Zinc in PDB 6bqu: Human Gr (418-507) in Complex with Monomeric Dna Binding Site
Protein crystallography data
The structure of Human Gr (418-507) in Complex with Monomeric Dna Binding Site, PDB code: 6bqu
was solved by
M.A.Pufall,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
51.95 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.231,
88.235,
103.905,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.3 /
24.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Human Gr (418-507) in Complex with Monomeric Dna Binding Site
(pdb code 6bqu). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Human Gr (418-507) in Complex with Monomeric Dna Binding Site, PDB code: 6bqu:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6bqu
Go back to
Zinc Binding Sites List in 6bqu
Zinc binding site 1 out
of 4 in the Human Gr (418-507) in Complex with Monomeric Dna Binding Site
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Human Gr (418-507) in Complex with Monomeric Dna Binding Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:54.0
occ:1.00
|
SG
|
B:CYS441
|
2.2
|
52.3
|
1.0
|
SG
|
B:CYS424
|
2.3
|
63.3
|
1.0
|
SG
|
B:CYS438
|
2.3
|
56.9
|
1.0
|
SG
|
B:CYS421
|
2.4
|
56.7
|
1.0
|
HB2
|
B:CYS441
|
2.9
|
66.1
|
1.0
|
HB3
|
B:CYS424
|
3.0
|
67.9
|
1.0
|
H
|
B:CYS424
|
3.0
|
68.2
|
1.0
|
H
|
B:CYS438
|
3.1
|
72.4
|
1.0
|
CB
|
B:CYS424
|
3.2
|
56.5
|
1.0
|
CB
|
B:CYS441
|
3.2
|
55.1
|
1.0
|
HB
|
B:VAL423
|
3.4
|
68.8
|
1.0
|
HB3
|
B:CYS438
|
3.5
|
73.9
|
1.0
|
HB3
|
B:CYS421
|
3.5
|
79.2
|
1.0
|
CB
|
B:CYS421
|
3.5
|
66.0
|
1.0
|
CB
|
B:CYS438
|
3.5
|
61.6
|
1.0
|
HH11
|
B:ARG470
|
3.6
|
79.4
|
1.0
|
HB2
|
B:CYS421
|
3.6
|
79.2
|
1.0
|
N
|
B:CYS424
|
3.6
|
56.9
|
1.0
|
H
|
B:CYS441
|
3.7
|
63.7
|
1.0
|
HB3
|
B:CYS441
|
3.8
|
66.1
|
1.0
|
HB3
|
B:ASP426
|
3.9
|
80.0
|
1.0
|
HH21
|
B:ARG477
|
3.9
|
61.4
|
1.0
|
HG
|
B:SER440
|
3.9
|
65.6
|
1.0
|
N
|
B:CYS438
|
3.9
|
60.4
|
1.0
|
CA
|
B:CYS424
|
4.0
|
56.4
|
1.0
|
HB2
|
B:CYS424
|
4.0
|
67.9
|
1.0
|
H
|
B:ASP426
|
4.1
|
83.6
|
1.0
|
NH1
|
B:ARG470
|
4.2
|
66.2
|
1.0
|
N
|
B:CYS441
|
4.2
|
53.1
|
1.0
|
HH12
|
B:ARG470
|
4.2
|
79.4
|
1.0
|
CA
|
B:CYS438
|
4.3
|
61.9
|
1.0
|
CA
|
B:CYS441
|
4.3
|
51.5
|
1.0
|
HB2
|
B:CYS438
|
4.3
|
73.9
|
1.0
|
CB
|
B:VAL423
|
4.3
|
57.3
|
1.0
|
OG
|
B:SER440
|
4.3
|
54.6
|
1.0
|
H
|
B:VAL423
|
4.3
|
77.5
|
1.0
|
HB
|
B:THR437
|
4.4
|
74.8
|
1.0
|
HD2
|
B:ARG470
|
4.4
|
67.3
|
1.0
|
HB2
|
B:ASP426
|
4.4
|
80.0
|
1.0
|
HG12
|
B:VAL423
|
4.5
|
69.2
|
1.0
|
H
|
B:SER425
|
4.5
|
74.3
|
1.0
|
CB
|
B:ASP426
|
4.6
|
66.7
|
1.0
|
HA
|
B:CYS441
|
4.6
|
61.7
|
1.0
|
C
|
B:VAL423
|
4.6
|
55.7
|
1.0
|
C
|
B:CYS424
|
4.6
|
63.0
|
1.0
|
NH2
|
B:ARG477
|
4.7
|
51.2
|
1.0
|
HA
|
B:THR437
|
4.8
|
76.5
|
1.0
|
N
|
B:SER425
|
4.8
|
61.9
|
1.0
|
HA
|
B:CYS424
|
4.8
|
67.7
|
1.0
|
CG1
|
B:VAL423
|
4.8
|
57.7
|
1.0
|
N
|
B:ASP426
|
4.8
|
69.7
|
1.0
|
HG11
|
B:VAL423
|
4.8
|
69.2
|
1.0
|
HE
|
B:ARG477
|
4.8
|
59.5
|
1.0
|
HD3
|
B:ARG470
|
4.8
|
67.3
|
1.0
|
C
|
B:CYS438
|
4.9
|
60.6
|
1.0
|
CA
|
B:VAL423
|
4.9
|
59.5
|
1.0
|
CA
|
B:CYS421
|
4.9
|
69.0
|
1.0
|
O
|
B:CYS438
|
4.9
|
60.1
|
1.0
|
N
|
B:VAL423
|
5.0
|
64.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6bqu
Go back to
Zinc Binding Sites List in 6bqu
Zinc binding site 2 out
of 4 in the Human Gr (418-507) in Complex with Monomeric Dna Binding Site
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Human Gr (418-507) in Complex with Monomeric Dna Binding Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:44.7
occ:1.00
|
SG
|
B:CYS463
|
2.2
|
40.5
|
1.0
|
SG
|
B:CYS457
|
2.2
|
45.7
|
1.0
|
SG
|
B:CYS473
|
2.3
|
38.7
|
1.0
|
SG
|
B:CYS476
|
2.3
|
53.3
|
1.0
|
HB2
|
B:CYS457
|
2.9
|
53.7
|
1.0
|
HB2
|
B:CYS463
|
3.0
|
55.6
|
1.0
|
CB
|
B:CYS457
|
3.2
|
44.7
|
1.0
|
HB2
|
B:CYS476
|
3.2
|
56.4
|
1.0
|
CB
|
B:CYS463
|
3.2
|
46.3
|
1.0
|
H
|
B:CYS463
|
3.3
|
54.3
|
1.0
|
CB
|
B:CYS473
|
3.4
|
39.5
|
1.0
|
CB
|
B:CYS476
|
3.4
|
47.0
|
1.0
|
HB3
|
B:CYS473
|
3.4
|
47.4
|
1.0
|
HB2
|
B:CYS473
|
3.4
|
47.4
|
1.0
|
O
|
B:HOH601
|
3.6
|
39.9
|
1.0
|
HA
|
B:CYS457
|
3.6
|
51.4
|
1.0
|
H
|
B:CYS476
|
3.8
|
55.0
|
1.0
|
H
|
B:ASP462
|
3.8
|
53.7
|
1.0
|
HA
|
B:ASN461
|
3.9
|
54.4
|
1.0
|
CA
|
B:CYS457
|
3.9
|
42.8
|
1.0
|
HB3
|
B:CYS463
|
3.9
|
55.6
|
1.0
|
HB3
|
B:CYS457
|
3.9
|
53.7
|
1.0
|
H
|
B:ALA458
|
4.0
|
53.2
|
1.0
|
H
|
B:GLY459
|
4.0
|
55.7
|
1.0
|
N
|
B:CYS463
|
4.0
|
45.3
|
1.0
|
HB3
|
B:CYS476
|
4.0
|
56.4
|
1.0
|
H
|
B:ASN461
|
4.1
|
61.4
|
1.0
|
CA
|
B:CYS463
|
4.2
|
45.3
|
1.0
|
N
|
B:CYS476
|
4.3
|
45.9
|
1.0
|
N
|
B:ASP462
|
4.4
|
44.8
|
1.0
|
CA
|
B:CYS476
|
4.4
|
46.2
|
1.0
|
HB3
|
B:ALA475
|
4.5
|
56.2
|
1.0
|
N
|
B:ALA458
|
4.5
|
44.3
|
1.0
|
H
|
B:ARG460
|
4.5
|
61.5
|
1.0
|
CA
|
B:ASN461
|
4.6
|
45.3
|
1.0
|
N
|
B:ASN461
|
4.6
|
51.1
|
1.0
|
HA
|
B:CYS463
|
4.6
|
54.4
|
1.0
|
C
|
B:CYS457
|
4.7
|
45.4
|
1.0
|
HA
|
B:CYS476
|
4.7
|
55.4
|
1.0
|
N
|
B:GLY459
|
4.8
|
46.4
|
1.0
|
CA
|
B:CYS473
|
4.8
|
41.5
|
1.0
|
HA3
|
B:GLY459
|
4.9
|
56.8
|
1.0
|
C
|
B:ASN461
|
4.9
|
44.3
|
1.0
|
HA
|
B:CYS473
|
4.9
|
49.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6bqu
Go back to
Zinc Binding Sites List in 6bqu
Zinc binding site 3 out
of 4 in the Human Gr (418-507) in Complex with Monomeric Dna Binding Site
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Human Gr (418-507) in Complex with Monomeric Dna Binding Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:41.6
occ:1.00
|
SG
|
A:CYS463
|
2.3
|
49.8
|
1.0
|
SG
|
A:CYS473
|
2.3
|
49.2
|
1.0
|
SG
|
A:CYS457
|
2.3
|
48.8
|
1.0
|
SG
|
A:CYS476
|
2.4
|
45.5
|
1.0
|
HB2
|
A:CYS463
|
3.0
|
61.2
|
1.0
|
HB2
|
A:CYS457
|
3.0
|
58.6
|
1.0
|
HB2
|
A:CYS476
|
3.1
|
53.0
|
1.0
|
CB
|
A:CYS457
|
3.2
|
48.8
|
1.0
|
CB
|
A:CYS463
|
3.2
|
51.0
|
1.0
|
H
|
A:CYS463
|
3.3
|
64.1
|
1.0
|
CB
|
A:CYS473
|
3.3
|
49.4
|
1.0
|
HB2
|
A:CYS473
|
3.3
|
59.3
|
1.0
|
HB3
|
A:CYS473
|
3.4
|
59.3
|
1.0
|
CB
|
A:CYS476
|
3.4
|
44.2
|
1.0
|
H
|
A:CYS476
|
3.6
|
49.0
|
1.0
|
HA
|
A:CYS457
|
3.6
|
58.0
|
1.0
|
HA
|
A:ASN461
|
3.6
|
65.0
|
1.0
|
H
|
A:GLY459
|
3.7
|
57.7
|
1.0
|
H
|
A:ASN461
|
3.9
|
63.7
|
1.0
|
HB3
|
A:CYS463
|
3.9
|
61.2
|
1.0
|
CA
|
A:CYS457
|
4.0
|
48.3
|
1.0
|
N
|
A:CYS463
|
4.0
|
53.4
|
1.0
|
H
|
A:ALA458
|
4.0
|
57.0
|
1.0
|
HB3
|
A:CYS457
|
4.0
|
58.6
|
1.0
|
HB3
|
A:CYS476
|
4.1
|
53.0
|
1.0
|
N
|
A:CYS476
|
4.2
|
40.8
|
1.0
|
HB3
|
A:ALA475
|
4.2
|
49.7
|
1.0
|
H
|
A:ASP462
|
4.2
|
65.6
|
1.0
|
CA
|
A:CYS463
|
4.2
|
52.8
|
1.0
|
CA
|
A:ASN461
|
4.4
|
54.1
|
1.0
|
CA
|
A:CYS476
|
4.4
|
42.4
|
1.0
|
N
|
A:ASN461
|
4.5
|
53.1
|
1.0
|
N
|
A:ALA458
|
4.5
|
47.5
|
1.0
|
N
|
A:ASP462
|
4.5
|
54.7
|
1.0
|
N
|
A:GLY459
|
4.6
|
48.1
|
1.0
|
C
|
A:CYS457
|
4.7
|
47.6
|
1.0
|
HA3
|
A:GLY459
|
4.7
|
59.1
|
1.0
|
HA
|
A:CYS476
|
4.7
|
50.9
|
1.0
|
CA
|
A:CYS473
|
4.7
|
50.1
|
1.0
|
HA
|
A:CYS463
|
4.7
|
63.4
|
1.0
|
C
|
A:ASN461
|
4.7
|
55.9
|
1.0
|
HA
|
A:CYS473
|
4.9
|
60.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6bqu
Go back to
Zinc Binding Sites List in 6bqu
Zinc binding site 4 out
of 4 in the Human Gr (418-507) in Complex with Monomeric Dna Binding Site
