Zinc in PDB 3g97: Gr Dna-Binding Domain:Gilz 16BP Complex-9
Protein crystallography data
The structure of Gr Dna-Binding Domain:Gilz 16BP Complex-9, PDB code: 3g97
was solved by
M.A.Pufall,
K.R.Yamamoto,
S.H.Meijsing,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.55 /
2.08
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.823,
38.589,
97.120,
90.00,
122.89,
90.00
|
R / Rfree (%)
|
20.3 /
24.2
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Gr Dna-Binding Domain:Gilz 16BP Complex-9
(pdb code 3g97). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Gr Dna-Binding Domain:Gilz 16BP Complex-9, PDB code: 3g97:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 3g97
Go back to
Zinc Binding Sites List in 3g97
Zinc binding site 1 out
of 4 in the Gr Dna-Binding Domain:Gilz 16BP Complex-9
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Gr Dna-Binding Domain:Gilz 16BP Complex-9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn526
b:97.0
occ:1.00
|
SG
|
B:CYS460
|
2.4
|
88.9
|
1.0
|
SG
|
B:CYS440
|
2.5
|
0.9
|
1.0
|
SG
|
B:CYS443
|
2.5
|
99.2
|
1.0
|
SG
|
B:CYS457
|
2.7
|
0.3
|
1.0
|
CB
|
B:CYS460
|
3.3
|
80.6
|
1.0
|
CB
|
B:CYS440
|
3.3
|
0.5
|
1.0
|
CB
|
B:CYS457
|
3.4
|
96.2
|
1.0
|
N
|
B:CYS443
|
3.4
|
0.6
|
1.0
|
CB
|
B:CYS443
|
3.4
|
0.9
|
1.0
|
N
|
B:CYS457
|
3.6
|
97.3
|
1.0
|
CA
|
B:CYS443
|
3.9
|
0.3
|
1.0
|
CA
|
B:CYS457
|
4.1
|
99.4
|
1.0
|
CB
|
B:VAL442
|
4.3
|
87.0
|
1.0
|
C
|
B:CYS443
|
4.4
|
0.1
|
1.0
|
CA
|
B:CYS460
|
4.5
|
80.0
|
1.0
|
CB
|
B:ASP445
|
4.5
|
0.5
|
1.0
|
N
|
B:CYS460
|
4.5
|
85.8
|
1.0
|
C
|
B:VAL442
|
4.5
|
94.6
|
1.0
|
N
|
B:SER444
|
4.6
|
0.9
|
1.0
|
C
|
B:THR456
|
4.7
|
99.9
|
1.0
|
N
|
B:ASP445
|
4.7
|
0.7
|
1.0
|
C
|
B:CYS457
|
4.8
|
96.9
|
1.0
|
CA
|
B:CYS440
|
4.8
|
0.3
|
1.0
|
OG
|
B:SER459
|
4.8
|
93.7
|
1.0
|
CA
|
B:VAL442
|
4.8
|
92.6
|
1.0
|
CA
|
B:THR456
|
4.8
|
98.7
|
1.0
|
NH1
|
B:ARG489
|
4.8
|
0.6
|
1.0
|
O
|
B:CYS457
|
4.8
|
93.6
|
1.0
|
N
|
B:VAL442
|
4.9
|
98.4
|
1.0
|
CB
|
B:THR456
|
4.9
|
95.8
|
1.0
|
O
|
B:CYS443
|
5.0
|
0.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 3g97
Go back to
Zinc Binding Sites List in 3g97
Zinc binding site 2 out
of 4 in the Gr Dna-Binding Domain:Gilz 16BP Complex-9
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Gr Dna-Binding Domain:Gilz 16BP Complex-9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn527
b:47.8
occ:1.00
|
SG
|
B:CYS482
|
2.2
|
42.7
|
1.0
|
SG
|
B:CYS476
|
2.2
|
41.0
|
1.0
|
SG
|
B:CYS492
|
2.3
|
43.6
|
1.0
|
SG
|
B:CYS495
|
2.5
|
52.0
|
1.0
|
CB
|
B:CYS482
|
3.2
|
45.8
|
1.0
|
CB
|
B:CYS492
|
3.4
|
43.1
|
1.0
|
CB
|
B:CYS495
|
3.4
|
36.4
|
1.0
|
CB
|
B:CYS476
|
3.4
|
32.4
|
1.0
|
O
|
B:HOH34
|
3.7
|
52.3
|
1.0
|
N
|
B:CYS482
|
3.9
|
48.0
|
1.0
|
CA
|
B:CYS476
|
4.0
|
38.5
|
1.0
|
O
|
B:HOH13
|
4.1
|
40.2
|
1.0
|
CA
|
B:CYS482
|
4.1
|
45.2
|
1.0
|
N
|
B:CYS495
|
4.3
|
46.6
|
1.0
|
CA
|
B:CYS495
|
4.4
|
47.3
|
1.0
|
O2
|
A:EDO1
|
4.5
|
46.1
|
1.0
|
N
|
B:ASP481
|
4.6
|
49.7
|
1.0
|
O
|
B:HOH14
|
4.6
|
57.2
|
1.0
|
N
|
B:ASN480
|
4.6
|
44.0
|
1.0
|
CA
|
