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Sodium in PDB 8qh4: Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide

Protein crystallography data

The structure of Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide, PDB code: 8qh4 was solved by D.Wohlwend, T.Friedrich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.15 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.527, 116.619, 190.01, 90, 90, 90
R / Rfree (%) 19.2 / 22.4

Other elements in 8qh4:

The structure of Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide also contains other interesting chemical elements:

Iron (Fe) 12 atoms
Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide (pdb code 8qh4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide, PDB code: 8qh4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8qh4

Go back to Sodium Binding Sites List in 8qh4
Sodium binding site 1 out of 8 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:49.5
occ:1.00
 OE1 B:GLU97 2.5 28.8 1.0
O2D B:A3D503 2.6 42.7 1.0
O B:HOH841 2.9 26.9 1.0
O B:HOH727 3.4 26.0 1.0
C2D B:A3D503 3.5 44.4 1.0
CD B:GLU97 3.5 26.3 1.0
OE2 B:GLU97 3.7 25.8 1.0
C1D B:A3D503 3.8 44.8 1.0
CG2 B:THR319 3.9 19.8 1.0
O B:HOH778 4.0 30.4 1.0
OG1 B:THR319 4.0 18.4 1.0
CD2 B:LEU297 4.3 21.7 1.0
N B:THR319 4.3 19.9 1.0
CA B:GLY68 4.4 23.9 1.0
O B:HOH800 4.4 37.5 1.0
CA B:GLY318 4.5 20.9 1.0
CB B:THR319 4.5 19.4 1.0
O B:HOH622 4.5 21.8 1.0
C B:GLY318 4.7 20.4 1.0
O B:GLY67 4.7 21.9 1.0
O4D B:A3D503 4.7 42.7 1.0
CB B:LEU297 4.8 20.4 1.0
CG B:GLU97 4.8 23.6 1.0
C3D B:A3D503 4.9 42.6 1.0
N1N B:A3D503 4.9 46.0 1.0

Sodium binding site 2 out of 8 in 8qh4

Go back to Sodium Binding Sites List in 8qh4
Sodium binding site 2 out of 8 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:48.5
occ:1.00
 OE2 B:GLU52 2.4 46.2 1.0
O B:HOH736 2.5 31.0 1.0
CD B:GLU52 3.5 44.4 1.0
CB B:VAL81 4.0 28.5 1.0
CG B:GLU52 4.1 42.0 1.0
CG2 B:VAL81 4.1 29.2 1.0
O3 B:SO4505 4.2 84.8 1.0
CG1 B:VAL81 4.3 27.0 1.0
CB B:PRO51 4.5 29.5 1.0
OE1 B:GLU52 4.5 44.0 1.0
CD1 B:ILE55 4.6 27.3 1.0
O B:HOH898 4.7 30.2 1.0
O B:ALA124 4.7 23.2 1.0
N B:GLU52 4.9 33.3 1.0

Sodium binding site 3 out of 8 in 8qh4

Go back to Sodium Binding Sites List in 8qh4
Sodium binding site 3 out of 8 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na508

b:51.6
occ:1.00
 OE1 B:GLU150 2.1 32.2 1.0
CE B:LYS154 3.3 41.5 1.0
CD B:GLU150 3.3 30.3 1.0
CD B:LYS154 3.7 39.1 1.0
CG B:GLU150 4.1 28.8 1.0
CB B:GLU150 4.1 27.3 1.0
O D:HOH897 4.2 45.3 1.0
O B:GLU150 4.2 24.4 1.0
OE2 B:GLU150 4.2 30.7 1.0
CA B:GLU150 4.3 25.1 1.0
O D:HOH848 4.4 43.2 1.0
CB B:LYS153 4.4 29.7 1.0
O D:HOH881 4.5 36.1 1.0
CD B:LYS153 4.5 33.1 1.0
NZ B:LYS154 4.5 42.0 1.0
CE B:LYS153 4.6 35.6 1.0
C B:GLU150 4.7 24.8 1.0
CG B:LYS154 4.9 37.8 1.0

