Zinc in PDB 3g8x: Gr Dna Binding Domain:Gilz 16BP Complex-65
Protein crystallography data
The structure of Gr Dna Binding Domain:Gilz 16BP Complex-65, PDB code: 3g8x
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)
|
35.36 /
2.05
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.213,
37.914,
96.993,
90.00,
123.22,
90.00
|
R / Rfree (%)
|
21 /
25.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Gr Dna Binding Domain:Gilz 16BP Complex-65
(pdb code 3g8x). 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-65, PDB code: 3g8x:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 3g8x
Go back to
Zinc Binding Sites List in 3g8x
Zinc binding site 1 out
of 4 in the Gr Dna Binding Domain:Gilz 16BP Complex-65
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-65 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn526
b:54.6
occ:1.00
|
SG
|
A:CYS457
|
2.2
|
59.5
|
1.0
|
SG
|
A:CYS443
|
2.3
|
63.9
|
1.0
|
SG
|
A:CYS460
|
2.3
|
55.2
|
1.0
|
SG
|
A:CYS440
|
2.4
|
51.2
|
1.0
|
CB
|
A:CYS443
|
3.0
|
55.2
|
1.0
|
CB
|
A:CYS440
|
3.2
|
50.7
|
1.0
|
CB
|
A:CYS460
|
3.2
|
41.4
|
1.0
|
N
|
A:CYS443
|
3.7
|
58.2
|
1.0
|
CB
|
A:CYS457
|
3.7
|
66.7
|
1.0
|
CA
|
A:CYS443
|
3.9
|
60.6
|
1.0
|
N
|
A:CYS457
|
4.0
|
53.6
|
1.0
|
OG
|
A:SER459
|
4.0
|
70.2
|
1.0
|
N
|
A:CYS460
|
4.2
|
41.6
|
1.0
|
CA
|
A:CYS460
|
4.3
|
38.8
|
1.0
|
CA
|
A:CYS457
|
4.3
|
63.4
|
1.0
|
CB
|
A:VAL442
|
4.5
|
38.9
|
1.0
|
C
|
A:CYS443
|
4.6
|
67.9
|
1.0
|
CA
|
A:CYS440
|
4.6
|
63.3
|
1.0
|
NH2
|
A:ARG496
|
4.6
|
52.1
|
1.0
|
CB
|
A:ASP445
|
4.7
|
76.5
|
1.0
|
NH1
|
A:ARG489
|
4.7
|
57.6
|
1.0
|
C
|
A:VAL442
|
4.7
|
58.8
|
1.0
|
O
|
A:CYS457
|
4.7
|
43.9
|
1.0
|
N
|
A:SER444
|
4.7
|
62.6
|
1.0
|
N
|
A:ASP445
|
4.8
|
63.4
|
1.0
|
C
|
A:CYS457
|
4.8
|
61.2
|
1.0
|
O
|
A:ASP445
|
4.9
|
84.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 3g8x
Go back to
Zinc Binding Sites List in 3g8x
Zinc binding site 2 out
of 4 in the Gr Dna Binding Domain:Gilz 16BP Complex-65
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-65 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn527
b:37.1
occ:1.00
|
SG
|
A:CYS476
|
2.2
|
37.0
|
1.0
|
SG
|
A:CYS492
|
2.2
|
37.2
|
1.0
|
SG
|
A:CYS482
|
2.2
|
36.8
|
1.0
|
SG
|
A:CYS495
|
2.4
|
36.4
|
1.0
|
O1
|
A:EDO528
|
3.1
|
57.5
|
1.0
|
CB
|
A:CYS482
|
3.2
|
47.4
|
1.0
|
CB
|
A:CYS476
|
3.3
|
34.7
|
1.0
|
CB
|
A:CYS492
|
3.4
|
33.9
|
1.0
|
CB
|
A:CYS495
|
3.4
|
27.6
|
1.0
|
CA
|
A:CYS476
|
3.9
|
37.2
|
1.0
|
N
|
A:CYS482
|
4.0
|
43.3
|
1.0
|
N
|
A:CYS495
|
4.1
|
32.8
|
1.0
|
CA
|
A:CYS482
|
4.2
|
41.7
|
1.0
|
C1
|
A:EDO528
|
4.3
|
45.6
|
1.0
|
CA
|
A:CYS495
|
4.3
|
33.5
|
1.0
|
CA
|
A:ASN480
|
4.4
|
45.2
|
1.0
|
C2
|
A:EDO528
|
4.4
|
54.7
|
1.0
|
O
|
A:HOH17
|
4.5
|
59.8
|
1.0
|
N
|
A:ASN480
|
4.5
|
48.2
|
1.0
|
O
|
A:HOH8
|
4.6
|
38.1
|
1.0
|
O2
|
A:EDO528
|
4.7
|
32.2
|
1.0
|
N
