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Cadmium in PDB 1g8h: Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi

Enzymatic activity of Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi

All present enzymatic activity of Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi:
2.7.7.4;

Protein crystallography data

The structure of Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi, PDB code: 1g8h 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) 24.87 / 2.80
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 186.011, 186.011, 223.812, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 24.5

Other elements in 1g8h:

The structure of Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Calcium (Ca) 6 atoms
Sodium (Na) 12 atoms

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 Ternary Product Complex with Aps and Ppi (pdb code 1g8h). 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 Ternary Product Complex with Aps and Ppi, PDB code: 1g8h:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 11 in 1g8h

Go back to Cadmium Binding Sites List in 1g8h
Cadmium binding site 1 out of 11 in the Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi


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 Ternary Product Complex with Aps and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd512

b:32.9
occ:1.00
 NE2 A:HIS235 2.4 29.3 1.0
NE2 A:HIS236 2.4 20.7 1.0
OD2 A:ASP168 2.5 30.2 1.0
OXT A:ACY556 2.6 28.9 1.0
O A:ACY556 2.6 31.9 1.0
C A:ACY556 2.9 31.0 1.0
CE1 A:HIS236 3.0 20.9 1.0
CE1 A:HIS235 3.3 28.0 1.0
CD2 A:HIS235 3.4 28.1 1.0
CG A:ASP168 3.5 29.9 1.0
CD2 A:HIS236 3.5 21.5 1.0
O A:HOH991 3.6 39.3 1.0
OD1 A:ASP168 4.0 32.5 1.0
O A:HOH705 4.0 26.7 1.0
ND1 A:HIS236 4.1 20.8 1.0
CG A:HIS236 4.4 22.0 1.0
CH3 A:ACY556 4.4 30.5 1.0
ND1 A:HIS235 4.5 28.5 1.0
CG A:HIS235 4.5 27.7 1.0
CB A:ASP168 4.6 29.4 1.0
NH1 A:ARG173 4.7 26.2 1.0

Cadmium binding site 2 out of 11 in 1g8h

Go back to Cadmium Binding Sites List in 1g8h
Cadmium binding site 2 out of 11 in the Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi


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 Ternary Product Complex with Aps and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd513

b:0.4
occ:1.00
 SG A:CYS43 2.5 27.9 1.0
O A:PRO39 2.6 26.7 1.0
O A:HOH1050 3.3 34.7 1.0
C A:PRO39 3.4 25.2 1.0
N A:CYS43 3.6 23.4 1.0
CB A:CYS43 3.6 25.3 1.0
CA A:CYS43 3.9 24.2 1.0
CB A:LEU42 4.1 26.9 1.0
CA A:PRO39 4.1 25.2 1.0
O A:GLY226 4.1 31.1 1.0
C A:LEU42 4.3 23.3 1.0
N A:ARG40 4.3 24.3 1.0
O A:HOH915 4.5 22.2 1.0
CB A:PRO39 4.5 25.2 1.0
CA A:ARG40 4.5 24.8 1.0
CA A:LEU42 4.6 24.9 1.0
C A:GLY226 4.7 29.3 1.0
N A:LEU42 4.8 25.2 1.0
C A:ARG40 4.9 25.8 1.0
O A:ARG40 5.0 25.0 1.0
CA A:GLY226 5.0 27.3 1.0

Cadmium binding site 3 out of 11 in 1g8h

Go back to Cadmium Binding Sites List in 1g8h
Cadmium binding site 3 out of 11 in the Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi


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 Ternary Product Complex with Aps and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd514

b:36.8
occ:1.00
 O A:LEU18 2.2 30.7 1.0
O A:ACY550 2.2 27.3 1.0
OE1 A:GLU22 2.6 32.7 1.0
OE2 A:GLU22 2.7 34.4 1.0
C A:ACY550 3.0 25.2 1.0
CD A:GLU22 3.0 33.4 1.0
OXT A:ACY550 3.1 26.0 1.0
C A:LEU18 3.2 30.9 1.0
CA A:LEU18 4.0 30.4 1.0
CB A:ASN21 4.1 34.6 1.0
N A:LYS19 4.1 31.1 1.0
N A:ASN21 4.2 33.6 1.0
OD1 A:ASN21 4.3 37.5 1.0
CA A:LYS19 4.4 33.4 1.0
CH3 A:ACY550 4.5 22.4 1.0
CG A:ASN21 4.5 35.3 1.0
N A:LYS20 4.5 33.3 1.0
CG A:GLU22 4.6 33.8 1.0
C A:LYS19 4.6 34.0 1.0
CB A:LEU18 4.6 30.1 1.0
CA A:ASN21 4.7 34.0 1.0
N A:GLU22 4.8 33.4 1.0
O A:ALA17 4.9 28.2 1.0

