Zinc in PDB 3fyl: Gr Dna Binding Domain:Cgt Complex
Protein crystallography data
The structure of Gr Dna Binding Domain:Cgt Complex, PDB code: 3fyl
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)
|
35.24 /
1.63
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.445,
37.770,
96.679,
90.00,
123.50,
90.00
|
R / Rfree (%)
|
19.6 /
23.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Gr Dna Binding Domain:Cgt Complex
(pdb code 3fyl). 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:Cgt Complex, PDB code: 3fyl:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 3fyl
Go back to
Zinc Binding Sites List in 3fyl
Zinc binding site 1 out
of 4 in the Gr Dna Binding Domain:Cgt Complex
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:Cgt Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn526
b:30.4
occ:0.56
|
SG
|
A:CYS460
|
2.2
|
27.6
|
0.5
|
SG
|
A:CYS440
|
2.3
|
29.7
|
0.6
|
SG
|
A:CYS443
|
2.3
|
34.1
|
0.7
|
SG
|
A:CYS457
|
2.4
|
36.3
|
0.7
|
CB
|
A:CYS460
|
3.2
|
33.6
|
0.8
|
CB
|
A:CYS440
|
3.2
|
41.5
|
1.0
|
CB
|
A:CYS443
|
3.3
|
35.6
|
0.7
|
CB
|
A:CYS457
|
3.7
|
40.3
|
0.8
|
N
|
A:CYS443
|
3.7
|
41.2
|
1.0
|
N
|
A:CYS457
|
3.9
|
41.4
|
1.0
|
CA
|
A:CYS443
|
4.1
|
33.4
|
0.7
|
N
|
A:CYS460
|
4.1
|
23.1
|
0.5
|
NH1
|
A:ARG489
|
4.2
|
37.1
|
0.8
|
CA
|
A:CYS460
|
4.2
|
27.9
|
0.8
|
CA
|
A:CYS457
|
4.4
|
34.8
|
0.8
|
OG
|
A:SER459
|
4.4
|
29.8
|
0.5
|
CB
|
A:VAL442
|
4.4
|
28.1
|
0.8
|
CB
|
A:ASP445
|
4.6
|
48.6
|
1.0
|
CA
|
A:CYS440
|
4.7
|
39.1
|
1.0
|
C
|
A:CYS443
|
4.7
|
44.6
|
1.0
|
C
|
A:VAL442
|
4.7
|
42.7
|
1.0
|
N
|
A:SER444
|
4.8
|
34.5
|
0.7
|
O
|
A:CYS457
|
4.9
|
32.8
|
0.7
|
C
|
A:CYS457
|
4.9
|
36.3
|
1.0
|
N
|
A:ASP445
|
4.9
|
45.8
|
0.7
|
NH2
|
A:ARG496
|
4.9
|
22.2
|
0.5
|
CD
|
A:ARG489
|
4.9
|
23.9
|
0.5
|
CB
|
A:THR456
|
5.0
|
38.9
|
1.0
|
CA
|
A:VAL442
|
5.0
|
29.4
|
0.8
|
N
|
A:VAL442
|
5.0
|
23.1
|
0.6
|
|
Zinc binding site 2 out
of 4 in 3fyl
Go back to
Zinc Binding Sites List in 3fyl
Zinc binding site 2 out
of 4 in the Gr Dna Binding Domain:Cgt Complex
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:Cgt Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn527
b:28.4
occ:0.64
|
SG
|
A:CYS482
|
2.2
|
24.7
|
0.5
|
SG
|
A:CYS476
|
2.3
|
34.8
|
1.0
|
SG
|
A:CYS495
|
2.3
|
23.9
|
0.6
|
SG
|
A:CYS492
|
2.4
|
23.9
|
0.5
|
CB
|
A:CYS482
|
3.2
|
29.2
|
0.7
|
CB
|
A:CYS492
|
3.2
|
31.4
|
1.0
|
CB
|
A:CYS476
|
3.3
|
33.7
|
1.0
|
CB
|
A:CYS495
|
3.4
|
36.0
|
1.0
|
O
|
A:HOH4
|
3.8
|
37.7
|
1.0
|
N
|
A:CYS482
|
3.9
|
29.9
|
0.6
|
CA
|
A:CYS476
|
4.0
|
27.0
|
0.7
|
N
|
A:CYS495
|
4.2
|
24.5
|
0.6
|
CA
|
A:CYS482
|
4.2
|
33.9
|
1.0
|
CA
|
A:CYS495
|
4.4
|
30.1
|
1.0
|
O
|
A:HOH58
|
4.4
|
53.1
|
1.0
|
CA
|
A:ASN480
|
4.4
|
38.0
|
0.8
|
N
|
A:ASP481
|
4.5
|
29.2
|
0.7
|
N
|
A:ASN480
|
