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Sodium in PDB 6q9g: Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129D and Nuof Bound to Nadh

Enzymatic activity of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129D and Nuof Bound to Nadh

All present enzymatic activity of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129D and Nuof Bound to Nadh:
1.6.5.11;

Protein crystallography data

The structure of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129D and Nuof Bound to Nadh, PDB code: 6q9g 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) 26.40 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.330, 116.180, 189.780, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.1

Other elements in 6q9g:

The structure of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129D and Nuof 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 G129D and Nuof Bound to Nadh (pdb code 6q9g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129D and Nuof Bound to Nadh, PDB code: 6q9g:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6q9g

Go back to Sodium Binding Sites List in 6q9g
Sodium binding site 1 out of 3 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129D and Nuof 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 G129D and Nuof Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:75.6
occ:1.00
 O B:HOH914 2.4 37.6 1.0
O B:HOH868 2.8 49.9 1.0
O B:HOH732 2.9 41.2 1.0
OE2 B:GLU33 3.0 26.2 1.0
O B:HOH711 3.7 23.8 1.0
O B:VAL28 3.7 21.8 1.0
CD B:GLU33 4.0 26.3 1.0
NH2 B:ARG27 4.0 23.2 1.0
N B:SER30 4.2 22.7 1.0
O B:HOH783 4.3 24.1 1.0
CB B:SER30 4.3 25.1 1.0
OG B:SER30 4.3 25.3 1.0
CG B:GLU33 4.7 26.4 1.0
C B:VAL28 4.8 20.8 1.0
OE1 B:GLU33 4.8 26.7 1.0
CA B:HIS29 4.9 21.0 1.0
CA B:SER30 4.9 23.4 1.0

Sodium binding site 2 out of 3 in 6q9g

Go back to Sodium Binding Sites List in 6q9g
Sodium binding site 2 out of 3 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129D and Nuof 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 G129D and Nuof Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:60.7
occ:1.00
 OE1 B:GLU53 2.9 38.7 1.0
NE1 B:TRP57 3.8 29.9 1.0
CD B:GLU53 3.9 37.6 1.0
CZ2 B:TRP57 4.0 30.2 1.0
CE2 B:TRP57 4.3 29.4 1.0
CG B:GLU53 4.3 35.7 1.0
OE2 B:GLU53 4.9 38.4 1.0
CD1 B:TRP57 5.0 28.8 1.0

Sodium binding site 3 out of 3 in 6q9g

Go back to Sodium Binding Sites List in 6q9g
Sodium binding site 3 out of 3 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129D and Nuof 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 G129D and Nuof Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na506

b:49.5
occ:1.00
 O D:HOH928 2.5 36.3 1.0
OD2 D:ASP310 2.6 33.1 1.0
O D:HOH605 3.1 35.7 1.0
O D:HOH937 3.5 42.6 1.0
CG D:PRO243 3.6 37.9 1.0
CG D:ASP310 3.7 32.0 1.0
CB D:PRO243 3.9 40.0 1.0
CB D:ASP310 4.1 31.0 1.0
O D:MET268 4.1 27.4 1.0
CB D:PRO308 4.2 31.0 1.0
CA D:ASN269 4.2 29.0 1.0
CB D:ASN269 4.4 30.5 1.0
CD2 D:TYR246 4.6 40.8 1.0
N D:ASN269 4.7 28.0 1.0
C D:MET268 4.7 27.2 1.0
CG D:PRO308 4.7 31.7 1.0
OD1 D:ASP310 4.8 31.6 1.0
CD D:PRO243 4.8 37.0 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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