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Cadmium in PDB 4c1k: Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase

Enzymatic activity of Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase

All present enzymatic activity of Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase:
2.5.1.54;

Protein crystallography data

The structure of Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase, PDB code: 4c1k was solved by A.R.Nazmi, L.R.Schofield, R.C.J.Dobson, G.B.Jameson, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.65 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.449, 79.670, 144.215, 90.00, 119.69, 90.00
R / Rfree (%) 18.859 / 23.088

Other elements in 4c1k:

The structure of Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase (pdb code 4c1k). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase, PDB code: 4c1k:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 4c1k

Go back to Cadmium Binding Sites List in 4c1k
Cadmium binding site 1 out of 6 in the Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase


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 Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1265

b:28.4
occ:0.50
 O A:HOH2009 1.9 26.0 0.5
OE2 A:GLU227 1.9 28.2 1.0
OD2 A:ASP238 2.0 52.8 1.0
SG A:CYS31 2.5 36.0 1.0
NE2 A:HIS201 2.5 36.1 1.0
CD A:GLU227 2.9 27.6 1.0
CG A:ASP238 3.1 55.2 1.0
CE1 A:HIS201 3.1 37.0 1.0
OE1 A:GLU227 3.1 28.4 1.0
CB A:CYS31 3.3 31.1 1.0
O1 A:PEP1264 3.6 24.2 0.5
CD2 A:HIS201 3.7 37.7 1.0
CB A:ASP238 3.8 53.2 1.0
NE2 A:GLN241 4.0 41.0 1.0
CA A:CYS31 4.1 31.2 1.0
OD1 A:ASP238 4.1 48.3 1.0
C1 A:PEP1264 4.1 22.9 0.5
CG A:GLU227 4.3 26.1 1.0
NZ A:LYS60 4.3 33.9 0.6
ND1 A:HIS201 4.3 37.2 1.0
C2 A:PEP1264 4.5 23.1 0.5
C3 A:PEP1264 4.6 23.6 0.5
CG A:HIS201 4.6 33.4 1.0
O2' A:PEP1264 4.8 21.4 0.5
NH2 A:ARG55 4.8 42.1 1.0
C A:CYS31 5.0 30.6 1.0

Cadmium binding site 2 out of 6 in 4c1k

Go back to Cadmium Binding Sites List in 4c1k
Cadmium binding site 2 out of 6 in the Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase


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 Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1264

b:25.9
occ:0.50
 O B:HOH2003 1.9 15.3 0.5
OE2 B:GLU227 2.3 32.9 1.0
OD2 B:ASP238 2.4 50.6 1.0
NE2 B:HIS201 2.4 32.6 1.0
SG B:CYS31 2.5 33.3 1.0
OE1 B:GLU227 2.9 26.1 1.0
CD B:GLU227 2.9 29.1 1.0
CE1 B:HIS201 3.1 33.0 1.0
CB B:CYS31 3.2 30.5 1.0
CG B:ASP238 3.5 51.7 1.0
CD2 B:HIS201 3.6 32.7 1.0
O2' B:PEP1263 3.8 22.1 0.5
CB B:ASP238 4.0 50.1 1.0
CA B:CYS31 4.0 28.4 1.0
NE2 B:GLN241 4.0 36.4 1.0
ND1 B:HIS201 4.2 33.8 1.0
NZ B:LYS60 4.3 40.9 0.6
C1 B:PEP1263 4.4 21.9 0.5
CG B:GLU227 4.4 26.4 1.0
C2 B:PEP1263 4.5 22.6 0.5
CG B:HIS201 4.5 30.1 1.0
OD1 B:ASP238 4.5 52.0 1.0
C3 B:PEP1263 4.6 22.4 0.5
NH2 B:ARG55 4.8 35.5 1.0
C B:CYS31 4.9 29.0 1.0
O B:CYS31 5.0 30.1 1.0

Cadmium binding site 3 out of 6 in 4c1k

Go back to Cadmium Binding Sites List in 4c1k
Cadmium binding site 3 out of 6 in the Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase


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 Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1265

b:38.4
occ:0.50
 OE2 C:GLU227 2.1 38.8 1.0
O C:HOH2005 2.2 32.8 0.5
SG C:CYS31 2.4 38.2 1.0
NE2 C:HIS201 2.6 39.0 1.0
OD2 C:ASP238 2.7 57.6 1.0
CD C:GLU227 3.0 35.6 1.0
CB C:CYS31 3.2 35.3 1.0
OE1 C:GLU227 3.2 36.1 1.0
CE1 C:HIS201 3.2 37.2 1.0
CG C:ASP238 3.6 62.5 1.0
CD2 C:HIS201 3.7 37.0 1.0
O1 C:PEP1263 3.7 23.5 0.5
NE2 C:GLN241 3.8 43.6 1.0
CB C:ASP238 3.9 64.4 1.0
CA C:CYS31 4.0 32.0 1.0
C1 C:PEP1263 4.2 21.8 0.5
NZ C:LYS60 4.2 39.3 0.6
C2 C:PEP1263 4.3 21.6 0.5
ND1 C:HIS201 4.4 36.9 1.0
CG C:GLU227 4.4 33.5 1.0
C3 C:PEP1263 4.4 21.0 0.5
CG C:HIS201 4.6 33.1 1.0
NH2 C:ARG55 4.7 35.6 1.0
OD1 C:ASP238 4.7 58.1 1.0
O2 C:PEP1263 4.8 22.4 0.5
C C:CYS31 4.9 31.4 1.0
O2' C:PEP1263 4.9 18.4 0.5
CD C:GLN241 5.0 42.5 1.0

