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Sodium in PDB 6q9j: Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129S and Nuof Bound to Nadh

Enzymatic activity of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129S and Nuof Bound to Nadh

All present enzymatic activity of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129S 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 G129S and Nuof Bound to Nadh, PDB code: 6q9j 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) 48.15 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.637, 116.339, 190.286, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.7

Other elements in 6q9j:

The structure of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129S 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 G129S and Nuof Bound to Nadh (pdb code 6q9j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129S and Nuof Bound to Nadh, PDB code: 6q9j:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6q9j

Go back to Sodium Binding Sites List in 6q9j
Sodium binding site 1 out of 4 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129S 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 G129S and Nuof Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:87.3
occ:1.00
 O B:HOH1113 2.4 47.0 1.0
OE2 B:GLU33 3.1 34.4 1.0
O B:HOH840 3.8 29.1 1.0
O B:HOH1043 3.9 28.1 1.0
CD B:GLU33 4.0 33.6 1.0
O B:VAL28 4.0 26.8 1.0
NH2 B:ARG27 4.1 29.4 1.0
N B:SER30 4.3 27.9 1.0
CB B:SER30 4.4 31.0 1.0
OG B:SER30 4.5 31.8 1.0
CG B:GLU33 4.6 33.0 1.0
OE1 B:GLU33 4.7 35.2 1.0
O B:HOH1119 4.9 46.4 1.0

Sodium binding site 2 out of 4 in 6q9j

Go back to Sodium Binding Sites List in 6q9j
Sodium binding site 2 out of 4 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129S 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 G129S and Nuof Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:53.9
occ:1.00
 O B:HOH916 2.3 33.6 1.0
OE1 B:GLU108 2.3 25.0 1.0
O B:HOH1024 2.5 33.6 1.0
CD B:GLU108 3.5 25.0 1.0
NE B:ARG109 3.6 23.1 1.0
CG2 B:ILE7 3.7 26.5 1.0
CB B:GLU108 3.8 23.7 1.0
CG2 B:ILE105 3.9 26.5 1.0
NH2 B:ARG109 3.9 23.8 1.0
CA B:ILE105 4.0 24.5 1.0
O B:ARG104 4.1 23.3 1.0
CZ B:ARG109 4.1 23.6 1.0
CG B:GLU108 4.2 24.1 1.0
O B:HOH1084 4.3 26.2 1.0
NE B:ARG104 4.3 22.0 1.0
CB B:ILE105 4.4 26.4 1.0
C B:ARG104 4.4 22.6 1.0
N B:ILE105 4.4 23.1 1.0
CG B:ARG104 4.4 21.4 1.0
OE2 B:GLU108 4.4 27.2 1.0
CG B:ARG109 4.5 22.7 1.0
CD B:ARG109 4.5 22.7 1.0
O B:PRO8 4.5 25.5 1.0
CD B:ARG104 4.7 21.6 1.0
CD1 B:ILE10 4.8 23.1 1.0
O B:HOH1012 4.8 23.0 1.0
CB B:ILE7 4.8 27.0 1.0
CD1 B:ILE7 4.9 27.0 1.0

Sodium binding site 3 out of 4 in 6q9j

Go back to Sodium Binding Sites List in 6q9j
Sodium binding site 3 out of 4 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129S 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 G129S and Nuof Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na508

b:60.7
occ:1.00
 OD1 D:ASN362 2.5 32.3 1.0
OE2 D:GLU359 2.9 28.4 1.0
O D:HOH863 3.0 48.2 1.0
CG D:ASN362 3.3 30.5 1.0
CB D:ASN362 3.8 28.2 1.0
CD D:GLU359 3.8 27.4 1.0
OE1 D:GLU359 4.0 28.2 1.0
O D:HOH631 4.4 40.3 1.0
CD2 D:LEU363 4.4 27.5 1.0
ND2 D:ASN362 4.5 32.4 1.0
NZ D:LYS366 4.5 38.2 1.0
CE D:LYS366 4.6 36.6 1.0
CE2 D:TYR358 4.6 28.9 1.0
CG D:LEU363 4.7 26.3 1.0
C D:ASN362 4.9 26.9 1.0
CA D:ASN362 4.9 27.0 1.0

Sodium binding site 4 out of 4 in 6q9j

Go back to Sodium Binding Sites List in 6q9j
Sodium binding site 4 out of 4 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129S 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 4 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe G129S and Nuof Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na509

b:51.8
occ:1.00
 O D:HOH638 2.4 34.1 1.0
OE1 D:GLU108 2.4 28.6 1.0
O D:HOH764 2.7 29.5 1.0
CD D:GLU108 3.6 27.3 1.0
NE D:ARG109 3.6 25.4 1.0
CG2 D:ILE7 3.7 27.5 1.0
CB D:GLU108 3.8 25.0 1.0
NH1 D:ARG109 3.9 27.0 1.0
CG2 D:ILE105 3.9 27.4 1.0
CA D:ILE105 4.0 24.7 1.0
CZ D:ARG109 4.2 26.3 1.0
O D:ARG104 4.2 23.1 1.0
CG D:GLU108 4.2 25.7 1.0
NE D:ARG104 4.3 23.6 1.0
O D:HOH893 4.3 31.4 1.0
CG D:ARG104 4.4 22.8 1.0
N D:ILE105 4.4 23.7 1.0
C D:ARG104 4.4 22.9 1.0
CB D:ILE105 4.5 26.7 1.0
CG D:ARG109 4.5 24.2 1.0
OE2 D:GLU108 4.5 29.4 1.0
O D:PRO8 4.6 27.5 1.0
CD D:ARG109 4.6 24.7 1.0
CD1 D:ILE10 4.7 24.6 1.0
CD D:ARG104 4.8 23.2 1.0
CB D:ILE7 4.8 28.1 1.0
CD1 D:ILE7 4.8 27.7 1.0
O D:HOH802 4.9 23.1 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 12:49:18 2024

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