Cadmium in PDB 1g8g: Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Enzymatic activity of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
All present enzymatic activity of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps:
2.7.7.4;
Protein crystallography data
The structure of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps, PDB code: 1g8g
was solved by
T.C.Ullrich,
M.Blaesse,
R.Huber,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.85 /
2.60
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
185.922,
185.922,
223.674,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.6 /
22.7
|
Other elements in 1g8g:
The structure of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps also contains other interesting chemical elements:
Cadmium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Cadmium atom in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
(pdb code 1g8g). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 11 binding sites of Cadmium where determined in the
Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps, PDB code: 1g8g:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 11 in 1g8g
Go back to
Cadmium Binding Sites List in 1g8g
Cadmium binding site 1 out
of 11 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd512
b:6.4
occ:0.50
|
OXT
|
A:ACY557
|
2.1
|
17.0
|
1.0
|
OD2
|
A:ASP168
|
2.1
|
23.3
|
1.0
|
NE2
|
A:HIS236
|
2.1
|
27.2
|
1.0
|
O
|
A:ACY557
|
2.2
|
22.9
|
1.0
|
NE2
|
A:HIS235
|
2.2
|
29.2
|
1.0
|
C
|
A:ACY557
|
2.4
|
19.9
|
1.0
|
CE1
|
A:HIS236
|
2.7
|
27.8
|
1.0
|
CE1
|
A:HIS235
|
3.1
|
31.9
|
1.0
|
CD2
|
A:HIS235
|
3.2
|
29.5
|
1.0
|
CG
|
A:ASP168
|
3.3
|
28.8
|
1.0
|
CD2
|
A:HIS236
|
3.3
|
26.8
|
1.0
|
ND1
|
A:HIS236
|
3.8
|
26.2
|
1.0
|
OD1
|
A:ASP168
|
3.9
|
25.5
|
1.0
|
CH3
|
A:ACY557
|
3.9
|
11.5
|
1.0
|
CG
|
A:HIS236
|
4.2
|
24.9
|
1.0
|
ND1
|
A:HIS235
|
4.3
|
30.3
|
1.0
|
CG
|
A:HIS235
|
4.4
|
29.6
|
1.0
|
CB
|
A:ASP168
|
4.4
|
29.4
|
1.0
|
|
Cadmium binding site 2 out
of 11 in 1g8g
Go back to
Cadmium Binding Sites List in 1g8g
Cadmium binding site 2 out
of 11 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd513
b:46.5
occ:0.50
|
O
|
A:PRO39
|
2.5
|
31.1
|
1.0
|
SG
|
A:CYS43
|
2.6
|
24.9
|
1.0
|
O
|
A:HOH1223
|
2.9
|
36.7
|
1.0
|
O
|
A:HOH1027
|
3.0
|
49.5
|
1.0
|
O
|
A:HOH1311
|
3.2
|
40.6
|
1.0
|
C
|
A:PRO39
|
3.3
|
28.0
|
1.0
|
CA
|
A:PRO39
|
3.8
|
27.8
|
1.0
|
CD1
|
A:LEU227
|
3.8
|
38.3
|
1.0
|
N
|
A:CYS43
|
3.8
|
25.3
|
1.0
|
CB
|
A:CYS43
|
3.9
|
24.9
|
1.0
|
CB
|
