Atomistry » Sodium » PDB 6pul-6qdr » 6q9j
Atomistry »
  Sodium »
    PDB 6pul-6qdr »
      6q9j »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy