Zinc in PDB 5cbz: Ancmr Dna Binding Domain - (+)Gre Complex
Protein crystallography data
The structure of Ancmr Dna Binding Domain - (+)Gre Complex, PDB code: 5cbz
was solved by
W.H.Hudson,
E.A.Ortlund,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.532,
81.150,
116.416,
90.00,
96.80,
90.00
|
R / Rfree (%)
|
19.6 /
23
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Ancmr Dna Binding Domain - (+)Gre Complex
(pdb code 5cbz). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Ancmr Dna Binding Domain - (+)Gre Complex, PDB code: 5cbz:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5cbz
Go back to
Zinc Binding Sites List in 5cbz
Zinc binding site 1 out
of 8 in the Ancmr Dna Binding Domain - (+)Gre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:45.8
occ:1.00
|
SG
|
A:CYS421
|
2.2
|
43.4
|
1.0
|
SG
|
A:CYS424
|
2.3
|
45.1
|
1.0
|
SG
|
A:CYS438
|
2.3
|
46.0
|
1.0
|
SG
|
A:CYS441
|
2.4
|
42.1
|
1.0
|
CB
|
A:CYS441
|
3.2
|
34.4
|
1.0
|
CB
|
A:CYS421
|
3.3
|
48.5
|
1.0
|
CB
|
A:CYS424
|
3.4
|
45.1
|
1.0
|
CB
|
A:CYS438
|
3.4
|
43.2
|
1.0
|
N
|
A:CYS424
|
3.5
|
45.7
|
1.0
|
N
|
A:CYS438
|
3.9
|
45.8
|
1.0
|
CA
|
A:CYS424
|
4.0
|
43.1
|
1.0
|
NH1
|
A:ARG470
|
4.2
|
42.3
|
1.0
|
CA
|
A:CYS438
|
4.2
|
45.7
|
1.0
|
CB
|
A:VAL423
|
4.3
|
40.1
|
1.0
|
N
|
A:CYS441
|
4.3
|
37.7
|
1.0
|
CA
|
A:CYS441
|
4.3
|
39.6
|
1.0
|
OG
|
A:SER440
|
4.4
|
41.8
|
1.0
|
C
|
A:VAL423
|
4.6
|
46.2
|
1.0
|
C
|
A:CYS424
|
4.6
|
51.1
|
1.0
|
CB
|
A:ASP426
|
4.7
|
48.5
|
1.0
|
N
|
A:GLY425
|
4.7
|
53.1
|
1.0
|
CA
|
A:CYS421
|
4.7
|
52.2
|
1.0
|
CG1
|
A:VAL423
|
4.7
|
41.2
|
1.0
|
CA
|
A:VAL423
|
4.8
|
47.5
|
1.0
|
N
|
A:ASP426
|
4.8
|
53.4
|
1.0
|
C
|
A:CYS438
|
4.9
|
47.3
|
1.0
|
N
|
A:VAL423
|
4.9
|
44.9
|
1.0
|
O
|
A:CYS438
|
5.0
|
43.5
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5cbz
Go back to
Zinc Binding Sites List in 5cbz
Zinc binding site 2 out
of 8 in the Ancmr Dna Binding Domain - (+)Gre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:34.6
occ:1.00
|
SG
|
A:CYS476
|
2.3
|
32.8
|
1.0
|
SG
|
A:CYS457
|
2.3
|
36.0
|
1.0
|
SG
|
A:CYS473
|