A:PRO39
|
4.1
|
27.7
|
1.0
|
CB
|
A:LEU42
|
4.2
|
27.1
|
1.0
|
CA
|
A:CYS43
|
4.2
|
24.7
|
1.0
|
N
|
A:ARG40
|
4.4
|
27.0
|
1.0
|
C
|
A:LEU42
|
4.6
|
25.9
|
1.0
|
CA
|
A:ARG40
|
4.6
|
27.1
|
1.0
|
O
|
A:HOH799
|
4.7
|
38.4
|
1.0
|
O
|
A:HOH1262
|
4.8
|
61.5
|
1.0
|
CA
|
A:LEU42
|
4.8
|
26.4
|
1.0
|
N
|
A:LEU42
|
5.0
|
25.6
|
1.0
|
|
Cadmium binding site 3 out
of 11 in 1g8g
Go back to
Cadmium Binding Sites List in 1g8g
Cadmium binding site 3 out
of 11 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd514
b:37.9
occ:1.00
|
OE1
|
A:GLU22
|
2.2
|
32.1
|
1.0
|
O
|
A:LEU18
|
2.3
|
33.5
|
1.0
|
OE2
|
A:GLU22
|
2.4
|
33.8
|
1.0
|
O
|
A:ACY551
|
2.5
|
35.4
|
1.0
|
CD
|
A:GLU22
|
2.6
|
33.4
|
1.0
|
OXT
|
A:ACY551
|
2.9
|
36.6
|
1.0
|
C
|
A:ACY551
|
3.0
|
35.4
|
1.0
|
C
|
A:LEU18
|
3.2
|
34.1
|
1.0
|
N
|
A:LYS19
|
4.0
|
34.0
|
1.0
|
CG
|
A:GLU22
|
4.1
|
33.1
|
1.0
|
CA
|
A:LEU18
|
4.1
|
34.0
|
1.0
|
CA
|
A:LYS19
|
4.2
|
33.1
|
1.0
|
CB
|
A:ASN21
|
4.3
|
32.6
|
1.0
|
N
|
A:ASN21
|
4.4
|
34.4
|
1.0
|
C
|
A:LYS19
|
4.5
|
32.8
|
1.0
|
CH3
|
A:ACY551
|
4.5
|
33.3
|
1.0
|
N
|
A:LYS20
|
4.6
|
31.0
|
1.0
|
CB
|
A:LEU18
|
4.6
|
31.1
|
1.0
|
N
|
A:GLU22
|
4.7
|
36.0
|
1.0
|
OD1
|
A:ASN21
|
4.8
|
34.3
|
1.0
|
CA
|
A:ASN21
|
4.9
|
35.2
|
1.0
|
CG
|
A:ASN21
|
4.9
|
33.0
|
1.0
|
|
Cadmium binding site 4 out
of 11 in 1g8g
Go back to
Cadmium Binding Sites List in 1g8g
Cadmium binding site 4 out
of 11 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd515
b:31.4
occ:1.00
|
OE1
|
A:GLU182
|
2.2
|
24.6
|
1.0
|
O
|
A:ACY555
|
2.3
|
21.1
|
1.0
|
OXT
|
A:ACY555
|
2.7
|
24.3
|
1.0
|
C
|
A:ACY555
|
2.8
|
23.0
|
1.0
|
CD
|
A:GLU182
|
2.9
|
27.0
|
1.0
|
OE2
|
A:GLU182
|
3.0
|
29.5
|
1.0
|
NZ
|
A:LYS174
|
4.2
|
20.9
|
1.0
|
CG
|
A:GLU182
|
4.3
|
26.3
|
1.0
|
CH3
|
A:ACY555
|
4.4
|
21.5
|
1.0
|
NH1
|
A:ARG186
|
4.5
|
29.7
|
1.0
|
CE
|
A:LYS174
|
4.6
|
20.7
|
1.0
|
OXT
|
A:ACY554
|
4.6
|
29.5
|
1.0
|
CE1
|
A:PHE255
|
4.8
|
24.7
|
1.0
|
CZ
|
A:PHE255
|
4.8
|
23.1
|
1.0
|
C
|
A:ACY554
|
5.0
|
27.8
|
1.0
|
O
|
A:ACY554
|
5.0
|
26.3
|
1.0
|
|
Cadmium binding site 5 out
of 11 in 1g8g
Go back to
Cadmium Binding Sites List in 1g8g
Cadmium binding site 5 out
of 11 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd516
b:20.4
occ:0.70
|
O
|
A:ACY556
|
2.0
|
42.2
|
1.0
|
O
|
A:ACY552
|
2.1
|
24.1
|
1.0
|
OD1
|
A:ASP189
|
2.1
|
28.0
|
1.0
|
OXT
|
A:ACY552
|
2.2
|
25.5
|
1.0
|
OXT
|
A:ACY556
|
2.3
|
43.8
|
1.0
|
OD2
|
A:ASP189
|
2.4
|
28.6
|
1.0
|
C
|
A:ACY556
|
2.4
|
44.5
|
1.0
|
C
|
A:ACY552
