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Sodium in PDB 8qh7: Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent)

Protein crystallography data

The structure of Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent), PDB code: 8qh7 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) 49.70 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.233, 116.449, 190.047, 90, 90, 90
R / Rfree (%) 17.1 / 20.1

Other elements in 8qh7:

The structure of Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) also contains other interesting chemical elements:

Iron (Fe) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) (pdb code 8qh7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent), PDB code: 8qh7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 8qh7

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Sodium binding site 1 out of 9 in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent)


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:28.0
occ:1.00
 OE2 A:GLU143 2.5 21.7 1.0
O B:GLU137 2.7 19.6 1.0
O A:LEU128 2.7 20.6 1.0
CD A:GLU143 3.2 21.8 1.0
OE1 A:GLU143 3.3 21.7 1.0
O B:HOH861 3.3 26.6 1.0
NH1 B:ARG104 3.5 23.7 1.0
CD1 B:TYR138 3.6 17.9 1.0
C A:LEU128 3.7 20.8 1.0
C B:GLU137 3.7 20.1 1.0
CB A:LEU128 3.8 20.9 1.0
CE1 B:TYR138 3.8 17.3 1.0
CA A:LEU128 4.1 20.6 1.0
CD2 A:LEU128 4.1 22.1 1.0
CB B:GLU137 4.1 20.7 1.0
SD A:MET138 4.2 25.0 1.0
NH2 B:ARG104 4.3 24.2 1.0
CZ B:ARG104 4.3 23.9 1.0
CG A:LEU128 4.5 21.7 1.0
CA B:GLU137 4.6 20.4 1.0
CG A:GLU143 4.6 22.1 1.0
N B:TYR138 4.7 19.0 1.0
CE A:MET138 4.7 25.2 1.0
CA B:TYR138 4.8 19.4 1.0
CG B:TYR138 4.9 17.9 1.0
N A:GLY129 4.9 20.5 1.0
CG A:MET138 4.9 23.8 1.0

Sodium binding site 2 out of 9 in 8qh7

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Sodium binding site 2 out of 9 in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent)


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:39.0
occ:1.00
 OE1 B:GLU108 2.4 23.8 1.0
O B:HOH743 2.5 28.5 1.0
O B:HOH885 2.5 26.3 1.0
NE B:ARG109 3.5 22.6 1.0
CD B:GLU108 3.6 24.2 1.0
CB B:GLU108 3.6 22.3 1.0
CG2 B:ILE105 3.8 25.3 1.0
CG2 B:ILE7 3.8 25.4 1.0
CA B:ILE105 3.9 23.3 1.0
NH2 B:ARG109 3.9 23.9 1.0
O B:ARG104 4.0 21.3 1.0
CZ B:ARG109 4.1 23.3 1.0
CG B:GLU108 4.1 22.8 1.0
CB B:ILE105 4.2 25.8 1.0
CG B:ARG109 4.3 21.5 1.0
NE B:ARG104 4.3 22.9 1.0
CD B:ARG109 4.3 21.6 1.0
N B:ILE105 4.4 21.5 1.0
C B:ARG104 4.4 21.6 1.0
O B:HOH886 4.4 27.6 1.0
CG B:ARG104 4.5 21.3 1.0
OE2 B:GLU108 4.6 27.7 1.0
O B:PRO8 4.7 22.4 1.0
O B:HOH800 4.7 22.4 1.0
CD B:ARG104 4.8 22.3 1.0
CD1 B:ILE7 4.8 26.1 1.0
O B:ILE105 4.9 22.2 1.0
CA B:GLU108 4.9 21.5 1.0
C B:ILE105 4.9 22.3 1.0
CB B:ILE7 5.0 25.2 1.0

Sodium binding site 3 out of 9 in 8qh7

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Sodium binding site 3 out of 9 in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent)


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na508

b:53.6
occ:1.00
 OE2 B:GLU170 2.1 43.9 1.0
O B:HOH755 2.4 22.7 1.0
CD B:GLU170 2.6 39.9 1.0
OE1 B:GLU170 2.9 43.1 1.0
O B:LEU169 3.1 27.4 1.0
N B:GLY159 3.3 28.1 1.0
CB B:LEU158 3.5 25.7 1.0
CA B:GLU170 3.5 29.3 1.0
CE B:LYS153 3.5 37.5 0.5
CG B:GLU170 3.7 36.4 1.0
CA B:GLY159 3.7 30.3 1.0
NZ B:LYS153 3.9 39.1 0.5
CB B:GLU170 4.0 32.3 1.0
C B:LEU158 4.0 28.2 1.0
C B:LEU169 4.0 27.9 1.0
CD B:LYS153 4.0 34.0 0.5
CD B:LYS153 4.0 35.6 0.5
CG B:LYS153 4.0 32.9 0.5
CG B:LYS153 4.0 34.0 0.5
N B:GLU170 4.2 28.8 1.0
NZ B:LYS153 4.2 36.1 0.5
CE B:LYS153 4.2 35.9 0.5
CA B:LEU158 4.3 26.4 1.0
CG B:LEU158 4.4 24.5 1.0
N B:ILE171 4.4 25.5 1.0
CD1 B:LEU158 4.5 24.0 1.0
CD2 B:LEU158 4.5 24.4 1.0
C B:GLU170 4.5 26.7 1.0
O B:HOH769 4.8 48.9 1.0
O B:LEU158 4.8 28.5 1.0
C B:GLY159 5.0 30.8 1.0
O2 B:GOL505 5.0 53.4 1.0

Sodium binding site 4 out of 9 in 8qh7

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Sodium binding site 4 out of 9 in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent)


