Zinc in PDB 3g9i: Gr Dna Binding Domain: Pal Complex-35
Protein crystallography data
The structure of Gr Dna Binding Domain: Pal Complex-35, PDB code: 3g9i
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)
|
48.81 /
1.85
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.513,
37.648,
95.448,
90.00,
123.08,
90.00
|
R / Rfree (%)
|
17 /
20.1
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Gr Dna Binding Domain: Pal Complex-35
(pdb code 3g9i). 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 Complex-35, PDB code: 3g9i:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 3g9i
Go back to
Zinc Binding Sites List in 3g9i
Zinc binding site 1 out
of 4 in the Gr Dna Binding Domain: Pal Complex-35
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 Complex-35 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn526
b:46.4
occ:1.00
|
SG
|
A:CYS443
|
2.2
|
44.2
|
1.0
|
SG
|
A:CYS457
|
2.3
|
46.5
|
1.0
|
SG
|
A:CYS460
|
2.3
|
40.5
|
1.0
|
SG
|
A:CYS440
|
2.4
|
47.9
|
1.0
|
CB
|
A:CYS460
|
3.1
|
38.8
|
1.0
|
CB
|
A:CYS440
|
3.3
|
55.4
|
1.0
|
CB
|
A:CYS443
|
3.3
|
43.1
|
1.0
|
CB
|
A:CYS457
|
3.5
|
48.4
|
1.0
|
N
|
A:CYS443
|
3.7
|
41.8
|
1.0
|
N
|
A:CYS457
|
3.8
|
47.3
|
1.0
|
CA
|
A:CYS443
|
4.0
|
46.0
|
1.0
|
N
|
A:CYS460
|
4.2
|
42.7
|
1.0
|
CA
|
A:CYS457
|
4.2
|
46.3
|
1.0
|
CA
|
A:CYS460
|
4.2
|
43.7
|
1.0
|
NH1
|
A:ARG489
|
4.4
|
46.3
|
1.0
|
CB
|
A:ASP445
|
4.4
|
50.7
|
1.0
|
OG
|
A:SER459
|
4.5
|
45.1
|
1.0
|
CB
|
A:VAL442
|
4.5
|
46.1
|
1.0
|
C
|
A:CYS443
|
4.6
|
51.4
|
1.0
|
C
|
A:VAL442
|
4.7
|
41.7
|
1.0
|
CA
|
A:CYS440
|
4.7
|
52.4
|
1.0
|
N
|
A:ASP445
|
4.8
|
51.6
|
1.0
|
N
|
A:SER444
|
4.8
|
53.9
|
1.0
|
C
|
A:CYS457
|
4.9
|
48.6
|
1.0
|
NH2
|
A:ARG496
|
4.9
|
36.9
|
1.0
|
CD
|
A:ARG489
|
4.9
|
45.4
|
1.0
|
C
|
A:THR456
|
4.9
|
53.7
|
1.0
|
N
|
A:VAL442
|
4.9
|
50.0
|
1.0
|
O
|
A:CYS457
|
5.0
|
48.8
|
1.0
|
CA
|
A:VAL442
|
5.0
|
42.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 3g9i
Go back to
Zinc Binding Sites List in 3g9i
Zinc binding site 2 out
of 4 in the Gr Dna Binding Domain: Pal Complex-35
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 Complex-35 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn527
b:28.4
occ:1.00
|
SG
|
A:CYS476
|
2.2
|
25.3
|
1.0
|
SG
|
A:CYS482
|
2.3
|
27.7
|
1.0
|
SG
|
A:CYS495
|
2.4
|
27.3
|
1.0
|
SG
|
A:CYS492
|
2.4
|
27.3
|
1.0
|
CB
|
A:CYS482
|
3.2
|
25.8
|
1.0
|
CB
|
A:CYS476
|
3.3
|
23.4
|
1.0
|
CB
|
A:CYS492
|
3.3
|
23.9
|
1.0
|
CB
|
A:CYS495
|
3.4
|
23.4
|
1.0
|
N
|
A:CYS482
|
3.9
|
31.7
|
1.0
|
CA
|
A:CYS476
|
4.0
|
20.7
|
1.0
|
O
|
A:HOH528
|
4.0
|
27.9
|
1.0
|
N
|
A:CYS495
|
4.2
|
27.2
|
1.0
|
CA
|
A:CYS482
|
4.2
|
29.4
|
1.0
|
O
|
A:HOH9
|
4.2
|
31.4
|
1.0
|
CA
|
A:CYS495
|
4.3
|
33.0
|
1.0
|
O
|
A:HOH18
|
4.6
|
35.4
|
1.0
|
CA
|
A:ASN480
|
4.6
|
24.9
|
1.0
|
N
|
A:ASP481
|
