Zinc in PDB 3g9m: Gr Dna-Binding Domain:Sgk 16BP Complex-44
Protein crystallography data
The structure of Gr Dna-Binding Domain:Sgk 16BP Complex-44, PDB code: 3g9m
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)
|
30.61 /
1.61
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.058,
38.713,
96.475,
90.00,
123.71,
90.00
|
R / Rfree (%)
|
18.7 /
19.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Gr Dna-Binding Domain:Sgk 16BP Complex-44
(pdb code 3g9m). 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:Sgk 16BP Complex-44, PDB code: 3g9m:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 3g9m
Go back to
Zinc Binding Sites List in 3g9m
Zinc binding site 1 out
of 4 in the Gr Dna-Binding Domain:Sgk 16BP Complex-44
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:Sgk 16BP Complex-44 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn526
b:27.2
occ:1.00
|
SG
|
A:CYS460
|
2.3
|
26.1
|
1.0
|
SG
|
A:CYS443
|
2.3
|
29.2
|
1.0
|
SG
|
A:CYS440
|
2.3
|
25.7
|
1.0
|
SG
|
A:CYS457
|
2.3
|
28.1
|
1.0
|
CB
|
A:CYS460
|
3.2
|
25.0
|
1.0
|
CB
|
A:CYS440
|
3.3
|
31.1
|
1.0
|
CB
|
A:CYS443
|
3.4
|
25.5
|
1.0
|
CB
|
A:CYS457
|
3.7
|
22.7
|
1.0
|
N
|
A:CYS443
|
3.7
|
27.7
|
1.0
|
N
|
A:CYS457
|
3.9
|
25.5
|
1.0
|
CA
|
A:CYS443
|
4.1
|
25.9
|
1.0
|
N
|
A:CYS460
|
4.2
|
23.1
|
1.0
|
CA
|
A:CYS460
|
4.3
|
26.3
|
1.0
|
NH1
|
A:ARG489
|
4.3
|
31.4
|
1.0
|
CA
|
A:CYS457
|
4.3
|
25.9
|
1.0
|
OG
|
A:SER459
|
4.5
|
28.2
|
1.0
|
CB
|
A:VAL442
|
4.5
|
22.9
|
1.0
|
CB
|
A:ASP445
|
4.5
|
37.3
|
1.0
|
C
|
A:VAL442
|
4.7
|
30.1
|
1.0
|
C
|
A:CYS443
|
4.7
|
38.1
|
1.0
|
CA
|
A:CYS440
|
4.7
|
32.7
|
1.0
|
N
|
A:SER444
|
4.8
|
30.9
|
1.0
|
N
|
A:ASP445
|
4.8
|
40.0
|
1.0
|
O
|
A:CYS457
|
4.8
|
26.0
|
1.0
|
NH2
|
A:ARG496
|
4.9
|
24.8
|
1.0
|
C
|
A:CYS457
|
4.9
|
26.8
|
1.0
|
CD
|
A:ARG489
|
4.9
|
29.5
|
1.0
|
CA
|
A:VAL442
|
5.0
|
28.7
|
1.0
|
N
|
A:VAL442
|
5.0
|
27.5
|
1.0
|
|
Zinc binding site 2 out
of 4 in 3g9m
Go back to
Zinc Binding Sites List in 3g9m
Zinc binding site 2 out
of 4 in the Gr Dna-Binding Domain:Sgk 16BP Complex-44
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:Sgk 16BP Complex-44 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn527
b:21.8
occ:1.00
|
SG
|
A:CYS482
|
2.3
|
22.1
|
1.0
|
SG
|
A:CYS492
|
2.3
|
21.3
|
1.0
|
SG
|
A:CYS495
|
2.3
|
22.5
|
1.0
|
SG
|
A:CYS476
|
2.4
|
22.5
|
1.0
|
CB
|
A:CYS482
|
3.2
|
25.1
|
1.0
|
CB
|
A:CYS492
|
3.3
|
22.1
|
1.0
|
CB
|
A:CYS476
|
3.4
|
19.8
|
1.0
|
CB
|
A:CYS495
|
3.5
|
18.7
|
1.0
|
O1
|
A:EDO1
|
3.7
|
24.2
|
1.0
|
N
|
A:CYS482
|
4.0
|
21.8
|
1.0
|
CA
|
A:CYS476
|
4.0
|
23.5
|
1.0
|
C1
|
A:EDO1
|
4.1
|
40.0
|
1.0
|
N
|
A:CYS495
|
4.1
|
20.9
|
1.0
|
CA
|
A:CYS482
|
4.2
|
24.3
|
1.0
|
CA
|
A:CYS495
|
4.4
|
19.3
|
1.0
|
CA
|
A:ASN480
|
4.4
|
26.6
|
1.0
|
N
|
A:ASN480
|
4.5
|
26.7
|
1.0
|
O
|
A:HOH7
|
4.6
|
23.6
|
1.0
|
C2
|