2.3
|
31.8
|
1.0
|
SG
|
A:CYS463
|
2.4
|
36.9
|
1.0
|
CB
|
A:CYS463
|
3.2
|
36.6
|
1.0
|
CB
|
A:CYS457
|
3.3
|
33.2
|
1.0
|
CB
|
A:CYS473
|
3.4
|
31.9
|
1.0
|
CB
|
A:CYS476
|
3.4
|
29.7
|
1.0
|
O
|
A:HOH604
|
3.9
|
29.4
|
1.0
|
NH2
|
A:ARG479
|
4.0
|
54.9
|
1.0
|
CA
|
A:CYS457
|
4.0
|
33.4
|
1.0
|
N
|
A:CYS463
|
4.0
|
39.5
|
1.0
|
CA
|
A:CYS463
|
4.2
|
39.0
|
1.0
|
CA
|
A:ASN461
|
4.3
|
47.0
|
1.0
|
N
|
A:CYS476
|
4.3
|
32.5
|
1.0
|
CA
|
A:CYS476
|
4.4
|
30.7
|
1.0
|
O
|
A:HOH601
|
4.5
|
43.8
|
1.0
|
N
|
A:ASN461
|
4.6
|
44.2
|
1.0
|
O
|
A:HOH621
|
4.7
|
42.5
|
1.0
|
N
|
A:ALA458
|
4.7
|
34.9
|
1.0
|
N
|
A:GLY459
|
4.7
|
38.8
|
1.0
|
C
|
A:ASN461
|
4.7
|
46.5
|
1.0
|
CA
|
A:CYS473
|
4.7
|
36.4
|
1.0
|
C
|
A:CYS457
|
4.8
|
35.0
|
1.0
|
N
|
A:ASP462
|
4.9
|
45.3
|
1.0
|
O
|
A:CYS473
|
5.0
|
31.3
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5cbz
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Zinc Binding Sites List in 5cbz
Zinc binding site 3 out
of 8 in the Ancmr Dna Binding Domain - (+)Gre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:40.6
occ:1.00
|
SG
|
B:CYS441
|
2.2
|
35.4
|
1.0
|
SG
|
B:CYS424
|
2.3
|
40.6
|
1.0
|
SG
|
B:CYS421
|
2.3
|
41.0
|
1.0
|
SG
|
B:CYS438
|
2.4
|
41.2
|
1.0
|
CB
|
B:CYS441
|
3.2
|
35.2
|
1.0
|
CB
|
B:CYS421
|
3.3
|
43.5
|
1.0
|
CB
|
B:CYS424
|
3.3
|
37.4
|
1.0
|
CB
|
B:CYS438
|
3.5
|
41.3
|
1.0
|
N
|
B:CYS424
|
3.6
|
39.6
|
1.0
|
N
|
B:CYS438
|
3.9
|
41.8
|
1.0
|
CA
|
B:CYS424
|
4.0
|
35.9
|
1.0
|
CA
|
B:CYS438
|
4.3
|
45.6
|
1.0
|
N
|
B:CYS441
|
4.3
|
36.9
|
1.0
|
CA
|
B:CYS441
|
4.3
|
41.2
|
1.0
|
CB
|
B:VAL423
|
4.3
|
41.3
|
1.0
|
OG
|
B:SER440
|
4.6
|
42.0
|
1.0
|
C
|
B:CYS424
|
4.6
|
43.7
|
1.0
|
CB
|
B:ASP426
|
4.6
|
47.7
|
1.0
|
NH1
|
B:ARG470
|
4.6
|
41.0
|
1.0
|
C
|
B:VAL423
|
4.7
|
43.9
|
1.0
|
N
|
B:GLY425
|
4.7
|
41.2
|
1.0
|
CA
|
B:CYS421
|
4.8
|
43.4
|
1.0
|
N
|
B:ASP426
|
4.9
|
46.4
|
1.0
|
CG1
|
B:VAL423
|
4.9
|
36.8
|
1.0
|
C
|
B:CYS438
|
4.9
|
42.6
|
1.0
|
O
|
B:CYS438
|
4.9
|
44.6
|
1.0
|
NH2
|
B:ARG477
|
4.9
|
36.7
|
1.0
|
CA
|
B:VAL423
|
4.9
|
38.8
