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Cadmium in PDB 1pl3: Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant

Enzymatic activity of Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant

All present enzymatic activity of Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant:
1.1.99.18;

Protein crystallography data

The structure of Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant, PDB code: 1pl3 was solved by F.A.J.Rotsaert, B.M.Hallberg, S.De Vries, P.Moenne-Loccoz, C.Divne, M.H.Gold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.00 / 1.90
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 139.033, 139.033, 52.668, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 19.8

Other elements in 1pl3:

The structure of Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant 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, M65H Mutant (pdb code 1pl3). 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, M65H Mutant, PDB code: 1pl3:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 1pl3

Go back to Cadmium Binding Sites List in 1pl3
Cadmium binding site 1 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant


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, M65H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:26.6
occ:1.00
O A:HOH629 2.1 20.1 1.0
O1A B:HEM401 2.2 30.1 1.0
O B:HOH628 2.3 23.3 1.0
O A:PRO21 2.3 22.9 1.0
OD1 A:ASP24 2.3 21.8 1.0
O2A B:HEM401 2.5 26.9 1.0
OD2 A:ASP24 2.5 21.1 1.0
CGA B:HEM401 2.7 29.3 1.0
CG A:ASP24 2.8 19.1 1.0
C A:PRO21 3.3 21.6 1.0
CA A:PRO21 3.7 22.1 1.0
CBA B:HEM401 4.2 28.5 1.0
CB A:PRO21 4.2 21.5 1.0
CB A:ASP24 4.3 20.8 1.0
O A:HOH733 4.4 40.5 1.0
O B:HOH1633 4.5 24.9 1.0
O A:HOH662 4.5 38.9 1.0
N A:VAL22 4.5 20.9 1.0
O A:HOH637 4.5 33.3 1.0
O A:HOH672 4.7 37.6 1.0
O A:VAL22 4.8 22.6 1.0
CA A:ASP24 4.9 20.2 1.0
N A:ASP24 4.9 20.4 1.0
C A:VAL22 4.9 21.0 1.0
CA A:VAL22 4.9 20.6 1.0

Cadmium binding site 2 out of 6 in 1pl3

Go back to Cadmium Binding Sites List in 1pl3
Cadmium binding site 2 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant


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, M65H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:52.8
occ:1.00
OE2 A:GLU107 2.4 27.8 1.0
O A:HOH721 2.6 30.0 1.0
O A:HOH779 2.6 45.8 1.0
OXT A:ASN186 2.8 48.3 1.0
O A:ASN186 3.2 52.6 1.0
C A:ASN186 3.3 49.4 1.0
CD A:GLU107 3.3 28.4 1.0
OE1 A:GLU107 3.6 26.7 1.0
O A:TYR184 3.7 32.8 1.0
O A:HOH740 4.0 41.2 1.0
O A:HOH709 4.1 41.4 1.0
C A:TYR184 4.5 33.6 1.0
CZ A:PHE13 4.6 27.8 1.0
O A:ASN183 4.6 28.7 1.0
CA A:ASN186 4.6 48.2 1.0
CG A:GLU107 4.7 25.9 1.0
N A:ASN186 4.8 44.8 1.0
C A:LEU185 4.9 41.8 1.0

Cadmium binding site 3 out of 6 in 1pl3

Go back to Cadmium Binding Sites List in 1pl3
Cadmium binding site 3 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant


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, M65H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd504

b:0.5
occ:1.00
OE1 A:GLU126 2.9 43.6 1.0
OE2 A:GLU126 2.9 48.0 1.0
CD A:GLU126 3.3 38.7 1.0
CG A:GLU126 4.8 29.8 1.0

Cadmium binding site 4 out of 6 in 1pl3

Go back to Cadmium Binding Sites List in 1pl3
Cadmium binding site 4 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant


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, M65H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:30.1
occ:1.00
O A:HOH627 2.4 24.4 1.0
OD2 B:ASP165 2.4 22.1 1.0
OD2 A:ASP165 2.4 19.9 1.0
O B:HOH1627 2.5 21.3 1.0
OD1 A:ASP165 2.5 18.5 1.0
OD1 B:ASP165 2.5 19.2 1.0
CG A:ASP165 2.8 18.0 1.0
CG B:ASP165 2.8 21.0 1.0
O B:PHE166 4.3 19.3 1.0
O A:PHE166 4.3 20.8 1.0
CB A:ASP165 4.3 21.0 1.0
CB B:ASP165 4.3 22.1 1.0
O B:HOH1612 4.5 27.6 1.0
CG2 B:VAL22 4.5 23.1 1.0
CH2 B:TRP143 4.6 19.4 1.0
CG2 A:VAL22 4.6 20.5 1.0
O A:HOH612 4.6 24.6 1.0
CH2 A:TRP143 4.6 20.6 1.0
O A:HOH677 4.7 54.0 1.0
O A:HOH1642 4.8 30.5 1.0
O B:HOH642 4.9 29.3 1.0

Cadmium binding site 5 out of 6 in 1pl3

Go back to Cadmium Binding Sites List in 1pl3
Cadmium binding site 5 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant


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, M65H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1502

b:29.0
occ:1.00
O B:HOH1629 2.0 25.4 1.0
O1A A:HEM401 2.2 28.6 1.0
O A:HOH1628 2.3 29.8 1.0
OD1 B:ASP24 2.3 21.2 1.0
O B:PRO21 2.4 25.6 1.0
OD2 B:ASP24 2.4 24.4 1.0
O2A A:HEM401 2.6 27.1 1.0
CG B:ASP24 2.8 24.6 1.0
CGA A:HEM401 2.8 26.8 1.0
C B:PRO21 3.4 23.8 1.0
CA B:PRO21 3.8 24.0 1.0
CB B:ASP24 4.3 23.5 1.0
CB B:PRO21 4.3 23.6 1.0
CBA A:HEM401 4.3 28.3 1.0
O A:HOH633 4.4 27.0 1.0
O B:HOH1754 4.4 48.7 1.0
O B:HOH1662 4.5 45.1 1.0
O B:HOH1672 4.5 43.1 1.0
N B:VAL22 4.6 23.5 1.0
O B:HOH1637 4.7 41.0 1.0
CA B:ASP24 4.9 23.4 1.0
O B:VAL22 4.9 24.5 1.0
N B:ASP24 4.9 23.0 1.0
C B:VAL22 5.0 24.2 1.0
CA B:VAL22 5.0 23.2 1.0
CZ A:PHE166 5.0 17.9 1.0

Cadmium binding site 6 out of 6 in 1pl3

Go back to Cadmium Binding Sites List in 1pl3
Cadmium binding site 6 out of 6 in the Cytochrome Domain of Cellobiose Dehydrogenase, M65H Mutant


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, M65H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1503

b:0.8
occ:1.00
OE2 B:GLU107 3.0 50.1 1.0
O B:HOH1734 3.2 45.2 1.0
OXT B:ASN186 3.2 58.0 1.0
O B:ASN186 3.5 57.6 1.0
O B:TYR184 3.5 42.7 1.0
C B:ASN186 3.5 56.7 1.0
O B:HOH1763 3.6 63.3 1.0
CD B:GLU107 3.7 43.2 1.0
OE1 B:GLU107 3.8 43.1 1.0
O B:HOH1709 4.1 51.1 1.0
C B:TYR184 4.3 44.3 1.0
O B:ASN183 4.3 43.3 1.0
N B:ASN186 4.4 53.9 1.0
CZ B:PHE13 4.5 51.3 1.0
C B:LEU185 4.5 51.3 1.0
CA B:ASN186 4.5 56.0 1.0
O B:LEU185 4.6 51.4 1.0
CA B:TYR184 4.9 43.6 1.0

Reference:

F.A.J.Rotsaert, B.M.Hallberg, S.De Vries, P.Moenne-Loccoz, C.Divne, V.Renganathan, M.H.Gold. Biophysical and Structural Analysis of A Novel Heme B Iron Ligation in the Flavocytochrome Cellobiose Dehydrogenase. J.Biol.Chem. V. 278 33224 2003.
ISSN: ISSN 0021-9258
PubMed: 12796496
DOI: 10.1074/JBC.M302653200
Page generated: Sat Dec 12 08:11:45 2020

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