|
A:ASP481
|
4.7
|
39.9
|
1.0
|
N
|
A:ALA477
|
4.7
|
40.6
|
1.0
|
CA
|
A:CYS492
|
4.7
|
37.8
|
1.0
|
C
|
A:CYS476
|
4.8
|
48.0
|
1.0
|
N
|
A:GLY478
|
4.8
|
40.4
|
1.0
|
C
|
A:ASN480
|
4.8
|
43.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 3g8x
Go back to
Zinc Binding Sites List in 3g8x
Zinc binding site 3 out
of 4 in the Gr Dna Binding Domain:Gilz 16BP Complex-65
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-65 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn526
b:96.2
occ:1.00
|
SG
|
B:CYS460
|
2.3
|
67.8
|
1.0
|
SG
|
B:CYS440
|
2.4
|
90.4
|
1.0
|
SG
|
B:CYS457
|
2.5
|
86.7
|
1.0
|
SG
|
B:CYS443
|
2.5
|
92.4
|
1.0
|
CB
|
B:CYS440
|
3.2
|
0.6
|
1.0
|
CB
|
B:CYS457
|
3.2
|
70.8
|
1.0
|
CB
|
B:CYS443
|
3.3
|
89.0
|
1.0
|
CB
|
B:CYS460
|
3.4
|
71.6
|
1.0
|
N
|
B:CYS443
|
3.4
|
89.1
|
1.0
|
N
|
B:CYS457
|
3.5
|
93.3
|
1.0
|
CA
|
B:CYS443
|
3.8
|
89.0
|
1.0
|
CA
|
B:CYS457
|
3.9
|
85.1
|
1.0
|
N
|
B:SER444
|
4.1
|
0.8
|
1.0
|
C
|
B:CYS443
|
4.2
|
98.7
|
1.0
|
CB
|
B:VAL442
|
4.3
|
63.9
|
1.0
|
N
|
B:ASP445
|
4.3
|
95.3
|
1.0
|
N
|
B:CYS460
|
4.5
|
69.0
|
1.0
|
CB
|
B:ASP445
|
4.5
|
84.3
|
1.0
|
CA
|
B:CYS460
|
4.5
|
63.4
|
1.0
|
C
|
B:THR456
|
4.6
|
90.6
|
1.0
|
C
|
B:VAL442
|
4.6
|
80.8
|
1.0
|
CA
|
B:CYS440
|
4.7
|
0.8
|
1.0
|
C
|
B:CYS457
|
4.7
|
82.8
|
1.0
|
CB
|
B:THR456
|
4.7
|
74.6
|
1.0
|
OG
|
B:SER459
|
4.8
|
73.7
|
1.0
|
CA
|
B:THR456
|
4.8
|
84.7
|
1.0
|
O
|
B:CYS457
|
4.8
|
81.2
|
1.0
|
CA
|
B:VAL442
|
4.9
|
72.2
|
1.0
|
N
|
B:VAL442
|
4.9
|
73.8
|
1.0
|
CG1
|
B:VAL442
|
4.9
|
67.3
|
1.0
|
CA
|
B:ASP445
|
5.0
|
98.8
|
1.0
|
|
Zinc binding site 4 out
of 4 in 3g8x
Go back to
Zinc Binding Sites List in 3g8x
Zinc binding site 4 out
of 4 in the Gr Dna Binding Domain:Gilz 16BP Complex-65
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-65 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn527
b:40.1
occ:1.00
|
SG
|
B:CYS476
|
2.2
|
36.4
|
1.0
|
SG
|
B:CYS482
|
2.3
|
41.8
|
1.0
|
SG
|
B:CYS492
|
2.4
|
38.4
|
1.0
|
SG
|
B:CYS495
|
2.4
|
40.1
|
1.0
|
CB
|
B:CYS482
|
3.1
|
44.8
|
1.0
|
CB
|
B:CYS492
|
3.3
|
39.4
|
1.0
|
CB
|
B:CYS476
|
3.3
|
27.6
|
1.0
|
CB
|
B:CYS495
|
3.4
|
38.5
|
1.0
|
O
|
B:HOH13
|
3.7
|
42.8
|
1.0
|
N
|
B:CYS482
|
3.8
|
45.2
|
1.0
|
CA
|
B:CYS476
|
3.9
|
40.7
|
1.0
|
O
|
B:HOH4
|
4.1
|
48.4
|
1.0
|
CA
|
B:CYS482
|
4.1
|
53.1
|
1.0
|
N
|
B:CYS495
|
4.2
|
44.6
|
1.0
|
CA
|
B:CYS495
|
4.4
|
44.5
|
1.0
|
CA
|
B:ASN480
|
4.5
|
47.9
|
1.0
|
N
|
B:ASN480
|
4.5
|
35.3
|
1.0
|
O2
|
A:EDO528
|
4.5
|
32.2
|
1.0
|
N
|
B:ALA477
|
4.6
|
32.7
|
1.0
|
N
|
B:ASP481
|
4.6
|
41.6
|
1.0
|
C
|
B:CYS476
|
4.7
|
36.2
|
1.0
|
O
|
B:HOH10
|
4.7
|
42.1
|
1.0
|
CA
|
B:CYS492
|
4.7
|
38.2
|
1.0
|
N
|
B:GLY478
|
4.7
|
43.1
|
1.0
|
C
|
B:ASN480
|
4.8
|
46.7
|
1.0
|
C
|
B:ASP481
|
5.0
|
46.3
|
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 13:35:49 2024
|