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Cadmium in PDB 1jec: Crystal Structure of Atp Sulfurylase in Complex with Thiosulfate

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

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

Protein crystallography data

The structure of Crystal Structure of Atp Sulfurylase in Complex with Thiosulfate, PDB code: 1jec 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) 24.34 / 2.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 186.688, 186.688, 115.900, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 23.6

Other elements in 1jec:

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

Magnesium (Mg) 1 atom
Calcium (Ca) 3 atoms
Sodium (Na) 3 atoms

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 7 in 1jec

Go back to Cadmium Binding Sites List in 1jec
Cadmium binding site 1 out of 7 in the Crystal Structure of Atp Sulfurylase in Complex with Thiosulfate


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 Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd512

b:50.1
occ:1.00
 OD2 A:ASP168 2.5 33.8 1.0
NE2 A:HIS235 2.5 32.8 1.0
CE1 A:HIS236 2.6 31.6 1.0
O2 A:SO4525 2.6 99.8 1.0
OXT A:ACY535 2.6 35.3 1.0
O A:ACY535 2.6 39.0 1.0
NE2 A:HIS236 2.8 32.4 1.0
C A:ACY535 2.9 38.6 1.0
CG A:ASP168 3.4 32.0 1.0
CD2 A:HIS235 3.5 32.1 1.0
CE1 A:HIS235 3.5 33.9 1.0
ND1 A:HIS236 3.7 30.5 1.0
O A:HOH1034 3.8 47.2 1.0
S A:SO4525 3.8 99.1 1.0
OD1 A:ASP168 3.8 31.7 1.0
CD2 A:HIS236 4.0 29.1 1.0
O3 A:SO4525 4.0 99.5 1.0
O4 A:SO4525 4.3 99.4 1.0
CG A:HIS236 4.4 30.6 1.0
CH3 A:ACY535 4.5 35.7 1.0
CB A:ASP168 4.6 30.5 1.0
ND1 A:HIS235 4.6 35.9 1.0
CG A:HIS235 4.6 33.9 1.0
NH1 A:ARG173 4.7 31.0 1.0
O1 A:SO4525 5.0 99.5 1.0

Cadmium binding site 2 out of 7 in 1jec

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Cadmium binding site 2 out of 7 in the Crystal Structure of Atp Sulfurylase in Complex with Thiosulfate


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 Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd513

b:55.6
occ:0.50
 O A:HOH827 2.4 64.4 1.0
O A:PRO39 2.4 33.6 1.0
SG A:CYS43 2.6 26.4 1.0
O A:HOH966 2.6 52.2 1.0
O A:HOH1035 2.8 42.6 1.0
C A:PRO39 3.4 31.5 1.0
O A:HOH881 3.4 41.9 1.0
N A:CYS43 3.8 28.9 1.0
CA A:PRO39 4.0 32.5 1.0
CB A:CYS43 4.0 25.7 1.0
CB A:LEU42 4.1 30.1 1.0
CB A:PRO39 4.2 33.0 1.0
CA A:CYS43 4.3 27.7 1.0
O A:HOH673 4.5 28.2 1.0
N A:ARG40 4.5 28.6 1.0
C A:LEU42 4.6 30.2 1.0
CG A:LEU227 4.6 33.1 1.0
CA A:ARG40 4.8 28.0 1.0
CD2 A:LEU227 4.8 30.3 1.0
CA A:LEU42 4.8 29.3 1.0
CD1 A:LEU227 5.0 31.4 1.0
N A:LEU42 5.0 27.4 1.0

Cadmium binding site 3 out of 7 in 1jec

Go back to Cadmium Binding Sites List in 1jec
Cadmium binding site 3 out of 7 in the Crystal Structure of Atp Sulfurylase in Complex with Thiosulfate


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 Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd514

b:32.4
occ:1.00
 O A:ACY526 2.3 31.2 1.0
OE1 A:GLU22 2.3 33.2 1.0
O A:HOH849 2.3 28.2 1.0
O A:LEU18 2.3 28.6 1.0
OXT A:ACY526 2.4 29.4 1.0
OE2 A:GLU22 2.5 31.6 1.0
C A:ACY526 2.7 29.8 1.0
CD A:GLU22 2.8 31.5 1.0
C A:LEU18 3.2 28.9 1.0
N A:LYS19 4.0 29.4 1.0
CA A:LEU18 4.1 28.1 1.0
CA A:LYS19 4.2 28.9 1.0
CH3 A:ACY526 4.2 28.2 1.0
CG A:GLU22 4.3 29.6 1.0
O A:HOH970 4.4 37.8 1.0
OD1 A:ASN21 4.5 31.2 1.0
CB A:ASN21 4.5 27.2 1.0
C A:LYS19 4.6 29.3 1.0
N A:ASN21 4.6 28.6 1.0
CB A:LEU18 4.6 27.1 1.0
N A:LYS20 4.7 27.9 1.0
N A:GLU22 4.9 31.7 1.0
CG A:ASN21 4.9 28.5 1.0

