CYS267
|
3.6
|
92.7
|
1.0
|
CB
|
A:CYS287
|
3.6
|
79.0
|
1.0
|
N
|
A:CYS284
|
3.8
|
81.5
|
1.0
|
CA
|
A:CYS284
|
3.9
|
84.3
|
1.0
|
SG
|
A:CYS284
|
3.9
|
0.3
|
1.0
|
CA
|
A:CYS270
|
4.0
|
98.3
|
1.0
|
N
|
A:CYS287
|
4.1
|
76.0
|
1.0
|
NH1
|
A:ARG316
|
4.1
|
80.5
|
1.0
|
CB
|
A:VAL269
|
4.3
|
91.4
|
1.0
|
NH2
|
A:ARG323
|
4.4
|
82.2
|
1.0
|
CA
|
A:CYS287
|
4.5
|
76.4
|
1.0
|
CB
|
A:ASP272
|
4.5
|
0.5
|
1.0
|
C
|
A:VAL269
|
4.7
|
94.3
|
1.0
|
C
|
A:CYS284
|
4.7
|
82.5
|
1.0
|
CA
|
A:VAL269
|
4.9
|
91.1
|
1.0
|
CG1
|
A:VAL269
|
4.9
|
90.9
|
1.0
|
N
|
A:ASP272
|
4.9
|
0.2
|
1.0
|
N
|
A:GLY271
|
5.0
|
97.2
|
1.0
|
N
|
A:VAL269
|
5.0
|
90.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 6lc1
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Zinc Binding Sites List in 6lc1
Zinc binding site 4 out
of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter
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 NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:0.8
occ:1.00
|
SG
|
A:CYS322
|
2.5
|
83.3
|
1.0
|
SG
|
A:CYS303
|
2.5
|
0.8
|
1.0
|
SG
|
A:CYS319
|
2.6
|
94.0
|
1.0
|
SG
|
A:CYS309
|
2.7
|
0.3
|
1.0
|
CB
|
A:CYS309
|
2.9
|
0.8
|
1.0
|
CB
|
A:CYS319
|
3.1
|
99.7
|
1.0
|
N
|
A:CYS309
|
3.5
|
0.6
|
1.0
|
CB
|
A:CYS303
|
3.6
|
95.0
|
1.0
|
CB
|
A:CYS322
|
3.6
|
90.3
|
1.0
|
CA
|
A:CYS309
|
3.8
|
0.9
|
1.0
|
CA
|
A:CYS303
|
4.4
|
96.7
|
1.0
|
N
|
A:ASP308
|
4.5
|
99.9
|
1.0
|
N
|
A:CYS322
|
4.6
|
87.7
|
1.0
|
CA
|
A:CYS319
|
4.7
|
0.2
|
1.0
|
CB
|
A:ALA305
|
4.7
|
0.2
|
1.0
|
C
|
A:ASP308
|
4.7
|
0.8
|
1.0
|
CA
|
A:CYS322
|
4.7
|
90.9
|
1.0
|
C
|
A:LYS307
|
4.7
|
0.7
|
1.0
|
CA
|
A:LYS307
|
4.9
|
0.4
|
1.0
|
N
|
A:LYS307
|
4.9
|
0.1
|
1.0
|
N
|
A:LEU304
|
4.9
|
0.3
|
1.0
|
C
|
A:CYS303
|
4.9
|
0.4
|
1.0
|
N
|
A:ALA305
|
4.9
|
0.0
|
1.0
|
C
|
A:CYS309
|
4.9
|
0.9
|
1.0
|
|
Zinc binding site 5 out
of 8 in 6lc1
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Zinc Binding Sites List in 6lc1
Zinc binding site 5 out
of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn401
b:83.2
occ:1.00
|
SG
|
D:CYS267
|
2.4
|
91.2
|
1.0
|
SG
|
D:CYS287
|