Sodium binding site 4 out of 8 in 8qh4

Go back to Sodium Binding Sites List in 8qh4
Sodium binding site 4 out of 8 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:28.2
occ:1.00
 OD1 B:ASP94 2.5 18.1 1.0
O B:HOH715 2.7 15.7 1.0
O B:HOH766 2.7 16.4 1.0
O B:ALA179 2.8 19.3 1.0
CG B:ASP94 3.2 18.1 1.0
OD2 B:ASP94 3.2 19.8 1.0
O B:HOH707 3.3 30.7 1.0
C B:ALA179 3.7 19.9 1.0
N B:ALA179 3.7 21.6 1.0
CB B:CYS182 4.0 20.4 1.0
CA B:GLY176 4.2 18.8 1.0
CB B:ARG135 4.2 16.7 1.0
CA B:ALA179 4.2 21.2 1.0
N B:GLY178 4.2 21.0 1.0
CA B:ARG135 4.3 16.6 1.0
N B:ALA177 4.3 20.2 1.0
CE1 B:TYR133 4.4 16.5 1.0
C B:GLY178 4.5 22.3 1.0
OH B:TYR133 4.6 18.8 1.0
N B:TYR180 4.6 19.6 1.0
CB B:ASP94 4.7 16.9 1.0
OG B:SER96 4.7 19.9 1.0
C B:GLY176 4.7 19.6 1.0
CA B:GLY178 4.8 21.8 1.0
CB B:ALA179 4.8 21.6 1.0
N B:GLY136 4.9 17.1 1.0
OE1 B:GLU137 4.9 17.8 1.0
O B:ASP94 4.9 18.5 1.0
SG B:CYS182 5.0 22.7 1.0
CA B:TYR180 5.0 19.4 1.0
CA B:CYS182 5.0 19.4 1.0

Sodium binding site 5 out of 8 in 8qh4

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Sodium binding site 5 out of 8 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na510

b:39.8
occ:1.00
 O B:GLY178 2.5 23.6 1.0
O A:HOH396 2.6 20.8 1.0
OE2 B:GLU345 2.7 23.8 1.0
O B:HOH894 2.8 34.7 1.0
CD B:GLU345 3.6 22.7 1.0
C B:GLY178 3.6 22.3 1.0
OD2 A:ASP71 3.7 30.5 1.0
CG A:GLN126 3.8 21.8 1.0
OE1 B:GLU345 3.8 22.6 1.0
O A:HOH372 4.0 29.1 1.0
CB A:GLN126 4.1 20.4 1.0
O A:HOH364 4.2 53.1 1.0
CA B:GLY178 4.4 21.8 1.0
O B:HOH637 4.5 19.0 1.0
O A:HOH375 4.5 23.0 1.0
CB A:ASP71 4.6 26.7 1.0
CG A:ASP71 4.6 28.3 1.0
N B:ALA179 4.6 21.6 1.0
N A:GLN126 4.8 19.9 1.0
OE2 B:GLU137 4.8 19.7 1.0
O B:HOH707 4.8 30.7 1.0
CA B:ALA179 4.8 21.2 1.0
N B:TYR180 4.9 19.6 1.0

Sodium binding site 6 out of 8 in 8qh4

Go back to Sodium Binding Sites List in 8qh4
Sodium binding site 6 out of 8 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na204

b:36.7
occ:1.00
 OE1 C:GLN126 2.5 27.8 1.0
O D:HOH785 2.8 21.9 1.0
O D:HOH699 2.9 25.6 1.0
OG C:SER88 2.9 17.9 1.0
CD C:GLN126 3.5 25.8 1.0
O D:LYS337 3.5 20.7 1.0
N D:PHE341 3.5 19.1 1.0
CA C:SER88 3.6 18.4 1.0
CA D:PHE341 3.6 18.5 1.0
CB C:SER88 3.6 17.9 1.0
CB D:PHE341 3.6 18.2 1.0
NE2 C:GLN126 3.9 26.2 1.0
O C:HOH387 4.1 29.9 1.0
C D:GLU340 4.2 19.9 1.0
O C:VAL87 4.3 19.5 1.0
N C:SER88 4.3 18.3 1.0
CB D:GLU340 4.3 20.8 1.0
CD1 D:PHE341 4.5 17.4 1.0
CG D:PHE341 4.5 17.7 1.0
C D:LYS337 4.6 20.9 1.0
C C:VAL87 4.6 19.1 1.0
O D:GLU340 4.7 20.7 1.0
C C:SER88 4.7 18.5 1.0
CG C:GLN126 4.7 23.9 1.0
N C:ILE89 4.8 19.1 1.0
CA D:GLU340 4.9 20.5 1.0
CB C:GLN126 4.9 22.0 1.0
CA C:GLN126 4.9 20.9 1.0

