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Sodium in PDB 6q9k: Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh

Enzymatic activity of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh

All present enzymatic activity of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh:
1.6.5.11;

Protein crystallography data

The structure of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh, PDB code: 6q9k was solved by D.Wohlwend, S.Gerhardt, E.Gnandt, T.Friedrich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.26 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.380, 115.940, 189.970, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 21.9

Other elements in 6q9k:

The structure of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh also contains other interesting chemical elements:

Iron (Fe) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh (pdb code 6q9k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh, PDB code: 6q9k:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6q9k

Go back to Sodium Binding Sites List in 6q9k
Sodium binding site 1 out of 5 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:58.4
occ:1.00
 O B:HOH926 2.4 26.1 1.0
O B:HOH753 3.0 35.5 1.0
OE2 B:GLU33 3.1 23.2 1.0
O B:HOH923 3.2 38.5 1.0
O B:HOH656 3.7 13.9 1.0
O B:VAL28 3.8 20.3 1.0
O B:HOH869 3.8 21.0 1.0
CD B:GLU33 4.0 23.6 1.0
NH2 B:ARG27 4.1 22.2 1.0
N B:SER30 4.1 20.8 1.0
CB B:SER30 4.2 22.6 1.0
OG B:SER30 4.3 22.6 1.0
CG B:GLU33 4.6 23.7 1.0
CA B:SER30 4.8 21.3 1.0
OE1 B:GLU33 4.8 24.2 1.0
C B:VAL28 4.9 19.3 1.0
CA B:HIS29 4.9 19.4 1.0
O B:HOH787 5.0 44.2 1.0

Sodium binding site 2 out of 5 in 6q9k

Go back to Sodium Binding Sites List in 6q9k
Sodium binding site 2 out of 5 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na508

b:38.3
occ:1.00
 OE1 B:GLU108 2.3 16.0 1.0
O B:HOH756 2.4 22.1 1.0
O B:HOH843 2.6 27.2 1.0
NE B:ARG109 3.5 16.1 1.0
CD B:GLU108 3.5 16.1 1.0
CB B:GLU108 3.7 15.9 1.0
CG2 B:ILE7 3.8 19.2 1.0
NH2 B:ARG109 3.9 16.6 1.0
CG2 B:ILE105 3.9 16.5 1.0
CA B:ILE105 3.9 15.6 1.0
O B:ARG104 4.0 14.8 1.0
CZ B:ARG109 4.1 16.4 1.0
CG B:GLU108 4.1 15.9 1.0
NE B:ARG104 4.3 15.4 1.0
O B:HOH875 4.3 16.1 1.0
CB B:ILE105 4.3 16.4 1.0
CG B:ARG109 4.3 16.0 1.0
CG B:ARG104 4.3 14.6 1.0
CD B:ARG109 4.4 16.0 1.0
C B:ARG104 4.4 14.7 1.0
N B:ILE105 4.4 15.0 1.0
OE2 B:GLU108 4.5 16.7 1.0
O B:PRO8 4.7 18.7 1.0
CD B:ARG104 4.7 15.0 1.0
O B:HOH781 4.8 13.4 1.0
CB B:ILE7 4.9 19.9 1.0
CD1 B:ILE7 4.9 19.7 1.0
CA B:GLU108 5.0 15.7 1.0
O B:ILE105 5.0 15.4 1.0
CD1 B:ILE10 5.0 16.1 1.0

Sodium binding site 3 out of 5 in 6q9k

Go back to Sodium Binding Sites List in 6q9k
Sodium binding site 3 out of 5 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na506

b:36.9
occ:1.00
 OD1 D:ASN362 2.4 23.3 1.0
OE2 D:GLU359 2.7 20.8 1.0
O D:HOH821 3.1 42.6 1.0
CG D:ASN362 3.2 22.5 1.0
CB D:ASN362 3.5 21.0 1.0
CD D:GLU359 3.6 20.1 1.0
OE1 D:GLU359 3.8 20.6 1.0
CE2 D:TYR358 4.3 21.5 1.0
O D:HOH651 4.3 35.2 1.0
ND2 D:ASN362 4.3 23.3 1.0
CD2 D:LEU363 4.5 21.6 1.0
CG D:LEU363 4.7 20.5 1.0
CA D:ASN362 4.7 20.6 1.0
C D:ASN362 4.8 20.9 1.0
N D:LEU363 4.8 20.4 1.0
CG D:GLU359 5.0 19.3 1.0
OH D:TYR358 5.0 23.4 1.0
CE D:LYS366 5.0 26.9 1.0