2.4
|
89.6
|
1.0
|
SG
|
D:CYS270
|
2.4
|
91.0
|
1.0
|
CB
|
D:CYS270
|
2.5
|
89.7
|
1.0
|
SG
|
D:CYS284
|
2.5
|
76.7
|
1.0
|
N
|
D:CYS270
|
3.0
|
91.3
|
1.0
|
CA
|
D:CYS270
|
3.3
|
89.2
|
1.0
|
CB
|
D:CYS284
|
3.4
|
82.1
|
1.0
|
CB
|
D:CYS267
|
3.6
|
91.5
|
1.0
|
N
|
D:CYS284
|
3.9
|
83.7
|
1.0
|
CB
|
D:CYS287
|
4.0
|
85.4
|
1.0
|
C
|
D:VAL269
|
4.1
|
95.6
|
1.0
|
N
|
D:GLY271
|
4.1
|
89.6
|
1.0
|
CA
|
D:CYS284
|
4.2
|
83.0
|
1.0
|
C
|
D:CYS270
|
4.2
|
85.1
|
1.0
|
NH1
|
D:ARG316
|
4.3
|
94.0
|
1.0
|
CB
|
D:VAL269
|
4.3
|
85.4
|
1.0
|
N
|
D:CYS287
|
4.5
|
79.9
|
1.0
|
CA
|
D:VAL269
|
4.5
|
91.1
|
1.0
|
N
|
D:VAL269
|
4.6
|
92.1
|
1.0
|
N
|
D:ASP272
|
4.7
|
91.2
|
1.0
|
CB
|
D:ASP272
|
4.7
|
96.0
|
1.0
|
CG1
|
D:VAL269
|
4.8
|
78.8
|
1.0
|
CA
|
D:CYS287
|
4.9
|
79.0
|
1.0
|
C
|
D:CYS284
|
4.9
|
84.6
|
1.0
|
CA
|
D:CYS267
|
4.9
|
90.9
|
1.0
|
O
|
D:CYS284
|
5.0
|
86.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 6lc1
Go back to
Zinc Binding Sites List in 6lc1
Zinc binding site 6 out
of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn402
b:98.7
occ:1.00
|
SG
|
D:CYS303
|
2.3
|
89.8
|
1.0
|
SG
|
D:CYS309
|
2.3
|
0.5
|
1.0
|
SG
|
D:CYS319
|
2.3
|
94.4
|
1.0
|
SG
|
D:CYS322
|
2.5
|
83.2
|
1.0
|
CB
|
D:CYS303
|
3.1
|
87.4
|
1.0
|
CB
|
D:CYS319
|
3.3
|
91.9
|
1.0
|
CB
|
D:CYS322
|
3.4
|
82.7
|
1.0
|
CB
|
D:CYS309
|
3.5
|
0.3
|
1.0
|
CA
|
D:CYS303
|
4.0
|
86.8
|
1.0
|
N
|
D:CYS309
|
4.2
|
0.6
|
1.0
|
N
|
D:CYS322
|
4.2
|
81.5
|
1.0
|
CA
|
D:CYS322
|
4.4
|
81.9
|
1.0
|
CA
|
D:CYS309
|
4.5
|
0.2
|
1.0
|
CA
|
D:LYS307
|
4.5
|
0.8
|
1.0
|
C
|
D:CYS303
|
4.6
|
93.5
|
1.0
|
CA
|
D:CYS319
|
4.7
|
85.1
|
1.0
|
N
|
D:LYS307
|
4.7
|
0.8
|
1.0
|
N
|
D:ASP308
|
4.7
|
0.5
|
1.0
|
N
|
D:LEU304
|
4.9
|
96.0
|
1.0
|
N
|
D:ALA305
|
4.9
|
0.4
|
1.0
|
CB
|
D:ALA305
|
4.9
|
96.7
|
1.0
|
C
|
D:LYS307
|
5.0
|
0.1
|
1.0
|
|
Zinc binding site 7 out
of 8 in 6lc1
Go back to
Zinc Binding Sites List in 6lc1
Zinc binding site 7 out
of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn401
b:77.1
occ:1.00
|
SG
|
G:CYS267
|
2.3
|
86.5
|
1.0
|
SG
|
G:CYS270
|
2.3
|
0.7
|
1.0