|
2.4
|
25.0
|
1.0
|
CG
|
A:ASP189
|
2.5
|
29.2
|
1.0
|
CH3
|
A:ACY556
|
4.0
|
43.3
|
1.0
|
CH3
|
A:ACY552
|
4.0
|
22.0
|
1.0
|
CB
|
A:ASP189
|
4.1
|
26.9
|
1.0
|
O
|
A:HOH755
|
4.3
|
26.7
|
1.0
|
O
|
A:HOH1023
|
4.7
|
44.4
|
1.0
|
CD
|
A:ARG190
|
4.8
|
25.5
|
1.0
|
CG
|
A:ARG190
|
4.9
|
24.6
|
1.0
|
CA
|
A:ASP189
|
5.0
|
27.3
|
1.0
|
|
Cadmium binding site 6 out
of 11 in 1g8g
Go back to
Cadmium Binding Sites List in 1g8g
Cadmium binding site 6 out
of 11 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd524
b:46.1
occ:1.00
|
O
|
A:HOH1212
|
2.1
|
32.2
|
1.0
|
OXT
|
A:ACY565
|
2.2
|
47.4
|
1.0
|
O
|
A:HOH1308
|
2.4
|
34.6
|
1.0
|
OD1
|
A:ASP71
|
2.5
|
36.1
|
1.0
|
OD2
|
A:ASP71
|
2.6
|
38.6
|
1.0
|
O
|
A:ACY565
|
2.7
|
49.6
|
1.0
|
C
|
A:ACY565
|
2.7
|
49.7
|
1.0
|
CG
|
A:ASP71
|
2.9
|
36.3
|
1.0
|
O
|
A:HOH721
|
3.1
|
30.4
|
1.0
|
CH3
|
A:ACY565
|
4.2
|
50.3
|
1.0
|
O
|
A:HOH909
|
4.2
|
58.0
|
1.0
|
CB
|
A:ASP71
|
4.4
|
36.8
|
1.0
|
NE
|
A:ARG73
|
4.6
|
27.5
|
1.0
|
CD
|
A:ARG73
|
4.6
|
30.3
|
1.0
|
O
|
A:ASP71
|
4.8
|
37.2
|
1.0
|
|
Cadmium binding site 7 out
of 11 in 1g8g
Go back to
Cadmium Binding Sites List in 1g8g
Cadmium binding site 7 out
of 11 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd530
b:6.3
occ:0.50
|
O
|
B:ACY564
|
2.0
|
16.3
|
1.0
|
OD2
|
B:ASP168
|
2.1
|
33.7
|
1.0
|
NE2
|
B:HIS236
|
2.1
|
29.7
|
1.0
|
OXT
|
B:ACY564
|
2.1
|
19.9
|
1.0
|
NE2
|
B:HIS235
|
2.2
|
26.5
|
1.0
|
C
|
B:ACY564
|
2.3
|
19.1
|
1.0
|
CE1
|
B:HIS236
|
2.8
|
30.1
|
1.0
|
CE1
|
B:HIS235
|
3.1
|
24.8
|
1.0
|
CD2
|
B:HIS236
|
3.2
|
28.3
|
1.0
|
CD2
|
B:HIS235
|
3.2
|
26.0
|
1.0
|
CG
|
B:ASP168
|
3.2
|
36.2
|
1.0
|
OD1
|
B:ASP168
|
3.8
|
38.5
|
1.0
|
CH3
|
B:ACY564
|
3.9
|
13.5
|
1.0
|
ND1
|
B:HIS236
|
3.9
|
28.4
|
1.0
|
CG
|
B:HIS236
|
4.1
|
28.4
|
1.0
|
ND1
|
B:HIS235
|
4.2
|
27.5
|
1.0
|
CG
|
B:HIS235
|
4.3
|
27.2
|
1.0
|
O
|
B:HOH953
|
4.4
|
50.2
|
1.0
|
CB
|
B:ASP168
|
4.4
|
35.4
|
1.0
|
NH1
|
B:ARG173
|
4.7
|
40.0
|
1.0
|
O
|
B:HOH995
|
4.7
|
23.5
|
1.0
|
|
Cadmium binding site 8 out
of 11 in 1g8g
Go back to
Cadmium Binding Sites List in 1g8g
Cadmium binding site 8 out
of 11 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd531
b:57.8
occ:0.50
|
O
|
B:PRO39
|
2.3
|
30.0
|
1.0
|
SG
|
B:CYS43
|
2.5
|
26.8
|
1.0
|
C
|
B:PRO39
|
3.3
|
28.0
|
1.0
|
N
|
B:CYS43
|
3.6
|
27.8
|
1.0
|
CB
|
B:CYS43
|
3.8
|
27.7
|
1.0
|
CA
|
B:PRO39
|
3.8
|
28.6
|
1.0
|
CD2
|
B:LEU227
|
3.8
|
40.1
|
1.0
|
CB
|
B:LEU42
|
3.9
|
31.1
|
1.0
|
CA
|
B:CYS43
|
4.1
|
26.9
|
1.0
