Zinc in PDB 3g9j: Gr Dna Binding Domain:Pal, 18BP Complex-36
Protein crystallography data
The structure of Gr Dna Binding Domain:Pal, 18BP Complex-36, PDB code: 3g9j
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)
|
49.13 /
2.32
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.069,
102.096,
112.076,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.4 /
22.6
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Gr Dna Binding Domain:Pal, 18BP Complex-36
(pdb code 3g9j). 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:Pal, 18BP Complex-36, PDB code: 3g9j:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 3g9j
Go back to
Zinc Binding Sites List in 3g9j
Zinc binding site 1 out
of 4 in the Gr Dna Binding Domain:Pal, 18BP Complex-36
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:Pal, 18BP Complex-36 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1514
b:45.3
occ:1.00
|
SG
|
A:CYS460
|
2.3
|
43.8
|
1.0
|
SG
|
A:CYS443
|
2.3
|
48.4
|
1.0
|
SG
|
A:CYS440
|
2.4
|
48.8
|
1.0
|
SG
|
A:CYS457
|
2.4
|
48.2
|
1.0
|
CB
|
A:CYS460
|
3.2
|
45.4
|
1.0
|
CB
|
A:CYS443
|
3.2
|
53.2
|
1.0
|
CB
|
A:CYS440
|
3.3
|
54.5
|
1.0
|
CB
|
A:CYS457
|
3.6
|
58.3
|
0.9
|
N
|
A:CYS443
|
3.7
|
52.1
|
1.0
|
CA
|
A:CYS443
|
4.0
|
47.8
|
1.0
|
N
|
A:CYS457
|
4.0
|
49.7
|
1.0
|
N
|
A:CYS460
|
4.3
|
36.6
|
1.0
|
CA
|
A:CYS457
|
4.3
|
58.2
|
1.0
|
CA
|
A:CYS460
|
4.3
|
39.7
|
1.0
|
NH1
|
A:ARG489
|
4.4
|
66.7
|
1.0
|
CB
|
A:VAL442
|
4.4
|
51.8
|
1.0
|
C
|
A:CYS443
|
4.6
|
54.5
|
1.0
|
OG
|
A:SER459
|
4.6
|
42.1
|
1.0
|
C
|
A:VAL442
|
4.6
|
55.4
|
1.0
|
CB
|
A:ASP445
|
4.7
|
74.7
|
1.0
|
CA
|
A:CYS440
|
4.8
|
55.4
|
1.0
|
N
|
A:SER444
|
4.8
|
50.7
|
1.0
|
CD
|
A:ARG489
|
4.8
|
52.6
|
1.0
|
CG1
|
A:VAL442
|
4.9
|
36.8
|
1.0
|
N
|
A:ASP445
|
4.9
|
43.2
|
1.0
|
NH2
|
A:ARG496
|
4.9
|
40.1
|
1.0
|
C
|
A:CYS457
|
4.9
|
48.8
|
1.0
|
CA
|
A:VAL442
|
4.9
|
54.4
|
1.0
|
O
|
A:CYS457
|
4.9
|
43.7
|
1.0
|
N
|
A:VAL442
|
5.0
|
58.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 3g9j
Go back to
Zinc Binding Sites List in 3g9j
Zinc binding site 2 out
of 4 in the Gr Dna Binding Domain:Pal, 18BP Complex-36
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:Pal, 18BP Complex-36 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1515
b:36.5
occ:1.00
|
SG
|
A:CYS482
|
2.2
|
31.6
|
1.0
|
SG
|
A:CYS476
|
2.3
|
33.3
|
1.0
|
SG
|
A:CYS492
|
2.4
|
36.7
|
1.0
|
SG
|
A:CYS495
|
2.4
|
41.3
|
1.0
|
CB
|
A:CYS482
|
3.1
|
27.6
|
1.0
|
CB
|
A:CYS476
|
3.3
|
30.6
|
1.0
|
CB
|
A:CYS492
|
3.3
|
26.9
|
1.0
|
CB
|
A:CYS495
|
3.4
|
24.1
|
1.0
|
O
|
A:HOH3
|
3.7
|
29.1
|
1.0
|
N
|
A:CYS482
|
3.9
|
40.6
|
1.0
|
CA
|
A:CYS476
|
3.9
|
25.9
|
0.9
|
CA
|
A:CYS482
|
4.1
|
41.1
|
1.0
|
N
|
A:CYS495
|
4.2
|
32.8
|
1.0
|
O
|
A:HOH526
|
4.3
|
37.4
|
1.0
|
CA
|
A:CYS495
|
4.4
|
31.3
|
1.0
|
CA
|
A:ASN480
|
4.5
|
41.6
|
1.0
|
N
|
A:ALA477
|
4.5
|
29.0
|
1.0
|
O
|
B:HOH8
|
4.6
|
