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Calcium in PDB 5ol2: The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile

Enzymatic activity of The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile

All present enzymatic activity of The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile:
1.3.8.1;

Protein crystallography data

The structure of The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile, PDB code: 5ol2 was solved by J.K.Demmer, N.P.Chowdhury, T.Selmer, U.Ermler, W.Buckel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.87 / 3.10
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 177.060, 177.060, 493.150, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile (pdb code 5ol2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile, PDB code: 5ol2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5ol2

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Calcium binding site 1 out of 5 in the The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:0.8
occ:1.00
 OD1 A:ASP188 2.4 0.7 1.0
OE2 A:GLU75 2.6 0.0 1.0
CG A:ASP188 3.6 0.6 1.0
NH1 A:ARG111 3.8 0.3 1.0
CD A:GLU75 3.8 0.0 1.0
O A:ALA187 4.1 0.4 1.0
OD2 A:ASP188 4.2 0.8 1.0
NZ A:LYS79 4.3 0.4 1.0
CD A:LYS79 4.5 0.5 1.0
CZ A:ARG111 4.5 0.1 1.0
NH2 A:ARG111 4.6 0.2 1.0
CG A:GLU75 4.7 0.8 1.0
OE1 A:GLU75 4.7 0.7 1.0
CB A:ASP188 4.7 0.7 1.0
CE A:LYS79 4.8 0.8 1.0
C A:ALA187 4.9 1.0 1.0
CA A:ASP188 5.0 0.2 1.0

Calcium binding site 2 out of 5 in 5ol2

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Calcium binding site 2 out of 5 in the The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:0.8
occ:1.00
 OE1 C:GLU29 2.9 0.4 1.0
OE2 C:GLU33 3.1 0.3 1.0
OE1 C:GLU33 3.1 0.2 1.0
CD C:GLU33 3.5 1.0 1.0
CD C:GLU29 4.1 0.2 1.0
NH2 C:ARG35 4.1 0.9 1.0
OE2 C:GLU29 4.9 0.2 1.0
CG C:GLU29 4.9 0.6 1.0

Calcium binding site 3 out of 5 in 5ol2

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Calcium binding site 3 out of 5 in the The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:0.2
occ:1.00
 OD1 D:ASP188 2.6 0.9 1.0
OE2 D:GLU75 2.6 0.7 1.0
NH1 D:ARG111 3.8 0.3 1.0
CG D:ASP188 3.8 0.2 1.0
CD D:GLU75 3.8 0.4 1.0
O D:ALA187 4.1 0.0 1.0
OD2 D:ASP188 4.5 0.2 1.0
CZ D:ARG111 4.5 0.4 1.0
NH2 D:ARG111 4.6 0.7 1.0
OE1 D:GLU75 4.6 0.7 1.0
CG D:GLU75 4.7 0.7 1.0
CD D:LYS79 4.7 0.2 1.0
CB D:ASP188 4.9 0.8 1.0
C D:ALA187 4.9 0.6 1.0

Calcium binding site 4 out of 5 in 5ol2

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Calcium binding site 4 out of 5 in the The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:0.5
occ:1.00
 OD2 E:ASP116 4.4 0.2 1.0
OD1 E:ASP116 4.5 0.7 1.0
CG E:ASP116 4.9 0.4 1.0

Calcium binding site 5 out of 5 in 5ol2

Go back to Calcium Binding Sites List in 5ol2
Calcium binding site 5 out of 5 in the The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca403

b:0.7
occ:1.00
 NH2 F:ARG35 2.3 0.7 1.0
OE1 F:GLU29 2.6 1.0 1.0
OE2 F:GLU33 2.9 0.7 1.0
OE1 F:GLU33 3.1 0.6 1.0
CD F:GLU33 3.4 0.5 1.0
CZ F:ARG35 3.6 0.4 1.0
CD F:GLU29 3.8 0.9 1.0
NE F:ARG35 4.3 0.6 1.0
CG F:GLU29 4.4 0.6 1.0
NH1 F:ARG35 4.6 0.1 1.0
OE2 F:GLU29 4.8 0.8 1.0
CG F:GLU33 4.9 1.0 1.0

Reference:

J.K.Demmer, N.Pal Chowdhury, T.Selmer, U.Ermler, W.Buckel. The Semiquinone Swing in the Bifurcating Electron Transferring Flavoprotein/Butyryl-Coa Dehydrogenase Complex From Clostridium Difficile. Nat Commun V. 8 1577 2017.
ISSN: ESSN 2041-1723
PubMed: 29146947
DOI: 10.1038/S41467-017-01746-3
Page generated: Mon Jul 15 09:47:49 2024

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