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5cbz
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Zinc Binding Sites List in 5cbz
Zinc binding site 4 out
of 8 in the Ancmr Dna Binding Domain - (+)Gre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:32.2
occ:1.00
|
SG
|
B:CYS473
|
2.2
|
32.9
|
1.0
|
SG
|
B:CYS457
|
2.3
|
31.4
|
1.0
|
SG
|
B:CYS476
|
2.3
|
33.1
|
1.0
|
SG
|
B:CYS463
|
2.5
|
33.9
|
1.0
|
CB
|
B:CYS463
|
3.1
|
28.3
|
1.0
|
CB
|
B:CYS457
|
3.3
|
31.5
|
1.0
|
CB
|
B:CYS473
|
3.3
|
32.8
|
1.0
|
CB
|
B:CYS476
|
3.4
|
30.5
|
1.0
|
O
|
A:HOH606
|
3.8
|
30.8
|
1.0
|
CA
|
B:CYS457
|
3.9
|
36.3
|
1.0
|
N
|
B:CYS463
|
4.1
|
34.5
|
1.0
|
N
|
B:CYS476
|
4.1
|
31.7
|
1.0
|
CA
|
B:CYS463
|
4.2
|
35.7
|
1.0
|
CA
|
B:CYS476
|
4.3
|
26.6
|
1.0
|
CA
|
B:ASN461
|
4.4
|
35.6
|
1.0
|
O
|
B:HOH615
|
4.5
|
40.0
|
1.0
|
N
|
B:ASN461
|
4.6
|
32.6
|
1.0
|
N
|
B:ALA458
|
4.7
|
30.8
|
1.0
|
CA
|
B:CYS473
|
4.7
|
31.4
|
1.0
|
O
|
A:HOH621
|
4.7
|
42.5
|
1.0
|
N
|
B:GLY459
|
4.8
|
33.4
|
1.0
|
C
|
B:CYS457
|
4.8
|
35.6
|
1.0
|
O
|
B:HOH607
|
4.8
|
32.4
|
1.0
|
C
|
B:ASN461
|
4.8
|
37.2
|
1.0
|
N
|
B:ASP462
|
4.9
|
37.8
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5cbz
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Zinc Binding Sites List in 5cbz
Zinc binding site 5 out
of 8 in the Ancmr Dna Binding Domain - (+)Gre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn501
b:34.2
occ:1.00
|
SG
|
E:CYS438
|
2.3
|
33.4
|
1.0
|
SG
|
E:CYS424
|
2.3
|
35.7
|
1.0
|
SG
|
E:CYS421
|
2.4
|
32.6
|
1.0
|
SG
|
E:CYS441
|
2.4
|
34.3
|
1.0
|
CB
|
E:CYS441
|
3.2
|
32.5
|
1.0
|
CB
|
E:CYS421
|
3.2
|
32.8
|
1.0
|
CB
|
E:CYS424
|
3.3
|
32.3
|
1.0
|
CB
|
E:CYS438
|
3.6
|
33.7
|
1.0
|
N
|
E:CYS424
|
3.6
|
34.4
|
1.0
|
N
|
E:CYS438
|
4.0
|
29.0
|
1.0
|
CA
|
E:CYS424
|
4.0
|
33.8
|
1.0
|
N
|
E:CYS441
|
4.3
|
31.4
|
1.0
|
CA
|
E:CYS438
|
4.3
|
34.3
|
1.0
|
CB
|
E:VAL423
|
4.3
|
36.3
|
1.0
|
CA
|
E:CYS441
|
4.3
|
35.3
|
1.0
|
NH1
|
E:ARG470
|
4.4
|
32.3
|
1.0
|
OG
|
E:SER440
|
4.5
|
37.3
|
1.0
|
CB
|
E:ASP426
|
4.6
|
42.6
|
1.0
|
C
|
E:CYS424
|
4.6
|
34.2
|
1.0
|
CA
|
E:CYS421
|
4.7
|
