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Cadmium in PDB 1jed: Crystal Structure of Atp Sulfurylase in Complex with Adp

Enzymatic activity of Crystal Structure of Atp Sulfurylase in Complex with Adp

All present enzymatic activity of Crystal Structure of Atp Sulfurylase in Complex with Adp:
2.7.7.4;

Protein crystallography data

The structure of Crystal Structure of Atp Sulfurylase in Complex with Adp, PDB code: 1jed was solved by T.C.Ullrich, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.81 / 2.95
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 186.135, 186.135, 223.253, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 22.7

Other elements in 1jed:

The structure of Crystal Structure of Atp Sulfurylase in Complex with Adp also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Calcium (Ca) 6 atoms
Sodium (Na) 12 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Atp Sulfurylase in Complex with Adp (pdb code 1jed). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 11 binding sites of Cadmium where determined in the Crystal Structure of Atp Sulfurylase in Complex with Adp, PDB code: 1jed:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11;

Cadmium binding site 1 out of 11 in 1jed

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Cadmium binding site 1 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd512

b:29.8
occ:1.00
NE2 A:HIS235 2.4 28.4 1.0
NE2 A:HIS236 2.5 23.0 1.0
O A:ACY557 2.5 21.8 1.0
OXT A:ACY557 2.5 17.8 1.0
OD2 A:ASP168 2.6 30.5 1.0
C A:ACY557 2.8 19.6 1.0
CE1 A:HIS236 3.0 23.0 1.0
CE1 A:HIS235 3.3 27.9 1.0
CD2 A:HIS235 3.4 28.1 1.0
CG A:ASP168 3.5 31.1 1.0
CD2 A:HIS236 3.5 24.0 1.0
OD1 A:ASP168 4.0 33.4 1.0
ND1 A:HIS236 4.1 23.1 1.0
CH3 A:ACY557 4.3 20.1 1.0
CG A:HIS236 4.4 23.6 1.0
O A:HOH1210 4.4 49.9 1.0
ND1 A:HIS235 4.4 26.6 1.0
CG A:HIS235 4.5 27.7 1.0
CB A:ASP168 4.7 31.3 1.0
O A:HOH738 4.9 32.6 1.0

Cadmium binding site 2 out of 11 in 1jed

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Cadmium binding site 2 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd513

b:74.1
occ:0.50
O A:HOH1213 2.7 51.8 1.0
SG A:CYS43 2.8 25.7 1.0
O A:PRO39 2.9 25.1 1.0
C A:PRO39 3.5 23.6 1.0
CA A:PRO39 3.9 23.1 1.0
CB A:PRO39 4.1 21.6 1.0
CB A:CYS43 4.2 25.3 1.0
CG A:LEU227 4.4 31.5 1.0
N A:CYS43 4.4 26.7 1.0
O A:GLY226 4.5 32.6 1.0
N A:ARG40 4.5 21.7 1.0
CA A:CYS43 4.7 27.4 1.0
CB A:LEU42 4.7 26.8 1.0
C A:GLY226 4.7 30.2 1.0
CD2 A:LEU227 4.8 31.2 1.0
CD1 A:LEU227 4.9 29.6 1.0
CA A:ARG40 4.9 23.0 1.0
CA A:GLY226 5.0 28.5 1.0

Cadmium binding site 3 out of 11 in 1jed

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Cadmium binding site 3 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd514

b:34.4
occ:1.00
O A:ACY551 2.3 27.3 1.0
O A:LEU18 2.3 31.7 1.0
O A:HOH673 2.4 6.3 1.0
OE1 A:GLU22 2.6 29.9 1.0
OE2 A:GLU22 2.7 31.6 1.0
OXT A:ACY551 2.8 26.8 1.0
C A:ACY551 2.9 26.6 1.0
CD A:GLU22 3.0 31.7 1.0
C A:LEU18 3.1 30.3 1.0
CA A:LEU18 3.8 28.7 1.0
N A:LYS19 4.0 30.1 1.0
CB A:LEU18 4.3 28.0 1.0
CB A:ASN21 4.3 33.3 1.0
CA A:LYS19 4.4 31.1 1.0
CH3 A:ACY551 4.4 26.4 1.0
OD1 A:ASN21 4.5 36.5 1.0
CG A:GLU22 4.5 32.1 1.0
N A:ASN21 4.5 33.5 1.0
C A:LYS19 4.6 31.7 1.0
CG A:ASN21 4.7 35.0 1.0
N A:LYS20 4.7 31.4 1.0
O A:ALA17 4.9 25.5 1.0
N A:GLU22 5.0 32.1 1.0
O A:HOH1192 5.0 37.0 1.0