A:EDO1
|
4.6
|
46.2
|
1.0
|
N
|
A:ASP481
|
4.6
|
23.6
|
1.0
|
N
|
A:ALA477
|
4.7
|
20.4
|
1.0
|
O
|
A:HOH32
|
4.7
|
37.4
|
1.0
|
CA
|
A:CYS492
|
4.8
|
18.2
|
1.0
|
C
|
A:ASN480
|
4.8
|
25.1
|
1.0
|
N
|
A:GLY478
|
4.8
|
24.5
|
1.0
|
O2
|
A:EDO1
|
4.8
|
28.3
|
1.0
|
C
|
A:CYS476
|
4.8
|
25.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 3g9m
Go back to
Zinc Binding Sites List in 3g9m
Zinc binding site 3 out
of 4 in the Gr Dna-Binding Domain:Sgk 16BP Complex-44
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:Sgk 16BP Complex-44 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn526
b:32.5
occ:1.00
|
SG
|
B:CYS443
|
2.3
|
32.9
|
1.0
|
SG
|
B:CYS460
|
2.3
|
31.0
|
1.0
|
SG
|
B:CYS440
|
2.4
|
33.0
|
1.0
|
SG
|
B:CYS457
|
2.4
|
34.0
|
1.0
|
CB
|
B:CYS460
|
3.2
|
30.2
|
1.0
|
CB
|
B:CYS440
|
3.3
|
34.2
|
1.0
|
CB
|
B:CYS443
|
3.3
|
29.8
|
1.0
|
CB
|
B:CYS457
|
3.6
|
29.9
|
1.0
|
N
|
B:CYS443
|
3.8
|
31.0
|
1.0
|
N
|
B:CYS457
|
3.9
|
34.9
|
1.0
|
CA
|
B:CYS443
|
4.1
|
34.6
|
1.0
|
N
|
B:CYS460
|
4.2
|
28.1
|
1.0
|
CA
|
B:CYS460
|
4.3
|
27.3
|
1.0
|
CA
|
B:CYS457
|
4.3
|
31.7
|
1.0
|
NH1
|
B:ARG489
|
4.4
|
38.9
|
1.0
|
OG
|
B:SER459
|
4.5
|
34.9
|
1.0
|
CB
|
B:VAL442
|
4.5
|
34.9
|
1.0
|
CB
|
B:ASP445
|
4.6
|
39.2
|
1.0
|
C
|
B:CYS443
|
4.7
|
37.2
|
1.0
|
CA
|
B:CYS440
|
4.7
|
35.8
|
1.0
|
C
|
B:VAL442
|
4.8
|
30.2
|
1.0
|
O
|
B:CYS457
|
4.8
|
32.4
|
1.0
|
NH2
|
B:ARG496
|
4.8
|
26.9
|
1.0
|
N
|
B:SER444
|
4.8
|
40.3
|
1.0
|
C
|
B:CYS457
|
4.9
|
31.7
|
1.0
|
CD
|
B:ARG489
|
4.9
|
30.4
|
1.0
|
N
|
B:ASP445
|
4.9
|
44.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 3g9m
Go back to
Zinc Binding Sites List in 3g9m
Zinc binding site 4 out
of 4 in the Gr Dna-Binding Domain:Sgk 16BP Complex-44
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:Sgk 16BP Complex-44 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn527
b:22.2
occ:1.00
|
SG
|
B:CYS482
|
2.3
|
22.9
|
1.0
|
SG
|
B:CYS476
|
2.3
|
21.2
|
1.0
|
SG
|
B:CYS492
|
2.4
|
21.8
|
1.0
|
SG
|
B:CYS495
|
2.4
|
23.4
|
1.0
|
CB
|
B:CYS482
|
3.2
|
23.0
|
1.0
|
CB
|
B:CYS492
|
3.3
|
18.6
|
1.0
|
CB
|
B:CYS495
|
3.3
|
18.9
|
1.0
|
CB
|
B:CYS476
|
3.4
|
18.7
|
1.0
|
O
|
A:HOH529
|
3.8
|
22.1
|
1.0
|
N
|
B:CYS482
|
3.9
|
25.7
|
1.0
|
CA
|
B:CYS476
|
4.0
|
19.7
|
1.0
|
O
|
B:HOH11
|
4.1
|
24.2
|
1.0
|
N
|
B:CYS495
|
4.1
|
21.2
|
1.0
|
CA
|
B:CYS482
|
4.2
|
24.2
|
1.0
|
CA
|
B:CYS495
|
4.3
|
20.7
|
1.0
|
O2
|
A:EDO1
|
4.5
|
28.3
|
1.0
|
CA
|
B:ASN480
|
4.6
|
23.7
|
1.0
|
N
|
B:ASP481
|
4.6
|
23.4
|
1.0
|
N
|
B:ASN480
|
4.7
|
22.3
|
1.0
|
O
|
B:HOH14
|
4.7
|
28.0
|
1.0
|
N
|
B:ALA477
|
4.7
|
20.5
|
1.0
|
CA
|
B:CYS492
|
4.7
|
20.8
|
1.0
|
C
|
B:CYS476
|
4.8
|
19.9
|
1.0
|
C
|
B:ASN480
|
4.9
|
27.2
|
1.0
|
N
|
B:GLY478
|
4.9
|
22.1
|
1.0
|
CB
|
B:ALA494
|
5.0
|
21.6
|
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 13:38:10 2024
|