Cadmium binding site 4 out of 11 in 1g8h

Go back to Cadmium Binding Sites List in 1g8h
Cadmium binding site 4 out of 11 in the Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi


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 Ternary Product Complex with Aps and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd515

b:78.3
occ:1.00
 O A:ACY554 2.7 21.3 1.0
OXT A:ACY554 2.8 19.7 1.0
OE1 A:GLU182 3.0 22.0 1.0
C A:ACY554 3.1 22.2 1.0
OE2 A:GLU182 3.5 24.6 1.0
CD A:GLU182 3.6 23.6 1.0
NZ A:LYS174 3.8 29.2 1.0
CE A:LYS174 4.0 27.6 1.0
CE1 A:PHE255 4.6 19.6 1.0
CZ A:PHE255 4.6 18.9 1.0
CH3 A:ACY554 4.6 23.0 1.0
NH1 A:ARG186 4.7 26.9 1.0
CG A:GLU182 4.9 21.6 1.0

Cadmium binding site 5 out of 11 in 1g8h

Go back to Cadmium Binding Sites List in 1g8h
Cadmium binding site 5 out of 11 in the Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi


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 Ternary Product Complex with Aps and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd516

b:43.5
occ:1.00
 OD1 A:ASP189 2.2 32.7 1.0
O A:ACY555 2.4 46.5 1.0
OXT A:ACY551 2.4 36.2 1.0
OD2 A:ASP189 2.6 35.2 1.0
OXT A:ACY555 2.6 49.4 1.0
CG A:ASP189 2.7 32.0 1.0
C A:ACY555 2.7 48.0 1.0
O A:ACY551 2.9 38.5 1.0
C A:ACY551 2.9 37.5 1.0
CH3 A:ACY555 4.1 48.0 1.0
CB A:ASP189 4.1 27.9 1.0
O A:HOH724 4.4 19.6 1.0
CH3 A:ACY551 4.5 35.9 1.0
O A:HOH1090 4.9 36.8 1.0
CD A:ARG190 4.9 31.0 1.0
CG A:ARG190 5.0 28.2 1.0

Cadmium binding site 6 out of 11 in 1g8h

Go back to Cadmium Binding Sites List in 1g8h
Cadmium binding site 6 out of 11 in the Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi


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 Ternary Product Complex with Aps and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd524

b:56.4
occ:1.00
 O A:ACY567 1.9 21.6 1.0
C A:ACY567 2.6 25.1 1.0
CH3 A:ACY567 2.7 24.4 1.0
OD2 A:ASP71 2.9 44.5 1.0
CG A:ASP71 3.5 42.9 1.0
OXT A:ACY567 3.8 27.5 1.0
O A:HOH762 3.9 30.9 1.0
OD1 A:ASP71 4.1 45.8 1.0
O A:HOH995 4.1 50.4 1.0
CB A:ASP71 4.2 38.7 1.0
CA A:ASP71 4.8 34.8 1.0
O A:ASP71 4.8 34.6 1.0
NE A:ARG73 5.0 25.7 1.0
CD A:ARG73 5.0 25.4 1.0

Cadmium binding site 7 out of 11 in 1g8h

Go back to Cadmium Binding Sites List in 1g8h
Cadmium binding site 7 out of 11 in the Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi


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 Ternary Product Complex with Aps and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd530

b:38.2
occ:1.00
 OD2 B:ASP168 2.3 30.8 1.0
OXT B:ACY566 2.3 25.0 1.0
NE2 B:HIS236 2.4 24.4 1.0
NE2 B:HIS235 2.5 30.2 1.0
O B:ACY566 2.6 22.8 1.0
C B:ACY566 2.7 25.6 1.0
CE1 B:HIS236 3.1 23.9 1.0
CG B:ASP168 3.3 30.9 1.0
CD2 B:HIS235 3.4 29.6 1.0
CD2 B:HIS236 3.4 22.3 1.0
CE1 B:HIS235 3.5 30.7 1.0
OD1 B:ASP168 3.8 34.3 1.0
O B:HOH980 3.9 41.4 1.0
O B:HOH646 4.0 18.1 1.0
ND1 B:HIS236 4.2 24.0 1.0
CH3 B:ACY566 4.3 25.7 1.0
CG B:HIS236 4.4 24.6 1.0
CB B:ASP168 4.4 28.9 1.0
NH1 B:ARG173 4.5 23.2 1.0
ND1 B:HIS235 4.6 31.8 1.0
CG B:HIS235 4.6 29.8 1.0