Cadmium binding site 4 out of 11 in 1jed

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Cadmium binding site 4 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd515

b:34.1
occ:1.00
O A:ACY555 2.3 23.4 1.0
OE1 A:GLU182 2.6 26.5 1.0
C A:ACY555 2.9 22.8 1.0
OXT A:ACY555 2.9 20.9 1.0
OE2 A:GLU182 3.3 28.4 1.0
CD A:GLU182 3.3 26.9 1.0
NH1 A:ARG186 4.2 21.2 1.0
NZ A:LYS174 4.3 17.6 1.0
CH3 A:ACY555 4.4 23.3 1.0
CE A:LYS174 4.6 16.8 1.0
CG A:GLU182 4.7 26.0 1.0
CE1 A:PHE255 4.8 20.5 1.0
CZ A:PHE255 4.8 21.3 1.0
OXT A:ACY554 4.9 24.8 1.0
O A:HOH1110 4.9 18.0 1.0

Cadmium binding site 5 out of 11 in 1jed

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Cadmium binding site 5 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd516

b:13.4
occ:0.70
OD1 A:ASP189 2.0 20.2 1.0
O A:ACY556 2.0 25.4 1.0
O A:ACY552 2.1 18.9 1.0
OXT A:ACY552 2.2 19.2 1.0
OD2 A:ASP189 2.3 22.7 1.0
C A:ACY552 2.4 18.7 1.0
CG A:ASP189 2.4 20.8 1.0
C A:ACY556 2.5 26.4 1.0
OXT A:ACY556 2.5 24.8 1.0
CH3 A:ACY556 3.9 25.6 1.0
CB A:ASP189 3.9 19.8 1.0
CH3 A:ACY552 4.0 17.2 1.0
O A:HOH756 4.7 20.1 1.0
CD A:ARG190 4.7 25.5 1.0
CG A:ARG190 4.8 21.6 1.0
CA A:ASP189 4.9 19.7 1.0
N A:ASP189 4.9 21.7 1.0

Cadmium binding site 6 out of 11 in 1jed

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Cadmium binding site 6 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd524

b:43.3
occ:1.00
O A:HOH681 2.1 24.4 1.0
O A:HOH732 2.2 49.9 1.0
O A:ACY565 2.3 32.4 1.0
OXT A:ACY565 2.4 33.2 1.0
C A:ACY565 2.6 33.6 1.0
OD2 A:ASP71 3.0 36.8 1.0
CG A:ASP71 3.4 35.2 1.0
OD1 A:ASP71 3.7 37.0 1.0
O A:HOH699 3.8 26.4 1.0
CH3 A:ACY565 4.1 33.0 1.0
CB A:ASP71 4.3 32.2 1.0
NE A:ARG73 4.7 19.0 1.0
O A:HOH881 4.7 41.4 1.0
CD A:ARG73 4.7 20.5 1.0
CA A:ASP71 4.9 29.1 1.0
O A:HOH1154 4.9 24.4 1.0
O A:ASP71 4.9 30.9 1.0

Cadmium binding site 7 out of 11 in 1jed

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Cadmium binding site 7 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd530

b:30.8
occ:1.00
OXT B:ACY564 2.2 19.1 1.0
OD2 B:ASP168 2.3 28.1 1.0
NE2 B:HIS235 2.4 29.5 1.0
NE2 B:HIS236 2.4 26.8 1.0
O B:ACY564 2.5 21.1 1.0
C B:ACY564 2.7 20.2 1.0
CE1 B:HIS236 3.0 26.0 1.0
CE1 B:HIS235 3.3 30.1 1.0
CG B:ASP168 3.3 29.4 1.0
CD2 B:HIS235 3.4 29.3 1.0
CD2 B:HIS236 3.4 26.4 1.0
OD1 B:ASP168 3.8 32.8 1.0
ND1 B:HIS236 4.1 26.0 1.0
CH3 B:ACY564 4.2 18.0 1.0
CG B:HIS236 4.3 26.7 1.0
O B:HOH936 4.4 41.3 1.0
ND1 B:HIS235 4.5 31.1 1.0
CB B:ASP168 4.5 30.0 1.0
CG B:HIS235 4.5 29.2 1.0

