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Cadmium in PDB 1d7d: Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5

Enzymatic activity of Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5

All present enzymatic activity of Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5:
1.1.3.25;

Protein crystallography data

The structure of Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5, PDB code: 1d7d was solved by B.M.Hallberg, T.Bergfors, K.Backbro, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.90
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 138.300, 138.300, 53.390, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 22.1

Other elements in 1d7d:

The structure of Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5 also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5 (pdb code 1d7d). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5, PDB code: 1d7d:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 1d7d

Go back to Cadmium Binding Sites List in 1d7d
Cadmium binding site 1 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:19.1
occ:1.00
 O A:HOH1629 1.9 24.9 1.0
O1A B:HEM401 2.0 21.3 1.0
O B:HOH1628 2.1 20.2 1.0
OD1 A:ASP24 2.3 16.1 1.0
O A:PRO21 2.3 19.2 1.0
OD2 A:ASP24 2.4 18.1 1.0
O2A B:HEM401 2.5 19.9 1.0
CGA B:HEM401 2.5 15.2 1.0
CG A:ASP24 2.7 13.5 1.0
C A:PRO21 3.4 16.2 1.0
CA A:PRO21 3.8 15.0 1.0
CBA B:HEM401 4.1 18.9 1.0
O A:HOH1661 4.2 36.6 1.0
CB A:ASP24 4.2 15.3 1.0
CB A:PRO21 4.3 16.1 1.0
O B:HOH2633 4.5 21.1 1.0
N A:VAL22 4.5 13.3 1.0
O A:HOH1637 4.7 27.2 1.0
O A:HOH1670 4.8 43.1 1.0
CA A:ASP24 4.8 17.2 1.0
O A:VAL22 4.8 17.5 1.0
N A:ASP24 4.8 12.0 1.0
C A:VAL22 4.9 23.7 1.0
CA A:VAL22 4.9 16.9 1.0
CZ B:PHE166 5.0 11.7 1.0

Cadmium binding site 2 out of 6 in 1d7d

Go back to Cadmium Binding Sites List in 1d7d
Cadmium binding site 2 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:28.3
occ:1.00
 O A:HOH1742 2.2 28.4 1.0
O A:HOH1743 2.2 32.4 1.0
OE2 A:GLU107 2.3 29.6 1.0
O A:HOH1702 2.3 21.4 1.0
OXT A:ASN186 2.4 48.3 1.0
O A:HOH1748 2.4 27.0 1.0
CD A:GLU107 3.2 28.7 1.0
C A:ASN186 3.4 56.0 1.0
OE1 A:GLU107 3.5 22.3 1.0
O A:ASN186 3.8 83.7 1.0
O A:TYR184 4.0 26.0 1.0
O A:HOH1741 4.0 27.4 1.0
O A:HOH1716 4.3 33.2 1.0
O A:ASN183 4.5 25.4 1.0
CG A:GLU107 4.6 18.7 1.0
CZ A:PHE13 4.7 19.6 1.0
C A:TYR184 4.7 23.8 1.0
CA A:ASN186 4.7 43.1 1.0
N A:ASN186 4.8 28.7 1.0
CG A:PRO106 4.9 26.0 1.0

Cadmium binding site 3 out of 6 in 1d7d

Go back to Cadmium Binding Sites List in 1d7d
Cadmium binding site 3 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd504

b:92.7
occ:1.00
 OE2 A:GLU126 3.2 66.9 1.0
CD A:GLU126 3.3 47.0 1.0
OE1 A:GLU126 3.4 57.3 1.0
O A:HOH1693 3.6 48.7 1.0
CG A:GLU126 4.2 32.8 1.0
O A:HOH1689 4.4 45.2 1.0