39.8
|
1.0
|
N
|
A:ASP481
|
4.6
|
33.9
|
1.0
|
N
|
A:ASN480
|
4.6
|
43.8
|
1.0
|
C
|
A:CYS476
|
4.7
|
33.8
|
1.0
|
N
|
A:GLY478
|
4.8
|
33.4
|
1.0
|
CA
|
A:CYS492
|
4.8
|
24.7
|
1.0
|
C
|
A:ASN480
|
4.9
|
46.7
|
1.0
|
O
|
A:HOH28
|
5.0
|
45.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 3g9j
Go back to
Zinc Binding Sites List in 3g9j
Zinc binding site 3 out
of 4 in the Gr Dna Binding Domain:Pal, 18BP Complex-36
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:Pal, 18BP Complex-36 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1512
b:41.4
occ:1.00
|
SG
|
B:CYS460
|
2.2
|
34.8
|
1.0
|
SG
|
B:CYS440
|
2.3
|
36.9
|
1.0
|
SG
|
B:CYS443
|
2.4
|
45.4
|
1.0
|
SG
|
B:CYS457
|
2.4
|
47.5
|
1.0
|
CB
|
B:CYS460
|
3.1
|
33.2
|
1.0
|
CB
|
B:CYS440
|
3.2
|
52.3
|
1.0
|
CB
|
B:CYS443
|
3.4
|
43.0
|
0.9
|
N
|
B:CYS443
|
3.6
|
44.7
|
1.0
|
CB
|
B:CYS457
|
3.7
|
50.0
|
1.0
|
N
|
B:CYS457
|
3.7
|
40.8
|
1.0
|
CA
|
B:CYS443
|
4.0
|
44.4
|
1.0
|
N
|
B:CYS460
|
4.1
|
31.4
|
1.0
|
CA
|
B:CYS460
|
4.2
|
34.6
|
1.0
|
NH1
|
B:ARG489
|
4.3
|
41.1
|
1.0
|
CA
|
B:CYS457
|
4.3
|
45.8
|
1.0
|
OG
|
B:SER459
|
4.4
|
39.3
|
1.0
|
CB
|
B:VAL442
|
4.5
|
46.1
|
1.0
|
CB
|
B:ASP445
|
4.5
|
61.1
|
1.0
|
C
|
B:VAL442
|
4.7
|
53.0
|
1.0
|
CA
|
B:CYS440
|
4.7
|
49.2
|
1.0
|
C
|
B:CYS443
|
4.7
|
49.9
|
1.0
|
N
|
B:ASP445
|
4.8
|
53.0
|
1.0
|
O
|
B:CYS457
|
4.8
|
43.5
|
1.0
|
C
|
B:THR456
|
4.8
|
49.9
|
1.0
|
N
|
B:SER444
|
4.8
|
53.0
|
1.0
|
C
|
B:CYS457
|
4.9
|
35.4
|
1.0
|
NH2
|
B:ARG496
|
4.9
|
36.7
|
1.0
|
CB
|
B:THR456
|
4.9
|
45.7
|
1.0
|
CA
|
B:THR456
|
5.0
|
44.6
|
1.0
|
CA
|
B:VAL442
|
5.0
|
49.2
|
1.0
|
|
Zinc binding site 4 out
of 4 in 3g9j
Go back to
Zinc Binding Sites List in 3g9j
Zinc binding site 4 out
of 4 in the Gr Dna Binding Domain:Pal, 18BP Complex-36
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:Pal, 18BP Complex-36 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1513
b:34.2
occ:0.98
|
SG
|
B:CYS482
|
2.2
|
30.2
|
1.0
|
SG
|
B:CYS476
|
2.3
|
35.7
|
1.0
|
SG
|
B:CYS492
|
2.3
|
34.1
|
1.0
|
SG
|
B:CYS495
|
2.4
|
36.1
|
1.0
|
CB
|
B:CYS482
|
3.3
|
27.1
|
1.0
|
CB
|
B:CYS492
|
3.4
|
35.3
|
1.0
|
CB
|
B:CYS495
|
3.4
|
28.1
|
1.0
|
CB
|
B:CYS476
|
3.4
|
29.5
|
1.0
|
O
|
B:HOH4
|
3.8
|
33.4
|
1.0
|
N
|
B:CYS482
|
4.0
|
36.0
|
1.0
|
CA
|
B:CYS476
|
4.0
|
35.2
|
1.0
|
N
|
B:CYS495
|
4.2
|
29.1
|
1.0
|
CA
|
B:CYS482
|
4.2
|
32.3
|
1.0
|
CA
|
B:ASN480
|
4.4
|
45.6
|
1.0
|
CA
|
B:CYS495
|
4.4
|
29.6
|
1.0
|
N
|
B:ASN480
|
4.5
|
39.0
|
1.0
|
O
|
B:HOH13
|
4.5
|
38.2
|
1.0
|
O
|
B:HOH20
|
4.6
|
45.2
|
1.0
|
N
|
B:ASP481
|
4.7
|
31.9
|
1.0
|
N
|
B:ALA477
|
4.7
|
36.6
|
1.0
|
CA
|
B:CYS492
|
4.8
|
31.9
|
1.0
|
N
|
B:GLY478
|
4.8
|
31.4
|
0.9
|
C
|
B:ASN480
|
4.8
|
38.2
|
1.0
|
C
|
B:CYS476
|
4.8
|
39.8
|
1.0
|
O
|
B:HOH8
|
4.9
|
39.8
|
1.0
|
CB
|
B:ALA494
|
5.0
|
25.2
|
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 13:37:35 2024
|