|
CB
|
B:PRO39
|
4.1
|
29.5
|
1.0
|
O
|
B:HOH952
|
4.2
|
36.2
|
1.0
|
C
|
B:LEU42
|
4.4
|
28.2
|
1.0
|
N
|
B:ARG40
|
4.4
|
27.0
|
1.0
|
CG
|
B:LEU227
|
4.5
|
38.8
|
1.0
|
CA
|
B:LEU42
|
4.6
|
29.4
|
1.0
|
CA
|
B:ARG40
|
4.6
|
27.9
|
1.0
|
N
|
B:LEU42
|
4.8
|
28.9
|
1.0
|
O
|
B:HOH678
|
4.9
|
48.8
|
1.0
|
CD1
|
B:LEU42
|
5.0
|
34.3
|
1.0
|
|
Cadmium binding site 9 out
of 11 in 1g8g
Go back to
Cadmium Binding Sites List in 1g8g
Cadmium binding site 9 out
of 11 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd532
b:42.2
occ:1.00
|
OE1
|
B:GLU22
|
1.9
|
41.0
|
1.0
|
O
|
B:LEU18
|
2.3
|
34.9
|
1.0
|
O
|
B:ACY558
|
2.3
|
37.5
|
1.0
|
OE2
|
B:GLU22
|
2.4
|
39.0
|
1.0
|
CD
|
B:GLU22
|
2.4
|
39.2
|
1.0
|
OXT
|
B:ACY558
|
2.8
|
37.5
|
1.0
|
C
|
B:ACY558
|
2.9
|
36.7
|
1.0
|
C
|
B:LEU18
|
3.3
|
34.1
|
1.0
|
CG
|
B:GLU22
|
3.9
|
37.7
|
1.0
|
N
|
B:LYS19
|
4.2
|
33.9
|
1.0
|
CA
|
B:LYS19
|
4.2
|
33.2
|
1.0
|
CB
|
B:ASN21
|
4.2
|
35.5
|
1.0
|
CA
|
B:LEU18
|
4.2
|
34.2
|
1.0
|
CH3
|
B:ACY558
|
4.4
|
35.4
|
1.0
|
C
|
B:LYS19
|
4.6
|
32.2
|
1.0
|
OD1
|
B:ASN21
|
4.6
|
37.2
|
1.0
|
N
|
B:ASN21
|
4.6
|
32.6
|
1.0
|
N
|
B:GLU22
|
4.7
|
35.9
|
1.0
|
N
|
B:LYS20
|
4.7
|
31.7
|
1.0
|
CG
|
B:ASN21
|
4.8
|
36.3
|
1.0
|
CB
|
B:LEU18
|
4.8
|
33.9
|
1.0
|
CA
|
B:ASN21
|
5.0
|
34.5
|
1.0
|
CB
|
B:GLU22
|
5.0
|
36.5
|
1.0
|
|
Cadmium binding site 10 out
of 11 in 1g8g
Go back to
Cadmium Binding Sites List in 1g8g
Cadmium binding site 10 out
of 11 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 10 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd533
b:70.7
occ:0.50
|
OE2
|
B:GLU182
|
2.2
|
28.2
|
1.0
|
OE1
|
B:GLU182
|
2.2
|
24.9
|
1.0
|
O
|
B:ACY562
|
2.3
|
28.3
|
1.0
|
CD
|
B:GLU182
|
2.5
|
26.1
|
1.0
|
C
|
B:ACY562
|
2.9
|
28.3
|
1.0
|
OXT
|
B:ACY562
|
3.0
|
25.3
|
1.0
|
CG
|
B:GLU182
|
4.0
|
26.9
|
1.0
|
NH1
|
B:ARG186
|
4.0
|
37.7
|
1.0
|
NH2
|
B:ARG186
|
4.2
|
34.2
|
1.0
|
CE1
|
B:PHE255
|
4.2
|
24.0
|
1.0
|
CH3
|
B:ACY562
|
4.4
|
29.1
|
1.0
|
CZ
|
B:PHE255
|
4.4
|
21.6
|
1.0
|
OXT
|
B:ACY561
|
4.4
|
36.4
|
1.0
|
NZ
|
B:LYS174
|
4.5
|
25.2
|
1.0
|
CE
|
B:LYS174
|
4.6
|
25.7
|
1.0
|
CZ
|
B:ARG186
|
4.6
|
35.9
|
1.0
|
CB
|
B:GLU182
|
4.8
|
24.4
|
1.0
|
C
|
B:ACY561
|
5.0
|
37.1
|
1.0
|
|
Reference:
T.C.Ullrich,
M.Blaesse,
R.Huber.
Crystal Structure of Atp Sulfurylase From Saccharomyces Cerevisiae, A Key Enzyme in Sulfate Activation. Embo J. V. 20 316 2001.
ISSN: ISSN 0261-4189
PubMed: 11157739
DOI: 10.1093/EMBOJ/20.3.316
Page generated: Fri Jul 19 13:23:36 2024
|