Cadmium binding site 4 out of 6 in 4c1k

Go back to Cadmium Binding Sites List in 4c1k
Cadmium binding site 4 out of 6 in the Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase


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 Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd1265

b:25.9
occ:0.50
 O D:HOH2019 1.7 24.5 0.5
OE2 D:GLU227 2.1 33.9 1.0
OD2 D:ASP238 2.3 52.6 1.0
SG D:CYS31 2.5 32.8 1.0
NE2 D:HIS201 2.6 34.5 1.0
OE1 D:GLU227 2.8 30.4 1.0
CD D:GLU227 2.8 29.2 1.0
CE1 D:HIS201 3.0 35.3 1.0
CB D:CYS31 3.2 27.5 1.0
CG D:ASP238 3.4 53.0 1.0
CD2 D:HIS201 3.8 34.1 1.0
O1 D:PEP1264 3.8 18.4 0.5
CB D:ASP238 3.9 49.0 1.0
CA D:CYS31 3.9 25.9 1.0
NE2 D:GLN241 4.0 39.3 1.0
ND1 D:HIS201 4.2 34.4 1.0
CG D:GLU227 4.3 26.3 1.0
C1 D:PEP1264 4.4 20.4 0.5
OD1 D:ASP238 4.4 53.1 1.0
CG D:HIS201 4.6 31.7 1.0
NZ D:LYS60 4.6 31.6 0.6
C2 D:PEP1264 4.7 21.8 0.5
NH2 D:ARG55 4.7 35.2 1.0
C D:CYS31 4.9 25.8 1.0

Cadmium binding site 5 out of 6 in 4c1k

Go back to Cadmium Binding Sites List in 4c1k
Cadmium binding site 5 out of 6 in the Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase


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 Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd1266

b:38.4
occ:0.50
 OE2 E:GLU227 2.2 41.7 1.0
OD2 E:ASP238 2.3 70.4 1.0
SG E:CYS31 2.5 40.0 1.0
NE2 E:HIS201 2.6 42.6 1.0
CE1 E:HIS201 3.0 41.6 1.0
CD E:GLU227 3.1 35.0 1.0
OE1 E:GLU227 3.2 36.8 1.0
CB E:CYS31 3.2 35.3 1.0
CG E:ASP238 3.4 72.1 1.0
O1 E:PEP1264 3.5 23.4 0.5
CD2 E:HIS201 3.8 39.8 1.0
CB E:ASP238 3.9 72.0 1.0
NE2 E:GLN241 3.9 38.9 1.0
CA E:CYS31 4.0 33.3 1.0
NZ E:LYS60 4.0 33.6 0.6
C1 E:PEP1264 4.1 22.9 0.5
ND1 E:HIS201 4.2 40.5 1.0
C2 E:PEP1264 4.3 24.0 0.5
OD1 E:ASP238 4.4 73.4 1.0
CG E:GLU227 4.5 34.0 1.0
C3 E:PEP1264 4.6 23.7 0.5
CG E:HIS201 4.6 37.4 1.0
NH2 E:ARG55 4.8 45.7 1.0
C E:CYS31 4.8 32.5 1.0
O2 E:PEP1264 4.9 24.7 0.5
O2' E:PEP1264 4.9 21.6 0.5
NH1 E:ARG55 5.0 41.7 1.0
CE E:LYS60 5.0 33.3 0.6
O E:CYS31 5.0 31.8 1.0

Cadmium binding site 6 out of 6 in 4c1k

Go back to Cadmium Binding Sites List in 4c1k
Cadmium binding site 6 out of 6 in the Crystal Structure of Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase


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 Pyrococcus Furiosus 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd1265

b:33.8
occ:0.50
 OE2 F:GLU227 2.2 44.9 1.0
OD2 F:ASP238 2.3 65.7 1.0
O F:HOH2006 2.5 41.0 0.5
SG F:CYS31 2.6 37.3 1.0
NE2 F:HIS201 2.6 41.8 1.0
CD F:GLU227 2.9 42.4 1.0
OE1 F:GLU227 2.9 39.7 1.0
CE1 F:HIS201 3.0 43.1 1.0
CB F:CYS31 3.3 31.9 1.0
CG F:ASP238 3.4 68.1 1.0
O1 F:PEP1264 3.6 25.4 0.5
CD2 F:HIS201 3.8 40.1 1.0
NE2 F:GLN241 3.8 42.2 1.0
CB F:ASP238 3.9 65.8 1.0
CA F:CYS31 4.0 32.7 1.0
NZ F:LYS60 4.1 45.9 0.6
ND1 F:HIS201 4.2 42.1 1.0
C1 F:PEP1264 4.3 25.6 0.5
CG F:GLU227 4.4 38.4 1.0
OD1 F:ASP238 4.4 70.0 1.0
CG F:HIS201 4.6 37.8 1.0
C2 F:PEP1264 4.6 25.8 0.5
C3 F:PEP1264 4.9 26.3 0.5
NH2 F:ARG55 4.9 46.9 1.0
C F:CYS31 4.9 33.7 1.0
CE F:LYS60 5.0 45.0 0.6

Reference:

A.R.Nazmi, L.R.Schofield, R.C.J.Dobson, G.B.Jameson, E.J.Parker. Destabilization of the Homotetrameric Assembly of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From the Hyperthermophile Pyrococcus Furiosus Enhances Enzymatic Activity J.Mol.Biol. V. 426 656 2014.
ISSN: ISSN 0022-2836
PubMed: 24239948
DOI: 10.1016/J.JMB.2013.11.008
Page generated: Sat Dec 12 08:24:12 2020

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