|
SG
|
G:CYS287
|
2.7
|
83.2
|
1.0
|
SG
|
G:CYS284
|
2.7
|
92.0
|
1.0
|
CB
|
G:CYS270
|
3.2
|
0.6
|
1.0
|
CB
|
G:CYS284
|
3.2
|
90.2
|
1.0
|
CB
|
G:CYS267
|
3.4
|
89.5
|
1.0
|
N
|
G:CYS270
|
3.6
|
96.4
|
1.0
|
CB
|
G:CYS287
|
3.7
|
80.5
|
1.0
|
N
|
G:CYS284
|
4.0
|
81.9
|
1.0
|
CA
|
G:CYS270
|
4.0
|
0.3
|
1.0
|
CA
|
G:CYS284
|
4.2
|
87.3
|
1.0
|
NH1
|
G:ARG316
|
4.3
|
98.8
|
1.0
|
N
|
G:CYS287
|
4.3
|
76.7
|
1.0
|
CB
|
G:VAL269
|
4.5
|
86.3
|
1.0
|
CB
|
G:ASP272
|
4.5
|
0.5
|
1.0
|
C
|
G:VAL269
|
4.6
|
96.5
|
1.0
|
CA
|
G:CYS287
|
4.6
|
77.3
|
1.0
|
CA
|
G:CYS267
|
4.8
|
88.3
|
1.0
|
N
|
G:VAL269
|
4.9
|
93.5
|
1.0
|
C
|
G:CYS284
|
4.9
|
89.9
|
1.0
|
CA
|
G:VAL269
|
4.9
|
90.9
|
1.0
|
N
|
G:ASP272
|
4.9
|
0.2
|
1.0
|
N
|
G:GLY271
|
5.0
|
0.1
|
1.0
|
|
Zinc binding site 8 out
of 8 in 6lc1
Go back to
Zinc Binding Sites List in 6lc1
Zinc binding site 8 out
of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn402
b:0.6
occ:1.00
|
SG
|
G:CYS319
|
2.4
|
99.4
|
1.0
|
SG
|
G:CYS303
|
2.4
|
0.8
|
1.0
|
SG
|
G:CYS322
|
2.4
|
100.0
|
1.0
|
SG
|
G:CYS309
|
2.5
|
0.9
|
1.0
|
CB
|
G:CYS309
|
3.1
|
0.1
|
1.0
|
CB
|
G:CYS303
|
3.2
|
0.3
|
1.0
|
CB
|
G:CYS319
|
3.2
|
0.1
|
1.0
|
CB
|
G:CYS322
|
3.4
|
97.5
|
1.0
|
N
|
G:CYS309
|
3.8
|
0.2
|
1.0
|
CA
|
G:CYS309
|
4.0
|
0.8
|
1.0
|
CA
|
G:CYS303
|
4.0
|
0.7
|
1.0
|
N
|
G:CYS322
|
4.2
|
89.6
|
1.0
|
C
|
G:ASP308
|
4.3
|
0.5
|
1.0
|
CA
|
G:CYS322
|
4.3
|
93.5
|
1.0
|
N
|
G:ASP308
|
4.4
|
0.6
|
1.0
|
CA
|
G:CYS319
|
4.6
|
0.4
|
1.0
|
C
|
G:LYS307
|
4.7
|
0.1
|
1.0
|
C
|
G:CYS303
|
4.7
|
0.2
|
1.0
|
CA
|
G:ASP308
|
4.8
|
0.2
|
1.0
|
O
|
G:ASP308
|
4.8
|
0.3
|
1.0
|
CB
|
G:ALA305
|
4.8
|
0.6
|
1.0
|
CD2
|
G:PHE321
|
4.8
|
95.0
|
1.0
|
CA
|
G:LYS307
|
4.9
|
0.9
|
1.0
|
N
|
G:LYS307
|
5.0
|
0.8
|
1.0
|
N
|
G:ALA305
|
5.0
|
0.7
|
1.0
|
|
Reference:
L.Jiang,
H.Wei,
N.Yan,
S.Dai,
J.Li,
L.Qu,
X.Chen,
M.Guo,
Z.Chen,
Y.Chen.
Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter. Biochem.Biophys.Res.Commun. 2019.
ISSN: ESSN 1090-2104
PubMed: 31822342
DOI: 10.1016/J.BBRC.2019.11.192
Page generated: Tue Oct 29 02:28:40 2024
|