34.2
|
1.0
|
C
|
E:VAL423
|
4.7
|
37.6
|
1.0
|
N
|
E:GLY425
|
4.7
|
34.3
|
1.0
|
N
|
E:ASP426
|
4.7
|
38.4
|
1.0
|
NH2
|
E:ARG477
|
4.9
|
33.8
|
1.0
|
CG1
|
E:VAL423
|
4.9
|
32.5
|
1.0
|
CA
|
E:VAL423
|
4.9
|
35.0
|
1.0
|
C
|
E:CYS438
|
5.0
|
35.4
|
1.0
|
O
|
E:CYS438
|
5.0
|
35.3
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5cbz
Go back to
Zinc Binding Sites List in 5cbz
Zinc binding site 6 out
of 8 in the Ancmr Dna Binding Domain - (+)Gre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn502
b:29.7
occ:1.00
|
SG
|
E:CYS457
|
2.2
|
31.4
|
1.0
|
SG
|
E:CYS476
|
2.2
|
29.2
|
1.0
|
SG
|
E:CYS473
|
2.3
|
30.9
|
1.0
|
SG
|
E:CYS463
|
2.3
|
33.7
|
1.0
|
CB
|
E:CYS457
|
3.2
|
30.9
|
1.0
|
CB
|
E:CYS463
|
3.3
|
36.7
|
1.0
|
CB
|
E:CYS473
|
3.3
|
30.3
|
1.0
|
CB
|
E:CYS476
|
3.3
|
26.3
|
1.0
|
CA
|
E:CYS457
|
3.9
|
33.6
|
1.0
|
O
|
E:HOH603
|
3.9
|
26.7
|
1.0
|
N
|
E:CYS463
|
4.0
|
33.6
|
1.0
|
N
|
E:CYS476
|
4.2
|
31.7
|
1.0
|
CA
|
E:CYS463
|
4.3
|
33.1
|
1.0
|
CA
|
E:CYS476
|
4.3
|
28.8
|
1.0
|
CA
|
E:ASN461
|
4.4
|
34.4
|
1.0
|
O
|
E:HOH615
|
4.5
|
37.2
|
1.0
|
N
|
E:ASN461
|
4.5
|
32.9
|
1.0
|
O
|
E:HOH621
|
4.7
|
31.5
|
1.0
|
N
|
E:ALA458
|
4.7
|
31.9
|
1.0
|
O
|
E:HOH632
|
4.7
|
31.8
|
1.0
|
C
|
E:ASN461
|
4.7
|
33.9
|
1.0
|
CA
|
E:CYS473
|
4.7
|
33.5
|
1.0
|
C
|
E:CYS457
|
4.7
|
30.4
|
1.0
|
N
|
E:GLY459
|
4.7
|
31.2
|
1.0
|
N
|
E:ASP462
|
4.7
|
39.4
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5cbz
Go back to
Zinc Binding Sites List in 5cbz
Zinc binding site 7 out
of 8 in the Ancmr Dna Binding Domain - (+)Gre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn501
b:38.0
occ:1.00
|
SG
|
F:CYS438
|
2.2
|
38.1
|
1.0
|
SG
|
F:CYS424
|
2.2
|
37.3
|
1.0
|
SG
|
F:CYS421
|
2.4
|
38.6
|
1.0
|
SG
|
F:CYS441
|
2.4
|
40.3
|
1.0
|
CB
|
F:CYS441
|
3.3
|
39.0
|
1.0
|
CB
|
F:CYS424
|
3.3
|
39.7
|
1.0
|
CB
|
F:CYS421
|
3.3
|
42.2
|
1.0
|
N
|
F:CYS424
|
3.4
|
41.1
|
1.0
|
CB
|
F:CYS438
|
3.5
|
41.8
|
1.0
|
CA
|
F:CYS424
|
3.9
|
37.2
|
1.0
|
N
|
F:CYS438
|
3.9
|
43.8
|
1.0
|
CA
|
F:CYS438
|
4.3
|
42.1
|
1.0
|
CB
|
F:VAL423
|
4.3
|
39.9
|
1.0