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:51.2
occ:1.00
 O B:HOH928 2.5 33.5 1.0
OE1 B:GLU129 2.6 33.9 1.0
O B:HOH735 2.8 42.9 1.0
CD B:GLU129 3.4 33.8 1.0
OE2 B:GLU129 3.6 34.2 1.0
O A:HOH367 3.7 27.4 1.0
OH B:TYR88 3.8 31.3 1.0
CB A:PRO24 3.8 32.1 1.0
CG A:PRO24 4.1 31.2 1.0
CE1 B:TYR88 4.3 29.2 1.0
CZ B:TYR88 4.5 29.6 1.0
O B:HOH981 4.5 45.1 1.0
O B:HOH955 4.6 32.7 1.0
CG B:GLU129 4.8 31.3 1.0

Sodium binding site 5 out of 9 in 8qh7

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Sodium binding site 5 out of 9 in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent)


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na510

b:39.9
occ:1.00
 O B:GLY178 2.6 25.4 1.0
OE2 B:GLU345 2.6 25.8 1.0
O A:HOH410 2.7 27.0 1.0
O B:HOH933 2.9 43.1 1.0
CD B:GLU345 3.5 23.9 1.0
OE1 B:GLU345 3.6 23.2 1.0
O A:HOH314 3.7 28.0 1.0
ND1 B:HIS344 3.7 36.7 1.0
C B:GLY178 3.8 23.6 1.0
OD2 A:ASP71 3.8 34.2 1.0
CG A:GLN126 3.8 26.1 1.0
CE1 B:HIS344 3.9 36.0 1.0
CB A:GLN126 4.1 24.3 1.0
O A:HOH420 4.4 44.7 1.0
O B:HOH664 4.5 22.7 1.0
O A:HOH366 4.5 24.2 1.0
CA B:GLY178 4.5 23.2 1.0
CB A:ASP71 4.6 30.0 1.0
CG A:ASP71 4.7 32.5 1.0
N B:ALA179 4.7 22.6 1.0
N B:TYR180 4.8 20.7 1.0
CA B:ALA179 4.8 22.2 1.0
N A:GLN126 4.8 23.8 1.0
OE2 B:GLU137 4.9 22.4 1.0
CG B:GLU345 4.9 22.4 1.0
O B:HOH816 4.9 36.3 1.0

Sodium binding site 6 out of 9 in 8qh7

Go back to Sodium Binding Sites List in 8qh7
Sodium binding site 6 out of 9 in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent)


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na204

b:57.1
occ:1.00
 O C:HOH416 2.4 37.3 1.0
O D:HOH957 2.6 45.8 1.0
O C:HOH372 3.7 30.5 1.0
CG2 C:VAL87 3.9 25.5 1.0
CB C:PRO124 3.9 29.7 1.0
CG C:PRO124 4.3 31.4 1.0
CG1 C:VAL87 4.4 25.6 1.0
CB C:VAL87 4.4 25.1 1.0
O C:HOH423 4.6 48.8 1.0

Sodium binding site 7 out of 9 in 8qh7

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Sodium binding site 7 out of 9 in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent)


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na507

b:63.7
occ:1.00
 O D:HOH969 2.5 30.6 1.0
O D:LYS154 2.8 31.6 1.0
C D:LYS154 3.4 32.2 1.0
O D:HOH647 3.6 27.8 1.0
CB D:LYS154 3.9 38.1 1.0
CD D:LYS155 4.0 33.6 1.0
N D:LYS155 4.0 30.3 1.0
CA D:LYS155 4.1 30.4 1.0
CA D:LYS154 4.2 34.1 1.0
CG D:LYS155 4.2 32.0 1.0
CE D:LYS155 4.5 34.5 1.0
O D:HOH844 4.6 39.9 1.0
CB D:LYS155 4.8 30.7 1.0
NZ D:LYS155 4.9 34.3 1.0

Sodium binding site 8 out of 9 in 8qh7

Go back to Sodium Binding Sites List in 8qh7
Sodium binding site 8 out of 9 in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent)


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na508

b:46.0
occ:1.00
 O D:HOH923 2.4 32.4 1.0
OE1 D:GLU129 2.6 29.1 1.0
O D:HOH670 2.9 39.0 1.0
OH D:TYR88 3.4 27.6 1.0
CD D:GLU129 3.5 29.2 1.0
OE2 D:GLU129 3.7 28.5 1.0
O D:HOH784 3.8 26.2 1.0
O D:HOH609 3.8 44.5 1.0
CE1 D:TYR88 4.1 25.5 1.0
CB C:PRO24 4.1 29.9 1.0
CZ D:TYR88 4.2 26.5 1.0
O C:HOH398 4.2 47.3 1.0
CG C:PRO24 4.3 28.8 1.0
O D:HOH968 4.6 30.1 1.0
O D:HOH626 4.8 32.9 1.0
CG D:GLU129 4.8 27.8 1.0

Sodium binding site 9 out of 9 in 8qh7

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Sodium binding site 9 out of 9 in the Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (Without Reducing Agent) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na509

b:50.4
occ:1.00
 O D:HOH764 2.3 29.3 1.0
OD1 D:ASP37 2.4 29.5 1.0
CG D:ASP37 3.5 30.9 1.0
NZ D:LYS21 3.6 37.1 1.0
CE D:LYS21 3.8 36.3 1.0
OD2 D:ASP37 4.0 30.3 1.0
O D:HOH650 4.0 31.6 1.0
CB D:ASP37 4.6 30.1 1.0
CA D:ASP37 4.7 30.8 1.0
O D:HOH867 4.9 50.4 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 13:10:35 2024

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