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Sodium in PDB 6q9c: Crystal Structure of Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions

Enzymatic activity of Crystal Structure of Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions

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

Protein crystallography data

The structure of Crystal Structure of Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions, PDB code: 6q9c 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) 49.44 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.279, 115.829, 189.832, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.7

Other elements in 6q9c:

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

Iron (Fe) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions (pdb code 6q9c). 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 Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions, PDB code: 6q9c:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6q9c

Go back to Sodium Binding Sites List in 6q9c
Sodium binding site 1 out of 5 in the Crystal Structure of Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions


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 Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:82.9
occ:1.00
 O B:HOH931 2.4 43.6 1.0
O B:HOH738 3.0 49.6 1.0
OE2 B:GLU33 3.2 32.9 1.0
O B:HOH851 3.7 35.3 1.0
O B:HOH672 3.9 28.4 1.0
O B:VAL28 4.0 27.6 1.0
CD B:GLU33 4.1 32.6 1.0
NH2 B:ARG27 4.2 29.8 1.0
N B:SER30 4.2 29.2 1.0
CB B:SER30 4.3 31.7 1.0
CG B:GLU33 4.5 32.4 1.0
OG B:SER30 4.5 32.5 1.0
CA B:SER30 4.9 29.7 1.0
CA B:HIS29 5.0 27.1 1.0
OE1 B:GLU33 5.0 34.2 1.0

Sodium binding site 2 out of 5 in 6q9c

Go back to Sodium Binding Sites List in 6q9c
Sodium binding site 2 out of 5 in the Crystal Structure of Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions


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 Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na508

b:47.8
occ:1.00
 O B:HOH748 2.3 34.0 1.0
OE1 B:GLU108 2.4 27.8 1.0
O B:HOH875 2.7 33.9 1.0
CD B:GLU108 3.6 27.1 1.0
NE B:ARG109 3.6 24.0 1.0
CG2 B:ILE7 3.8 26.5 1.0
CB B:GLU108 3.8 25.2 1.0
CG2 B:ILE105 3.9 26.9 1.0
NH2 B:ARG109 3.9 24.7 1.0
CA B:ILE105 4.0 25.5 1.0
O B:ARG104 4.1 23.9 1.0
CZ B:ARG109 4.2 24.4 1.0
NE B:ARG104 4.2 24.9 1.0
CG B:GLU108 4.2 26.0 1.0
CG B:ARG104 4.3 24.0 1.0
O B:HOH878 4.3 30.5 1.0
CB B:ILE105 4.3 27.1 1.0
C B:ARG104 4.4 23.8 1.0
N B:ILE105 4.4 24.3 1.0
CG B:ARG109 4.5 23.6 1.0
CD B:ARG109 4.5 23.8 1.0
O B:PRO8 4.5 26.0 1.0
OE2 B:GLU108 4.6 29.3 1.0
CD B:ARG104 4.6 24.6 1.0
CD1 B:ILE10 4.8 24.6 1.0
O B:HOH827 4.9 24.1 1.0
CB B:ILE7 4.9 27.0 1.0
CD1 B:ILE7 4.9 27.3 1.0

Sodium binding site 3 out of 5 in 6q9c

Go back to Sodium Binding Sites List in 6q9c
Sodium binding site 3 out of 5 in the Crystal Structure of Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions


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 Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na507

b:57.5
occ:1.00
 O D:HOH863 2.3 45.3 1.0
OD1 D:ASN362 2.6 30.8 1.0
OE2 D:GLU359 2.9 28.0 1.0
O D:HOH763 3.1 43.6 1.0
CG D:ASN362 3.4 29.1 1.0
CB D:ASN362 3.7 26.9 1.0
CD D:GLU359 3.7 27.0 1.0
OE1 D:GLU359 3.9 27.5 1.0
CE2 D:TYR358 4.4 29.2 1.0
CD2 D:LEU363 4.4 27.0 1.0
ND2 D:ASN362 4.5 30.4 1.0
O D:HOH743 4.7 41.0 1.0
CG D:LEU363 4.8 26.1 1.0
CE D:LYS366 4.8 34.9 1.0
NZ D:LYS366 4.9 36.1 1.0
C D:ASN362 4.9 26.1 1.0
CA D:ASN362 4.9 26.0 1.0
N D:LEU363 5.0 25.6 1.0

Sodium binding site 4 out of 5 in 6q9c

Go back to Sodium Binding Sites List in 6q9c
Sodium binding site 4 out of 5 in the Crystal Structure of Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions


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 Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na508

b:61.6
occ:1.00
 O D:HOH925 2.3 40.5 1.0
OD2 D:ASP310 2.6 39.2 1.0
O D:HOH647 3.1 44.7 1.0
O D:HOH945 3.5 50.5 1.0
CG D:ASP310 3.7 38.0 1.0
CG D:PRO243 3.9 42.7 1.0
CB D:PRO308 4.1 37.0 1.0
CB D:PRO243 4.1 44.9 1.0
CB D:ASP310 4.2 37.0 1.0
O D:MET268 4.2 34.1 1.0
CA D:ASN269 4.3 36.5 1.0
CG D:PRO308 4.5 37.5 1.0
CB D:ASN269 4.5 38.2 1.0
CD2 D:TYR246 4.7 43.8 1.0
OD1 D:ASP310 4.8 37.6 1.0
N D:ASN269 4.8 35.3 1.0
C D:MET268 4.8 34.2 1.0
O D:HOH616 4.8 41.5 1.0

Sodium binding site 5 out of 5 in 6q9c

Go back to Sodium Binding Sites List in 6q9c
Sodium binding site 5 out of 5 in the Crystal Structure of Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions


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 Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof Bound to Nadh Under Anaerobic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na509

b:46.4
occ:1.00
 O D:HOH735 2.3 34.6 1.0
OE1 D:GLU108 2.5 29.8 1.0
O D:HOH819 2.5 30.0 1.0
NE D:ARG109 3.6 25.7 1.0
CD D:GLU108 3.6 28.3 1.0
CB D:GLU108 3.7 26.5 1.0
CG2 D:ILE7 3.8 28.6 1.0
NH1 D:ARG109 3.9 26.8 1.0
CG2 D:ILE105 3.9 27.9 1.0
CA D:ILE105 4.0 26.1 1.0
O D:ARG104 4.1 25.5 1.0
CZ D:ARG109 4.1 26.4 1.0
CG D:GLU108 4.2 27.0 1.0
NE D:ARG104 4.2 25.9 1.0
O D:HOH890 4.3 31.2 1.0
CG D:ARG104 4.4 25.3 1.0
CG D:ARG109 4.4 25.0 1.0
C D:ARG104 4.4 25.1 1.0
CB D:ILE105 4.4 27.4 1.0
N D:ILE105 4.5 25.4 1.0
CD D:ARG109 4.5 25.4 1.0
O D:PRO8 4.6 28.3 1.0
OE2 D:GLU108 4.6 30.2 1.0
CD D:ARG104 4.7 25.7 1.0
CD1 D:ILE10 4.7 25.9 1.0
CD1 D:ILE7 4.8 29.0 1.0
CB D:ILE7 4.9 29.2 1.0
O D:HOH823 4.9 28.5 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 12:49:16 2024

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