Sodium binding site 7 out of 8 in 8qh4

Go back to Sodium Binding Sites List in 8qh4
Sodium binding site 7 out of 8 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na507

b:41.5
occ:1.00
 OE1 D:GLU108 2.4 22.6 1.0
O D:HOH639 2.6 21.7 1.0
O D:HOH824 2.7 20.9 1.0
CD D:GLU108 3.5 21.8 1.0
NE D:ARG109 3.5 19.2 1.0
CB D:GLU108 3.6 19.9 1.0
CG2 D:ILE105 3.8 24.1 1.0
CA D:ILE105 3.9 21.4 1.0
CG2 D:ILE7 3.9 22.7 1.0
O D:ARG104 4.0 21.1 1.0
NH1 D:ARG109 4.0 19.4 1.0
CG D:GLU108 4.1 20.6 1.0
CZ D:ARG109 4.2 19.6 1.0
NE D:ARG104 4.2 19.0 1.0
CB D:ILE105 4.3 24.1 1.0
CG D:ARG104 4.3 18.8 1.0
C D:ARG104 4.3 19.7 1.0
N D:ILE105 4.3 20.2 1.0
CG D:ARG109 4.4 18.9 1.0
CD D:ARG109 4.4 19.1 1.0
OE2 D:GLU108 4.5 24.2 1.0
O D:HOH870 4.6 21.8 1.0
CD D:ARG104 4.7 18.7 1.0
O D:PRO8 4.8 23.3 1.0
CA D:GLU108 4.9 19.2 1.0
O D:HOH834 4.9 22.0 1.0
C D:ILE105 4.9 20.7 1.0
O D:ILE105 4.9 20.5 1.0
CD1 D:ILE7 5.0 24.1 1.0
CD1 D:ILE10 5.0 20.7 1.0
CB D:ARG104 5.0 18.4 1.0

Sodium binding site 8 out of 8 in 8qh4

Go back to Sodium Binding Sites List in 8qh4
Sodium binding site 8 out of 8 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na508

b:59.4
occ:1.00
 OE2 D:GLU170 2.2 38.0 1.0
O D:HOH801 2.5 21.6 1.0
CD D:GLU170 2.7 32.9 1.0
OE1 D:GLU170 3.0 36.7 1.0
O D:LEU169 3.4 20.1 1.0
N D:GLY159 3.5 22.2 1.0
CE D:LYS153 3.6 32.2 1.0
CB D:LEU158 3.6 21.6 1.0
CG D:LYS153 3.7 29.0 1.0
CA D:GLU170 3.8 22.2 1.0
CA D:GLY159 3.8 22.9 1.0
CG D:GLU170 3.9 29.2 1.0
CD D:LYS153 3.9 30.8 1.0
C D:LEU158 4.0 22.5 1.0
CB D:GLU170 4.1 25.2 1.0
C D:LEU169 4.3 20.4 1.0
CA D:LEU158 4.4 21.9 1.0
N D:GLU170 4.5 21.5 1.0
CG D:LEU158 4.5 20.9 1.0
CD1 D:LEU158 4.6 20.6 1.0
N D:ILE171 4.7 19.1 1.0
O D:LEU158 4.8 22.9 1.0
C D:GLU170 4.8 20.4 1.0
CD2 D:LEU158 4.9 20.6 1.0

Reference:

D.Wohlwend, L.Merono, S.Bucka, K.Ritter, H.J.Jessen, T.Friedrich. Structures of 3-Acetylpyridine Adenine Dinucleotide and Adp-Ribose Bound to the Electron Input Module of Respiratory Complex I. Structure 2024.
ISSN: ISSN 0969-2126
PubMed: 38503292
DOI: 10.1016/J.STR.2024.02.013
Page generated: Wed Oct 9 13:10:34 2024

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