4.6
|
43.2
|
1.0
|
O
|
A:HOH7
|
4.6
|
33.2
|
1.0
|
O
|
A:HOH2
|
4.7
|
39.5
|
1.0
|
CA
|
A:CYS492
|
4.7
|
23.6
|
0.6
|
C
|
A:ASN480
|
4.7
|
36.3
|
0.9
|
N
|
A:GLY478
|
4.8
|
34.6
|
0.8
|
N
|
A:ALA477
|
4.8
|
25.7
|
0.5
|
C
|
A:CYS476
|
4.9
|
26.2
|
0.7
|
|
Zinc binding site 3 out
of 4 in 3fyl
Go back to
Zinc Binding Sites List in 3fyl
Zinc binding site 3 out
of 4 in the Gr Dna Binding Domain:Cgt Complex
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:Cgt Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn526
b:50.5
occ:1.00
|
SG
|
B:CYS460
|
2.3
|
42.0
|
0.8
|
SG
|
B:CYS457
|
2.3
|
51.8
|
1.0
|
SG
|
B:CYS443
|
2.3
|
49.9
|
1.0
|
SG
|
B:CYS440
|
2.4
|
41.4
|
0.6
|
CB
|
B:CYS460
|
3.1
|
35.9
|
0.7
|
CB
|
B:CYS440
|
3.2
|
48.8
|
1.0
|
CB
|
B:CYS443
|
3.4
|
50.9
|
1.0
|
CB
|
B:CYS457
|
3.6
|
46.8
|
1.0
|
N
|
B:CYS443
|
3.8
|
47.7
|
1.0
|
N
|
B:CYS457
|
3.9
|
53.0
|
1.0
|
CA
|
B:CYS443
|
4.1
|
46.3
|
0.9
|
N
|
B:CYS460
|
4.2
|
40.0
|
0.8
|
CA
|
B:CYS460
|
4.2
|
42.5
|
0.9
|
CA
|
B:CYS457
|
4.4
|
49.6
|
1.0
|
NH1
|
B:ARG489
|
4.4
|
44.0
|
0.8
|
CB
|
B:ASP445
|
4.5
|
49.4
|
0.8
|
OG
|
B:SER459
|
4.5
|
37.6
|
0.5
|
CB
|
B:VAL442
|
4.5
|
37.6
|
0.6
|
CA
|
B:CYS440
|
4.7
|
53.1
|
1.0
|
C
|
B:CYS443
|
4.7
|
53.2
|
1.0
|
N
|
B:ASP445
|
4.8
|
55.2
|
0.8
|
C
|
B:VAL442
|
4.8
|
47.7
|
1.0
|
N
|
B:SER444
|
4.8
|
52.3
|
1.0
|
NH2
|
B:ARG496
|
4.8
|
34.0
|
0.6
|
CD
|
B:ARG489
|
4.9
|
43.8
|
1.0
|
C
|
B:CYS457
|
5.0
|
52.8
|
1.0
|
O
|
B:CYS457
|
5.0
|
53.2
|
1.0
|
CG1
|
B:VAL442
|
5.0
|
35.1
|
0.6
|
|
Zinc binding site 4 out
of 4 in 3fyl
Go back to
Zinc Binding Sites List in 3fyl
Zinc binding site 4 out
of 4 in the Gr Dna Binding Domain:Cgt Complex
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:Cgt Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn527
b:35.3
occ:1.00
|
SG
|
B:CYS482
|
2.2
|
29.4
|
0.7
|
SG
|
B:CYS476
|
2.3
|
26.5
|
0.7
|
SG
|
B:CYS495
|
2.3
|
20.2
|
0.5
|
SG
|
B:CYS492
|
2.4
|
23.4
|
0.5
|
CB
|
B:CYS482
|
3.2
|
31.7
|
0.8
|
CB
|
B:CYS495
|
3.3
|
33.7
|
1.0
|
CB
|
B:CYS492
|
3.3
|
25.8
|
0.7
|
CB
|
B:CYS476
|
3.4
|
18.5
|
0.5
|
O
|
A:HOH13
|
3.8
|
32.8
|
1.0
|
N
|
B:CYS482
|
3.9
|
37.3
|
0.8
|
CA
|
B:CYS476
|
4.0
|
21.4
|
0.6
|
N
|
B:CYS495
|
4.1
|
24.9
|
0.6
|
CA
|
B:CYS482
|
4.2
|
37.6
|
1.0
|
O
|
B:HOH11
|
4.2
|
38.0
|
1.0
|
CA
|
B:CYS495
|
4.3
|
38.0
|
1.0
|
O
|
A:HOH2
|
4.5
|
39.5
|
1.0
|
N
|
B:ASP481
|
4.6
|
22.8
|
0.5
|
CA
|
B:ASN480
|
4.6
|
37.1
|
1.0
|
N
|
B:ASN480
|
4.7
|
25.5
|
0.6
|
CA
|
B:CYS492
|
4.7
|
28.3
|
0.8
|
N
|
B:ALA477
|
4.8
|
18.1
|
0.5
|
N
|
B:GLY478
|
4.8
|
20.4
|
0.5
|
O
|
B:HOH32
|
4.8
|
44.1
|
1.0
|
C
|
B:CYS476
|
4.9
|
25.2
|
0.8
|
C
|
B:ASN480
|
4.9
|
34.8
|
0.8
|
CB
|
B:ALA494
|
4.9
|
33.2
|
0.8
|
|
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 13:28:09 2024
|