|
N
|
F:CYS441
|
4.4
|
36.6
|
1.0
|
OG
|
F:SER440
|
4.4
|
37.7
|
1.0
|
CA
|
F:CYS441
|
4.4
|
39.2
|
1.0
|
NH1
|
F:ARG470
|
4.4
|
35.7
|
1.0
|
CB
|
F:ASP426
|
4.4
|
44.7
|
1.0
|
C
|
F:VAL423
|
4.5
|
42.2
|
1.0
|
C
|
F:CYS424
|
4.6
|
42.6
|
1.0
|
N
|
F:GLY425
|
4.7
|
44.3
|
1.0
|
N
|
F:ASP426
|
4.7
|
45.7
|
1.0
|
CA
|
F:CYS421
|
4.8
|
45.7
|
1.0
|
NH2
|
F:ARG477
|
4.8
|
34.1
|
1.0
|
CA
|
F:VAL423
|
4.8
|
40.9
|
1.0
|
N
|
F:VAL423
|
4.9
|
40.3
|
1.0
|
C
|
F:CYS438
|
4.9
|
41.4
|
1.0
|
CG1
|
F:VAL423
|
4.9
|
40.2
|
1.0
|
O
|
F:CYS438
|
5.0
|
43.9
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5cbz
Go back to
Zinc Binding Sites List in 5cbz
Zinc binding site 8 out
of 8 in the Ancmr Dna Binding Domain - (+)Gre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn502
b:33.6
occ:1.00
|
SG
|
F:CYS473
|
2.3
|
29.6
|
1.0
|
SG
|
F:CYS457
|
2.3
|
31.9
|
1.0
|
SG
|
F:CYS463
|
2.3
|
31.6
|
1.0
|
SG
|
F:CYS476
|
2.4
|
31.9
|
1.0
|
CB
|
F:CYS463
|
3.1
|
31.8
|
1.0
|
CB
|
F:CYS457
|
3.3
|
29.5
|
1.0
|
CB
|
F:CYS473
|
3.3
|
29.3
|
1.0
|
CB
|
F:CYS476
|
3.5
|
32.4
|
1.0
|
N
|
F:CYS463
|
3.9
|
33.6
|
1.0
|
O
|
E:HOH616
|
3.9
|
31.8
|
1.0
|
CA
|
F:CYS457
|
4.0
|
30.6
|
1.0
|
CA
|
F:CYS463
|
4.1
|
30.6
|
1.0
|
N
|
F:CYS476
|
4.3
|
31.8
|
1.0
|
O
|
F:HOH603
|
4.4
|
32.9
|
1.0
|
CA
|
F:ASN461
|
4.4
|
33.6
|
1.0
|
CA
|
F:CYS476
|
4.4
|
30.1
|
1.0
|
O
|
F:HOH608
|
4.5
|
38.4
|
1.0
|
N
|
F:ASN461
|
4.6
|
34.7
|
1.0
|
O
|
E:HOH632
|
4.7
|
31.8
|
1.0
|
CA
|
F:CYS473
|
4.7
|
27.8
|
1.0
|
N
|
F:ALA458
|
4.7
|
28.6
|
1.0
|
C
|
F:ASN461
|
4.7
|
37.0
|
1.0
|
N
|
F:ASP462
|
4.8
|
31.6
|
1.0
|
C
|
F:CYS457
|
4.8
|
32.4
|
1.0
|
N
|
F:GLY459
|
4.9
|
30.7
|
1.0
|
|
Reference:
W.H.Hudson,
B.R.Kossmann,
I.M.De Vera,
S.W.Chuo,
E.R.Weikum,
G.N.Eick,
J.W.Thornton,
I.N.Ivanov,
D.J.Kojetin,
E.A.Ortlund.
Distal Substitutions Drive Divergent Dna Specificity Among Paralogous Transcription Factors Through Subdivision of Conformational Space. Proc.Natl.Acad.Sci.Usa V. 113 326 2016.
ISSN: ESSN 1091-6490
PubMed: 26715749
DOI: 10.1073/PNAS.1518960113
Page generated: Sun Oct 27 14:06:11 2024
|