Cadmium binding site 8 out of 11 in 1g8h

Go back to Cadmium Binding Sites List in 1g8h
Cadmium binding site 8 out of 11 in the Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi


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 Ternary Product Complex with Aps and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd531

b:0.8
occ:1.00
 SG B:CYS43 2.5 27.3 1.0
O B:HOH1225 2.7 56.7 1.0
O B:PRO39 2.9 28.4 1.0
O B:HOH933 3.5 39.5 1.0
N B:CYS43 3.7 24.9 1.0
CB B:CYS43 3.7 26.3 1.0
C B:PRO39 3.7 25.8 1.0
O B:HOH662 3.9 16.4 1.0
CA B:CYS43 4.0 24.3 1.0
O B:GLY226 4.0 30.9 1.0
CB B:LEU42 4.1 28.7 1.0
C B:LEU42 4.3 25.4 1.0
CA B:PRO39 4.3 25.7 1.0
C B:GLY226 4.6 28.9 1.0
N B:ARG40 4.7 24.3 1.0
CA B:LEU42 4.7 26.2 1.0
CB B:PRO39 4.7 25.9 1.0
CA B:GLY226 4.8 27.4 1.0
CA B:ARG40 4.8 24.6 1.0
O B:HOH711 4.9 26.8 1.0
N B:LEU42 4.9 25.9 1.0

Cadmium binding site 9 out of 11 in 1g8h

Go back to Cadmium Binding Sites List in 1g8h
Cadmium binding site 9 out of 11 in the Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi


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 Ternary Product Complex with Aps and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd532

b:40.5
occ:1.00
 OE1 B:GLU22 1.8 34.9 1.0
O B:LEU18 2.3 31.3 1.0
O B:ACY560 2.3 30.8 1.0
CD B:GLU22 2.4 33.7 1.0
OE2 B:GLU22 2.4 35.9 1.0
C B:ACY560 3.0 30.1 1.0
OXT B:ACY560 3.0 31.1 1.0
C B:LEU18 3.4 32.5 1.0
CG B:GLU22 3.9 33.7 1.0
N B:LYS19 4.3 34.0 1.0
CB B:ASN21 4.3 34.4 1.0
CA B:LYS19 4.3 34.7 1.0
CA B:LEU18 4.3 31.3 1.0
CH3 B:ACY560 4.5 29.7 1.0
N B:GLU22 4.5 34.3 1.0
N B:ASN21 4.6 33.5 1.0
C B:LYS19 4.6 34.3 1.0
OD1 B:ASN21 4.8 35.7 1.0
N B:LYS20 4.8 34.4 1.0
CB B:LEU18 4.9 29.8 1.0
CG B:ASN21 4.9 35.7 1.0
CA B:ASN21 4.9 34.2 1.0
CB B:GLU22 4.9 35.0 1.0

Cadmium binding site 10 out of 11 in 1g8h

Go back to Cadmium Binding Sites List in 1g8h
Cadmium binding site 10 out of 11 in the Atp Sulfurylase From S. Cerevisiae: the Ternary Product Complex with Aps and Ppi


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 Ternary Product Complex with Aps and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd533

b:47.2
occ:1.00
 OE1 B:GLU182 2.4 25.9 1.0
OE2 B:GLU182 2.9 25.7 1.0
CD B:GLU182 3.0 26.2 1.0
O B:ACY564 3.7 22.9 1.0
NZ B:LYS174 3.8 29.9 1.0
OXT B:ACY564 3.9 22.9 1.0
C B:ACY564 4.1 25.4 1.0
CE B:LYS174 4.2 28.1 1.0
O B:ACY563 4.2 33.1 1.0
OXT B:ACY563 4.3 34.6 1.0
C B:ACY563 4.4 33.8 1.0
CG B:GLU182 4.5 24.0 1.0
NH1 B:ARG186 4.7 29.2 1.0
CE1 B:PHE255 4.8 20.9 1.0
CZ B:PHE255 4.9 19.5 1.0
NH2 B:ARG186 4.9 30.3 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 13:23:42 2024

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