Sodium in PDB 1e7p: Quinol:Fumarate Reductase From Wolinella Succinogenes

All present enzymatic activity of Quinol:Fumarate Reductase From Wolinella Succinogenes:
1.3.5.1; 1.3.5.4;

The structure of Quinol:Fumarate Reductase From Wolinella Succinogenes, PDB code: 1e7p was solved by C.R.D.Lancaster, A.Kroeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.074, 290.240, 153.614, 90.00, 95.73, 90.00
R / Rfree (%)	28.3 / 29.1

The structure of Quinol:Fumarate Reductase From Wolinella Succinogenes also contains other interesting chemical elements:

Iron

(Fe)

44 atoms

The binding sites of Sodium atom in the Quinol:Fumarate Reductase From Wolinella Succinogenes (pdb code 1e7p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Quinol:Fumarate Reductase From Wolinella Succinogenes, PDB code: 1e7p:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Quinol:Fumarate Reductase From Wolinella Succinogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Quinol:Fumarate Reductase From Wolinella Succinogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:81.9 occ:1.00 O A:MET372 2.5 80.2 1.0 O A:ALA395 2.8 72.2 1.0 OH A:TYR370 2.9 84.0 1.0 C A:MET372 3.3 79.8 1.0 O A:GLU393 3.5 69.4 1.0 O A:SER371 3.5 80.7 1.0 CA A:MET372 3.6 80.7 1.0 CA A:GLU393 3.8 67.3 1.0 CZ A:TYR370 3.8 83.2 1.0 C A:GLU393 3.9 68.8 1.0 C A:ALA395 4.0 72.1 1.0 CD2 A:HIS400 4.0 77.6 1.0 CE2 A:TYR370 4.1 82.4 1.0 C A:SER371 4.3 81.3 1.0 O A:GLY373 4.3 78.4 1.0 O A:GLY392 4.3 64.2 1.0 N A:MET372 4.4 81.5 1.0 OE1 A:GLU412 4.5 84.8 1.0 N A:GLY373 4.5 78.9 1.0 N A:GLU393 4.5 65.8 1.0 OE2 A:GLU412 4.6 81.0 1.0 NE2 A:HIS400 4.7 77.9 1.0 C A:GLY392 4.7 64.8 1.0 CA A:CYS396 4.8 73.7 1.0 CB A:MET372 4.8 80.2 1.0 N A:CYS396 4.8 72.9 1.0 N A:ALA395 4.9 71.0 1.0 C A:GLY373 4.9 77.8 1.0 CG A:HIS400 4.9 77.8 1.0 CB A:GLU393 4.9 66.2 1.0 CE1 A:TYR370 5.0 83.5 1.0

Sodium binding site 2 out of 4 in the Quinol:Fumarate Reductase From Wolinella Succinogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Quinol:Fumarate Reductase From Wolinella Succinogenes within 5.0Å range: probe atom residue distance (Å) B Occ D:Na703 b:64.8 occ:1.00 O D:MET372 2.5 48.0 1.0 O D:ALA395 2.8 56.1 1.0 OH D:TYR370 2.9 59.3 1.0 C D:MET372 3.3 47.6 1.0 O D:GLU393 3.5 61.5 1.0 O D:SER371 3.5 50.2 1.0 CA D:MET372 3.6 48.0 1.0 CA D:GLU393 3.8 60.7 1.0 CZ D:TYR370 3.8 58.0 1.0 C D:GLU393 3.9 61.0 1.0 C D:ALA395 4.0 57.1 1.0 CD2 D:HIS400 4.0 58.1 1.0 CE2 D:TYR370 4.1 57.7 1.0 C D:SER371 4.3 50.2 1.0 O D:GLY373 4.3 50.0 1.0 O D:GLY392 4.3 62.3 1.0 N D:MET372 4.4 49.1 1.0 OE1 D:GLU412 4.5 65.2 1.0 N D:GLY373 4.5 47.5 1.0 N D:GLU393 4.5 60.9 1.0 OE2 D:GLU412 4.6 64.3 1.0 NE2 D:HIS400 4.7 58.1 1.0 C D:GLY392 4.7 61.1 1.0 CA D:CYS396 4.8 58.9 1.0 CB D:MET372 4.8 46.7 1.0 N D:CYS396 4.8 57.3 1.0 N D:ALA395 4.9 59.2 1.0 C D:GLY373 4.9 49.6 1.0 CG D:HIS400 4.9 57.6 1.0 CB D:GLU393 4.9 60.1 1.0 CE1 D:TYR370 5.0 57.7 1.0