Sodium binding site 4 out of 5 in 6q9k

Go back to Sodium Binding Sites List in 6q9k
Sodium binding site 4 out of 5 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na507

b:47.6
occ:1.00
 O D:HOH919 2.3 32.5 1.0
OD2 D:ASP310 2.7 29.4 1.0
O D:HOH608 2.9 37.5 1.0
CG D:PRO243 3.7 34.3 1.0
CG D:ASP310 3.8 28.0 1.0
CB D:PRO243 4.0 36.6 1.0
CB D:PRO308 4.1 27.8 1.0
CB D:ASP310 4.3 27.0 1.0
CA D:ASN269 4.4 27.1 1.0
O D:MET268 4.4 24.8 1.0
CB D:ASN269 4.5 28.9 1.0
CG D:PRO308 4.6 28.4 1.0
CD2 D:TYR246 4.6 36.2 1.0
OD1 D:ASP310 4.8 27.4 1.0
CD D:PRO243 4.8 33.5 1.0
N D:ASN269 4.9 25.9 1.0
C D:MET268 4.9 24.8 1.0
O D:HOH667 4.9 37.3 1.0

Sodium binding site 5 out of 5 in 6q9k

Go back to Sodium Binding Sites List in 6q9k
Sodium binding site 5 out of 5 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na508

b:33.1
occ:1.00
 O D:HOH734 2.3 18.6 1.0
OE1 D:GLU108 2.4 18.1 1.0
O D:HOH724 2.6 21.9 1.0
CD D:GLU108 3.5 17.7 1.0
NE D:ARG109 3.5 18.5 1.0
CB D:GLU108 3.7 17.3 1.0
CG2 D:ILE7 3.7 20.3 1.0
NH1 D:ARG109 3.9 19.4 1.0
CA D:ILE105 4.0 17.1 1.0
CG2 D:ILE105 4.1 18.3 1.0
CZ D:ARG109 4.1 19.0 1.0
CG D:GLU108 4.1 17.3 1.0
O D:ARG104 4.2 16.1 1.0
NE D:ARG104 4.3 17.0 1.0
O D:HOH847 4.4 22.2 1.0
CG D:ARG109 4.4 17.8 1.0
CG D:ARG104 4.4 16.1 1.0
CB D:ILE105 4.5 18.1 1.0
CD D:ARG109 4.5 18.1 1.0
N D:ILE105 4.5 16.3 1.0
C D:ARG104 4.5 15.8 1.0
OE2 D:GLU108 4.5 18.2 1.0
O D:PRO8 4.7 20.4 1.0
CD D:ARG104 4.8 16.5 1.0
O D:HOH831 4.8 18.2 1.0
CD1 D:ILE7 4.8 20.4 1.0
CB D:ILE7 4.8 21.1 1.0
CD1 D:ILE10 4.9 17.5 1.0
CA D:GLU108 5.0 16.7 1.0

Reference:

M.Schulte, K.Frick, E.Gnandt, S.Jurkovic, S.Burschel, R.Labatzke, K.Aierstock, D.Fiegen, D.Wohlwend, S.Gerhardt, O.Einsle, T.Friedrich. A Mechanism to Prevent Production of Reactive Oxygen Species By Escherichia Coli Respiratory Complex I. Nat Commun V. 10 2551 2019.
ISSN: ESSN 2041-1723
PubMed: 31186428
DOI: 10.1038/S41467-019-10429-0
Page generated: Tue Oct 8 12:49:38 2024

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