Cadmium binding site 8 out of 11 in 1jed

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Cadmium binding site 8 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd531

b:92.9
occ:0.50
SG B:CYS43 2.7 23.1 1.0
O B:HOH1117 2.7 44.9 1.0
O B:HOH1142 2.9 29.4 1.0
O B:PRO39 3.0 23.0 1.0
O B:HOH949 3.5 18.9 1.0
C B:PRO39 3.9 22.5 1.0
CB B:CYS43 4.1 24.2 1.0
N B:CYS43 4.2 25.5 1.0
CA B:PRO39 4.3 22.6 1.0
CA B:CYS43 4.5 24.1 1.0
CB B:LEU42 4.5 27.2 1.0
CB B:PRO39 4.6 21.6 1.0
O B:GLY226 4.6 32.8 1.0
C B:GLY226 4.8 30.2 1.0
CA B:GLY226 4.8 27.4 1.0
CG B:LEU227 4.8 30.8 1.0
C B:LEU42 4.8 26.5 1.0
N B:ARG40 4.9 22.1 1.0

Cadmium binding site 9 out of 11 in 1jed

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Cadmium binding site 9 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd532

b:33.6
occ:1.00
OE1 B:GLU22 1.9 29.5 1.0
OE2 B:GLU22 2.3 33.7 1.0
CD B:GLU22 2.4 30.9 1.0
O B:ACY558 2.4 29.4 1.0
O B:LEU18 2.5 28.4 1.0
OXT B:ACY558 2.8 29.0 1.0
C B:ACY558 2.9 29.4 1.0
C B:LEU18 3.4 28.8 1.0
CG B:GLU22 3.8 30.6 1.0
N B:LYS19 4.2 30.6 1.0
CA B:LEU18 4.2 28.0 1.0
CA B:LYS19 4.3 30.9 1.0
CB B:ASN21 4.4 32.6 1.0
CH3 B:ACY558 4.4 29.7 1.0
C B:LYS19 4.6 30.7 1.0
CB B:LEU18 4.7 27.1 1.0
N B:GLU22 4.7 32.7 1.0
N B:ASN21 4.7 32.4 1.0
CB B:GLU22 4.9 31.0 1.0
OD1 B:ASN21 4.9 34.6 1.0
N B:LYS20 5.0 30.6 1.0

Cadmium binding site 10 out of 11 in 1jed

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Cadmium binding site 10 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd533

b:45.5
occ:0.50
OE1 B:GLU182 2.0 26.3 1.0
O B:ACY562 2.6 22.0 1.0
OE2 B:GLU182 2.6 24.2 1.0
CD B:GLU182 2.6 25.2 1.0
C B:ACY562 3.5 21.3 1.0
OXT B:ACY562 3.8 21.4 1.0
OXT B:ACY561 3.8 28.7 1.0
CG B:GLU182 4.1 23.8 1.0
C B:ACY561 4.2 26.9 1.0
NZ B:LYS174 4.4 20.4 1.0
NH1 B:ARG186 4.4 21.8 1.0
O B:ACY561 4.6 26.8 1.0
NH2 B:ARG186 4.6 22.6 1.0
CE B:LYS174 4.7 16.9 1.0
CH3 B:ACY562 4.9 20.3 1.0
CH3 B:ACY561 5.0 23.3 1.0

Cadmium binding site 11 out of 11 in 1jed

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Cadmium binding site 11 out of 11 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd534

b:12.1
occ:0.70
OD1 B:ASP189 2.0 19.8 1.0
O B:ACY563 2.1 28.5 1.0
OXT B:ACY559 2.1 18.2 1.0
OXT B:ACY563 2.3 26.6 1.0
OD2 B:ASP189 2.3 23.7 1.0
O B:ACY559 2.3 17.0 1.0
C B:ACY563 2.4 28.6 1.0
C B:ACY559 2.5 18.1 1.0
CG B:ASP189 2.5 19.8 1.0
CH3 B:ACY563 4.0 29.0 1.0
CB B:ASP189 4.0 18.6 1.0
CH3 B:ACY559 4.0 19.0 1.0
O B:HOH809 4.4 50.9 1.0
CD B:ARG190 4.7 23.6 1.0
CG B:ARG190 4.7 20.3 1.0
O B:HOH724 4.7 14.9 1.0
CA B:ASP189 4.9 18.9 1.0

Reference:

T.C.Ullrich, R.Huber. The Complex Structures of Atp Sulfurylase with Thiosulfate, Adp and Chlorate Reveal New Insights in Inhibitory Effects and the Catalytic Cycle. J.Mol.Biol. V. 313 1117 2001.
ISSN: ISSN 0022-2836
PubMed: 11700067
DOI: 10.1006/JMBI.2001.5098
Page generated: Wed Oct 28 09:53:39 2020
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