Sodium binding site 3 out of 4 in the Quinol:Fumarate Reductase From Wolinella Succinogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Quinol:Fumarate Reductase From Wolinella Succinogenes within 5.0Å range: probe atom residue distance (Å) B Occ G:Na703 b:48.4 occ:1.00 O G:MET372 2.5 80.4 1.0 O G:ALA395 2.8 76.2 1.0 OH G:TYR370 2.9 75.2 1.0 C G:MET372 3.3 80.9 1.0 O G:GLU393 3.5 81.0 1.0 O G:SER371 3.5 81.5 1.0 CA G:MET372 3.6 81.5 1.0 CA G:GLU393 3.8 81.4 1.0 CZ G:TYR370 3.8 76.0 1.0 C G:GLU393 3.9 81.1 1.0 C G:ALA395 4.0 76.9 1.0 CD2 G:HIS400 4.0 77.1 1.0 CE2 G:TYR370 4.1 76.6 1.0 C G:SER371 4.3 81.4 1.0 O G:GLY373 4.3 80.3 1.0 O G:GLY392 4.3 82.0 1.0 N G:MET372 4.4 81.7 1.0 OE1 G:GLU412 4.5 75.8 1.0 N G:GLY373 4.5 80.6 1.0 N G:GLU393 4.5 81.2 1.0 OE2 G:GLU412 4.6 74.3 1.0 NE2 G:HIS400 4.7 76.8 1.0 C G:GLY392 4.7 81.1 1.0 CA G:CYS396 4.8 76.2 1.0 CB G:MET372 4.8 81.8 1.0 N G:CYS396 4.8 76.8 1.0 N G:ALA395 4.9 78.0 1.0 C G:GLY373 4.9 80.1 1.0 CG G:HIS400 4.9 77.0 1.0 CB G:GLU393 4.9 82.1 1.0 CE1 G:TYR370 5.0 75.6 1.0

Sodium binding site 4 out of 4 in the Quinol:Fumarate Reductase From Wolinella Succinogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Quinol:Fumarate Reductase From Wolinella Succinogenes within 5.0Å range: probe atom residue distance (Å) B Occ J:Na703 b:41.8 occ:1.00 O J:MET372 2.5 86.8 1.0 O J:ALA395 2.8 82.5 1.0 OH J:TYR370 2.9 75.7 1.0 C J:MET372 3.3 86.7 1.0 O J:GLU393 3.5 88.1 1.0 O J:SER371 3.5 86.8 1.0 CA J:MET372 3.6 87.3 1.0 CA J:GLU393 3.8 87.1 1.0 CZ J:TYR370 3.8 76.3 1.0 C J:GLU393 3.9 87.4 1.0 C J:ALA395 4.0 83.6 1.0 CD2 J:HIS400 4.0 97.2 1.0 CE2 J:TYR370 4.1 76.4 1.0 C J:SER371 4.3 86.3 1.0 O J:GLY373 4.3 83.1 1.0 O J:GLY392 4.3 87.1 1.0 N J:MET372 4.4 87.3 1.0 OE1 J:GLU412 4.5 90.5 1.0 N J:GLY373 4.5 86.0 1.0 N J:GLU393 4.5 87.3 1.0 OE2 J:GLU412 4.6 90.9 1.0 NE2 J:HIS400 4.7 97.8 1.0 C J:GLY392 4.7 87.7 1.0 CA J:CYS396 4.8 82.0 1.0 CB J:MET372 4.8 88.1 1.0 N J:CYS396 4.8 82.7 1.0 N J:ALA395 4.9 85.2 1.0 C J:GLY373 4.9 83.5 1.0 CG J:HIS400 4.9 96.0 1.0 CB J:GLU393 4.9 85.3 1.0 CE1 J:TYR370 5.0 76.9 1.0

C.R.D.Lancaster, R.Gross, J.Simon. A Third Crystal Form of Wolinella Succinogenes Quinol:Fumarate Reductase Reveals Domain Closure at the Site of Fumarate Reduction Eur.J.Biochem. V. 268 1820 2001.
ISSN: ISSN 0014-2956
PubMed: 11248702
DOI: 10.1046/J.1432-1327.2001.02053.X