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Human Gr (418-507) in Complex with Monomeric Dna Binding Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:51.9
occ:1.00
|
SG
|
A:CYS438
|
2.2
|
64.3
|
1.0
|
SG
|
A:CYS441
|
2.2
|
54.5
|
1.0
|
SG
|
A:CYS424
|
2.3
|
58.0
|
1.0
|
SG
|
A:CYS421
|
2.4
|
52.7
|
1.0
|
HB3
|
A:CYS438
|
2.9
|
73.5
|
1.0
|
HB2
|
A:CYS441
|
2.9
|
66.6
|
1.0
|
H
|
A:CYS438
|
3.0
|
67.2
|
1.0
|
H
|
A:CYS424
|
3.0
|
64.8
|
1.0
|
CB
|
A:CYS438
|
3.1
|
61.3
|
1.0
|
CB
|
A:CYS441
|
3.2
|
55.5
|
1.0
|
HB3
|
A:CYS424
|
3.2
|
63.8
|
1.0
|
HB3
|
A:CYS421
|
3.4
|
74.0
|
1.0
|
CB
|
A:CYS424
|
3.4
|
53.2
|
1.0
|
CB
|
A:CYS421
|
3.4
|
61.7
|
1.0
|
H
|
A:CYS441
|
3.5
|
65.0
|
1.0
|
HB
|
A:VAL423
|
3.5
|
63.5
|
1.0
|
HB2
|
A:CYS421
|
3.5
|
74.0
|
1.0
|
HH11
|
A:ARG470
|
3.6
|
75.7
|
1.0
|
N
|
A:CYS424
|
3.7
|
54.0
|
1.0
|
N
|
A:CYS438
|
3.7
|
56.0
|
1.0
|
HB3
|
A:CYS441
|
3.8
|
66.6
|
1.0
|
HH21
|
A:ARG477
|
3.8
|
57.1
|
1.0
|
HB2
|
A:CYS438
|
3.9
|
73.5
|
1.0
|
H
|
A:ASP426
|
3.9
|
75.9
|
1.0
|
CA
|
A:CYS438
|
4.0
|
58.4
|
1.0
|
HB3
|
A:ASP426
|
4.0
|
79.5
|
1.0
|
CA
|
A:CYS424
|
4.1
|
53.7
|
1.0
|
HB2
|
A:ASP426
|
4.1
|
79.5
|
1.0
|
N
|
A:CYS441
|
4.2
|
54.2
|
1.0
|
HB2
|
A:CYS424
|
4.2
|
63.8
|
1.0
|
NH1
|
A:ARG470
|
4.2
|
63.0
|
1.0
|
H
|
A:SER425
|
4.2
|
69.8
|
1.0
|
CA
|
A:CYS441
|
4.3
|
54.2
|
1.0
|
HH12
|
A:ARG470
|
4.3
|
75.7
|
1.0
|
HD2
|
A:ARG470
|
4.3
|
70.2
|
1.0
|
HG
|
A:SER440
|
4.4
|
85.9
|
1.0
|
H
|
A:VAL423
|
4.4
|
66.5
|
1.0
|
HB
|
A:THR437
|
4.5
|
66.3
|
1.0
|
CB
|
A:VAL423
|
4.5
|
52.9
|
1.0
|
CB
|
A:ASP426
|
4.5
|
66.3
|
1.0
|
NH2
|
A:ARG477
|
4.6
|
47.6
|
1.0
|
N
|
A:SER425
|
4.6
|
58.2
|
1.0
|
HA
|
A:CYS441
|
4.7
|
65.1
|
1.0
|
C
|
A:CYS424
|
4.7
|
61.3
|
1.0
|
C
|
A:CYS438
|
4.7
|
60.4
|
1.0
|
HA
|
A:THR437
|
4.7
|
70.2
|
1.0
|
HG12
|
A:VAL423
|
4.7
|
56.8
|
1.0
|
N
|
A:ASP426
|
4.7
|
63.2
|
1.0
|
C
|
A:VAL423
|
4.8
|
53.0
|
1.0
|
OG
|
A:SER440
|
4.8
|
71.6
|
1.0
|
HA
|
A:CYS438
|
4.8
|
70.0
|
1.0
|
HD3
|
A:ARG470
|
4.8
|
70.2
|
1.0
|
HE
|
A:ARG477
|
4.8
|
54.7
|
1.0
|
CA
|
A:CYS421
|
4.9
|
62.8
|
1.0
|
C
|
A:THR437
|
4.9
|
61.8
|
1.0
|
O
|
A:CYS438
|
4.9
|
58.3
|
1.0
|
HA
|
A:CYS424
|
4.9
|
64.4
|
1.0
|
CD
|
A:ARG470
|
5.0
|
58.5
|
1.0
|
|
Reference:
M.A.Pufall,
M.A.Pufall.
N/A N/A.
Page generated: Mon Oct 28 18:12:21 2024
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