Cadmium binding site 4 out of 7 in 1jec

Go back to Cadmium Binding Sites List in 1jec
Cadmium binding site 4 out of 7 in the Crystal Structure of Atp Sulfurylase in Complex with Thiosulfate


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 Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd515

b:36.6
occ:0.50
 OE1 A:GLU182 1.6 29.5 1.0
O A:ACY533 1.8 32.5 1.0
C A:ACY533 2.6 34.5 1.0
CD A:GLU182 2.7 32.4 1.0
OXT A:ACY533 2.9 38.0 1.0
OE2 A:GLU182 3.2 35.0 1.0
NZ A:LYS174 3.9 28.4 1.0
CG A:GLU182 4.0 26.8 1.0
CH3 A:ACY533 4.1 32.5 1.0
CE A:LYS174 4.3 28.3 1.0
NH1 A:ARG186 4.4 28.5 1.0
OXT A:ACY529 4.5 51.3 1.0
CE1 A:PHE255 4.8 22.2 1.0
CZ A:PHE255 4.8 21.6 1.0
C A:ACY529 5.0 52.9 1.0

Cadmium binding site 5 out of 7 in 1jec

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Cadmium binding site 5 out of 7 in the Crystal Structure of Atp Sulfurylase in Complex with Thiosulfate


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 Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd516

b:43.3
occ:1.00
 OXT A:ACY527 2.4 42.8 1.0
O A:ACY534 2.4 49.8 1.0
O A:ACY527 2.4 40.0 1.0
OD2 A:ASP189 2.4 38.9 1.0
OXT A:ACY534 2.7 51.0 1.0
OD1 A:ASP189 2.7 37.6 1.0
C A:ACY527 2.7 41.0 1.0
C A:ACY534 2.8 51.5 1.0
CG A:ASP189 2.9 36.5 1.0
CH3 A:ACY527 4.3 38.8 1.0
O A:HOH968 4.3 38.3 1.0
CB A:ASP189 4.4 33.3 1.0
CH3 A:ACY534 4.4 52.0 1.0
CD A:ARG190 4.9 23.1 1.0
CG A:ARG190 4.9 25.2 1.0

Cadmium binding site 6 out of 7 in 1jec

Go back to Cadmium Binding Sites List in 1jec
Cadmium binding site 6 out of 7 in the Crystal Structure of Atp Sulfurylase in Complex with Thiosulfate


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 Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd518

b:74.0
occ:0.70
 OE2 A:GLU409 2.4 55.6 1.0
O A:HOH1038 2.5 43.9 1.0
CD A:GLU409 3.5 50.8 1.0
OE1 A:GLU409 4.0 51.0 1.0
CG A:GLU409 4.8 46.1 1.0
CB A:GLU409 4.9 37.4 1.0

Cadmium binding site 7 out of 7 in 1jec

Go back to Cadmium Binding Sites List in 1jec
Cadmium binding site 7 out of 7 in the Crystal Structure of Atp Sulfurylase in Complex with Thiosulfate


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 Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd600

b:40.6
occ:1.00
 S2 A:THJ540 2.6 27.1 1.0
O A:HOH1033 2.7 29.9 1.0
O1 A:THJ540 3.2 27.6 1.0
S1 A:THJ540 3.5 28.7 1.0
O A:HOH1027 3.7 45.1 1.0
O A:HOH714 3.8 41.7 1.0
O2 A:THJ540 4.0 30.6 1.0
O A:HOH770 4.1 37.1 1.0
NA A:NA1537 4.2 40.6 1.0
O A:GLN195 4.3 25.0 1.0
CD2 A:HIS292 4.4 27.9 1.0
O A:HOH638 4.4 25.6 1.0
O3 A:THJ540 4.8 29.3 1.0
NE2 A:HIS292 4.9 29.6 1.0
CA A:GLY289 4.9 28.7 1.0
CG A:HIS292 5.0 29.5 1.0
CA A:HIS292 5.0 30.0 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: Fri Jul 19 13:37:44 2024

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