Cadmium binding site 4 out of 6 in 1d7d

Go back to Cadmium Binding Sites List in 1d7d
Cadmium binding site 4 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:21.2
occ:1.00
 OD2 B:ASP165 2.3 19.6 1.0
O B:HOH2627 2.4 13.7 1.0
OD2 A:ASP165 2.4 16.5 1.0
OD1 A:ASP165 2.4 11.6 1.0
O A:HOH1627 2.4 16.1 1.0
OD1 B:ASP165 2.5 12.3 1.0
CG B:ASP165 2.7 14.8 1.0
CG A:ASP165 2.8 13.0 1.0
CB B:ASP165 4.3 15.3 1.0
O B:PHE166 4.3 15.6 1.0
CB A:ASP165 4.3 12.2 1.0
O A:PHE166 4.3 13.5 1.0
CG2 B:VAL22 4.5 21.2 1.0
O A:HOH1612 4.5 17.3 1.0
O B:HOH2612 4.5 19.6 1.0
CH2 B:TRP143 4.6 13.3 1.0
O A:HOH1674 4.6 42.6 1.0
CH2 A:TRP143 4.6 12.3 1.0
O A:HOH2642 4.7 20.8 1.0
CG2 A:VAL22 4.8 20.5 1.0
O B:HOH2674 4.8 43.7 1.0
O B:HOH1642 4.9 26.6 1.0
CB B:VAL22 5.0 20.5 1.0

Cadmium binding site 5 out of 6 in 1d7d

Go back to Cadmium Binding Sites List in 1d7d
Cadmium binding site 5 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:20.5
occ:1.00
 O B:HOH2629 1.7 18.0 1.0
O1A A:HEM401 2.3 22.3 1.0
O B:HOH2628 2.3 25.3 1.0
OD1 B:ASP24 2.4 18.3 1.0
O B:PRO21 2.4 17.9 1.0
OD2 B:ASP24 2.4 22.9 1.0
O2A A:HEM401 2.5 23.2 1.0
CGA A:HEM401 2.6 13.6 1.0
CG B:ASP24 2.7 14.9 1.0
C B:PRO21 3.4 19.3 1.0
CA B:PRO21 3.8 14.7 1.0
CBA A:HEM401 4.2 21.1 1.0
CB B:ASP24 4.2 16.8 1.0
CB B:PRO21 4.3 14.8 1.0
O B:HOH2661 4.4 36.6 1.0
O B:HOH2637 4.5 28.0 1.0
O A:HOH1633 4.5 23.6 1.0
N B:VAL22 4.6 13.2 1.0
O B:HOH2670 4.8 49.7 1.0
CA B:ASP24 4.8 19.6 1.0
N B:ASP24 4.8 12.9 1.0
O B:VAL22 4.9 17.9 1.0
C B:VAL22 4.9 23.5 1.0
CA B:VAL22 4.9 15.2 1.0
CZ A:PHE166 5.0 13.9 1.0

Cadmium binding site 6 out of 6 in 1d7d

Go back to Cadmium Binding Sites List in 1d7d
Cadmium binding site 6 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Cytochrome Domain of Cellobiose Dehydrogenase, HP3 Fragment, pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd503

b:63.7
occ:1.00
 OXT B:ASN186 2.1 51.9 1.0
OE2 B:GLU107 2.5 35.2 1.0
C B:ASN186 3.3 56.2 1.0
CD B:GLU107 3.4 28.9 1.0
O B:TYR184 3.6 32.3 1.0
OE1 B:GLU107 3.6 31.3 1.0
O B:ASN186 3.8 82.3 1.0
N B:ASN186 4.4 35.6 1.0
CA B:ASN186 4.4 46.1 1.0
C B:TYR184 4.5 27.2 1.0
O B:ASN183 4.6 33.0 1.0
CZ B:PHE13 4.6 25.0 1.0
C B:LEU185 4.6 34.3 1.0
CG B:PRO106 4.6 27.8 1.0
O B:LEU185 4.7 44.0 1.0
CG B:GLU107 4.8 20.7 1.0
CD B:PRO106 4.9 20.9 1.0

Reference:

B.M.Hallberg, T.Bergfors, K.Backbro, G.Pettersson, G.Henriksson, C.Divne. A New Scaffold For Binding Haem in the Cytochrome Domain of the Extracellular Flavocytochrome Cellobiose Dehydrogenase. Structure Fold.Des. V. 8 79 2000.
ISSN: ISSN 0969-2126
PubMed: 10673428
DOI: 10.1016/S0969-2126(00)00082-4
Page generated: Sat Dec 12 08:08:42 2020

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