4.6
|
21.5
|
1.0
|
O
|
A:HOH8
|
4.6
|
29.2
|
1.0
|
N
|
A:ALA477
|
4.6
|
21.8
|
1.0
|
N
|
A:ASN480
|
4.7
|
24.9
|
1.0
|
CA
|
A:CYS492
|
4.7
|
23.1
|
1.0
|
C
|
A:CYS476
|
4.8
|
24.6
|
1.0
|
N
|
A:GLY478
|
4.8
|
27.3
|
1.0
|
C
|
A:ASN480
|
4.8
|
28.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 3g9i
Go back to
Zinc Binding Sites List in 3g9i
Zinc binding site 3 out
of 4 in the Gr Dna Binding Domain: Pal Complex-35
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 Complex-35 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn526
b:31.6
occ:1.00
|
SG
|
B:CYS460
|
2.3
|
28.3
|
1.0
|
SG
|
B:CYS443
|
2.3
|
31.6
|
1.0
|
SG
|
B:CYS457
|
2.3
|
32.6
|
1.0
|
SG
|
B:CYS440
|
2.4
|
28.9
|
1.0
|
CB
|
B:CYS460
|
3.2
|
29.2
|
1.0
|
CB
|
B:CYS443
|
3.3
|
25.2
|
1.0
|
CB
|
B:CYS440
|
3.3
|
41.8
|
1.0
|
CB
|
B:CYS457
|
3.5
|
33.6
|
1.0
|
N
|
B:CYS443
|
3.7
|
30.5
|
1.0
|
N
|
B:CYS457
|
3.9
|
30.1
|
1.0
|
CA
|
B:CYS443
|
4.0
|
30.8
|
1.0
|
N
|
B:CYS460
|
4.2
|
26.1
|
1.0
|
CA
|
B:CYS460
|
4.2
|
24.6
|
1.0
|
CA
|
B:CYS457
|
4.3
|
33.0
|
1.0
|
NH1
|
B:ARG489
|
4.3
|
36.4
|
1.0
|
CB
|
B:VAL442
|
4.4
|
23.1
|
1.0
|
OG
|
B:SER459
|
4.5
|
31.6
|
1.0
|
CB
|
B:ASP445
|
4.6
|
48.5
|
1.0
|
C
|
B:CYS443
|
4.7
|
37.9
|
1.0
|
C
|
B:VAL442
|
4.7
|
32.2
|
1.0
|
CA
|
B:CYS440
|
4.8
|
34.0
|
1.0
|
N
|
B:SER444
|
4.8
|
36.3
|
1.0
|
N
|
B:ASP445
|
4.8
|
48.4
|
1.0
|
C
|
B:CYS457
|
4.8
|
34.0
|
1.0
|
NH2
|
B:ARG496
|
4.8
|
27.6
|
1.0
|
O
|
B:CYS457
|
4.9
|
30.8
|
1.0
|
CD
|
B:ARG489
|
4.9
|
27.4
|
1.0
|
CB
|
B:THR456
|
4.9
|
31.3
|
1.0
|
CA
|
B:VAL442
|
5.0
|
28.7
|
1.0
|
C
|
B:THR456
|
5.0
|
40.5
|
1.0
|
|
Zinc binding site 4 out
of 4 in 3g9i
Go back to
Zinc Binding Sites List in 3g9i
Zinc binding site 4 out
of 4 in the Gr Dna Binding Domain: Pal Complex-35
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 Complex-35 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn527
b:26.4
occ:1.00
|
SG
|
B:CYS482
|
2.2
|
24.2
|
1.0
|
SG
|
B:CYS476
|
2.3
|
26.4
|
1.0
|
SG
|
B:CYS495
|
2.3
|
25.4
|
1.0
|
SG
|
B:CYS492
|
2.4
|
24.6
|
1.0
|
CB
|
B:CYS482
|
3.1
|
25.9
|
1.0
|
CB
|
B:CYS492
|
3.3
|
20.2
|
1.0
|
CB
|
B:CYS476
|
3.3
|
26.5
|
1.0
|
CB
|
B:CYS495
|
3.4
|
20.6
|
1.0
|
O
|
A:HOH1
|
3.9
|
23.2
|
1.0
|
N
|
B:CYS482
|
3.9
|
26.4
|
1.0
|
CA
|
B:CYS476
|
4.0
|
27.3
|
1.0
|
CA
|
B:CYS482
|
4.2
|
19.0
|
1.0
|
N
|
B:CYS495
|
4.2
|
20.9
|
1.0
|
CA
|
B:CYS495
|
4.4
|
23.0
|
1.0
|
O
|
B:HOH34
|
4.4
|
49.6
|
1.0
|
CA
|
B:ASN480
|
4.4
|
34.7
|
1.0
|
N
|
B:ASN480
|
4.5
|
32.5
|
1.0
|
O
|
A:HOH8
|
4.6
|
29.2
|
1.0
|
N
|
B:ASP481
|
4.6
|
27.2
|
1.0
|
O
|
B:HOH5
|
4.7
|
23.4
|
1.0
|
N
|
B:ALA477
|
4.7
|
28.4
|
1.0
|
CA
|
B:CYS492
|
4.7
|
22.2
|
1.0
|
C
|
B:CYS476
|
4.8
|
32.4
|
1.0
|
N
|
B:GLY478
|
4.8
|
29.2
|
1.0
|
C
|
B:ASN480
|
4.8
|
35.9
|
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
|