B:ASN480
|
4.6
|
48.8
|
1.0
|
N
|
B:ALA477
|
4.6
|
35.4
|
1.0
|
N
|
B:GLY478
|
4.8
|
47.1
|
1.0
|
CA
|
B:CYS492
|
4.8
|
43.8
|
1.0
|
C
|
B:CYS476
|
4.8
|
37.9
|
1.0
|
C
|
B:ASN480
|
4.9
|
50.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 3g97
Go back to
Zinc Binding Sites List in 3g97
Zinc binding site 3 out
of 4 in the Gr Dna-Binding Domain:Gilz 16BP Complex-9
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Gr Dna-Binding Domain:Gilz 16BP Complex-9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn526
b:62.5
occ:1.00
|
SG
|
A:CYS460
|
2.2
|
56.7
|
1.0
|
SG
|
A:CYS457
|
2.3
|
77.1
|
1.0
|
SG
|
A:CYS443
|
2.3
|
60.8
|
1.0
|
SG
|
A:CYS440
|
2.6
|
53.8
|
1.0
|
CB
|
A:CYS443
|
3.0
|
58.7
|
1.0
|
CB
|
A:CYS440
|
3.1
|
53.5
|
1.0
|
CB
|
A:CYS460
|
3.4
|
51.8
|
1.0
|
CG2
|
A:VAL442
|
3.7
|
68.6
|
1.0
|
N
|
A:CYS443
|
3.7
|
72.4
|
1.0
|
CB
|
A:CYS457
|
3.7
|
68.4
|
1.0
|
CA
|
A:CYS443
|
3.9
|
64.7
|
1.0
|
N
|
A:CYS457
|
3.9
|
69.4
|
1.0
|
OG
|
A:SER459
|
4.0
|
67.0
|
1.0
|
N
|
A:CYS460
|
4.3
|
41.8
|
1.0
|
CA
|
A:CYS457
|
4.4
|
62.9
|
1.0
|
CA
|
A:CYS460
|
4.4
|
33.1
|
1.0
|
C
|
A:CYS443
|
4.4
|
73.3
|
1.0
|
CB
|
A:ASP445
|
4.5
|
78.5
|
1.0
|
CA
|
A:CYS440
|
4.6
|
59.5
|
1.0
|
N
|
A:ASP445
|
4.6
|
75.0
|
1.0
|
N
|
A:SER444
|
4.7
|
78.0
|
1.0
|
O
|
A:CYS457
|
4.7
|
51.6
|
1.0
|
C
|
A:VAL442
|
4.8
|
66.4
|
1.0
|
NH2
|
A:ARG496
|
4.8
|
63.1
|
1.0
|
C
|
A:CYS457
|
4.8
|
58.1
|
1.0
|
CD
|
A:ARG489
|
4.9
|
72.2
|
1.0
|
NH1
|
A:ARG489
|
5.0
|
53.4
|
1.0
|
|
Zinc binding site 4 out
of 4 in 3g97
Go back to
Zinc Binding Sites List in 3g97
Zinc binding site 4 out
of 4 in the Gr Dna-Binding Domain:Gilz 16BP Complex-9
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Gr Dna-Binding Domain:Gilz 16BP Complex-9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn527
b:40.6
occ:1.00
|
SG
|
A:CYS482
|
2.2
|
44.2
|
1.0
|
SG
|
A:CYS476
|
2.3
|
38.8
|
1.0
|
SG
|
A:CYS492
|
2.3
|
41.0
|
1.0
|
SG
|
A:CYS495
|
2.4
|
43.6
|
1.0
|
CB
|
A:CYS482
|
3.2
|
57.6
|
1.0
|
CB
|
A:CYS495
|
3.3
|
32.3
|
1.0
|
CB
|
A:CYS492
|
3.4
|
36.6
|
1.0
|
CB
|
A:CYS476
|
3.4
|
29.2
|
1.0
|
C1
|
A:EDO1
|
3.7
|
50.9
|
1.0
|
N
|
A:CYS482
|
3.9
|
44.2
|
1.0
|
CA
|
A:CYS476
|
4.0
|
38.3
|
1.0
|
N
|
A:CYS495
|
4.1
|
27.6
|
1.0
|
CA
|
A:CYS482
|
4.2
|
49.1
|
1.0
|
CA
|
A:CYS495
|
4.3
|
31.8
|
1.0
|
CA
|
A:ASN480
|
4.3
|
45.8
|
1.0
|
N
|
A:ASN480
|
4.4
|
55.7
|
1.0
|
O
|
A:HOH529
|
4.5
|
35.7
|
1.0
|
O1
|
A:EDO1
|
4.6
|
47.6
|
1.0
|
N
|
A:ASP481
|
4.6
|
37.0
|
1.0
|
O2
|
A:EDO1
|
4.7
|
46.1
|
1.0
|
N
|
A:ALA477
|
4.7
|
46.4
|
1.0
|
O
|
A:HOH7
|
4.7
|
54.0
|
1.0
|
C
|
A:ASN480
|
4.8
|
42.6
|
1.0
|
CA
|
A:CYS492
|
4.8
|
37.5
|
1.0
|
C
|
A:CYS476
|
4.8
|
48.5
|
1.0
|
C2
|
A:EDO1
|
4.8
|
57.1
|
1.0
|
N
|
A:GLY478
|
4.8
|
46.7
|
1.0
|
CB
|
A:ALA494
|
4.9
|
41.8
|
1.0
|
|
Reference:
S.H.Meijsing,
M.A.Pufall,
A.Y.So,
D.L.Bates,
L.Chen,
K.R.Yamamoto.
Dna Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity. Science V. 324 407 2009.
ISSN: ISSN 0036-8075
PubMed: 19372434
DOI: 10.1126/SCIENCE.1164265
Page generated: Thu Oct 24 13:36:23 2024
|