Atomistry » Sodium » PDB 8qaw-8qyi » 8qh7
Atomistry »
  Sodium »
    PDB 8qaw-8qyi »
      8qh7 »

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

Go back to Sodium Binding Sites List in 8qh7
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

Go back to Sodium Binding Sites List in 8qh7
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

Go back to Sodium Binding Sites List in 8qh7
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

Go back to Sodium Binding Sites List in 8qh7
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

Go back to Sodium Binding Sites List in 8qh7
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

Go back to Sodium Binding Sites List in 8qh7
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

Go back to Sodium Binding Sites List in 8qh7
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

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