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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 1e7p:

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

Iron (Fe) 44 atoms

Sodium Binding Sites:

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 1e7p

Go back to Sodium Binding Sites List in 1e7p
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 1e7p

Go back to Sodium Binding Sites List in 1e7p
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 1e7p

Go back to Sodium Binding Sites List in 1e7p
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 1e7p

Go back to Sodium Binding Sites List in 1e7p
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

Reference:

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
Page generated: Sun Oct 6 18:21:24 2024

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