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

Protein crystallography data

The structure of Crystal Structure of Oxidized Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide, PDB code: 8qgw 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) 49.63 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.537, 116.328, 189.621, 90, 90, 90
R / Rfree (%) 16.2 / 18.7

Other elements in 8qgw:

The structure of Crystal Structure of Oxidized 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
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Oxidized Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide (pdb code 8qgw). 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 Oxidized Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Oxidized 3-Acetylpyridine Adenine Dinucleotide, PDB code: 8qgw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8qgw

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Sodium binding site 1 out of 8 in the Crystal Structure of Oxidized 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 Oxidized 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:40.9
occ:1.00
 OE1 B:GLU108 2.4 22.7 1.0
O B:HOH696 2.5 23.1 1.0
O B:HOH921 2.5 22.2 1.0
CD B:GLU108 3.5 20.8 1.0
NE B:ARG109 3.5 16.9 1.0
CB B:GLU108 3.5 17.9 1.0
CG2 B:ILE105 3.8 22.9 1.0
CG2 B:ILE7 3.8 22.1 1.0
CA B:ILE105 3.9 18.1 1.0
NH2 B:ARG109 4.0 18.2 1.0
O B:ARG104 4.0 15.2 1.0
CG B:GLU108 4.0 18.2 1.0
CZ B:ARG109 4.2 18.1 1.0
CB B:ILE105 4.2 22.5 1.0
CG B:ARG109 4.3 16.0 1.0
NE B:ARG104 4.3 16.3 1.0
CD B:ARG109 4.3 16.0 1.0
C B:ARG104 4.4 15.3 1.0
O B:HOH929 4.4 21.2 1.0
CG B:ARG104 4.5 15.3 1.0
N B:ILE105 4.5 15.4 1.0
OE2 B:GLU108 4.6 25.9 1.0
O B:HOH862 4.7 18.1 1.0
O B:PRO8 4.7 17.4 1.0
CD1 B:ILE7 4.8 24.5 1.0
CA B:GLU108 4.8 15.8 1.0
CD B:ARG104 4.8 15.8 1.0
O B:ILE105 4.9 16.2 1.0
C B:ILE105 4.9 16.6 1.0
CD1 B:ILE10 5.0 16.2 1.0
CB B:ILE7 5.0 21.6 1.0

Sodium binding site 2 out of 8 in 8qgw

Go back to Sodium Binding Sites List in 8qgw
Sodium binding site 2 out of 8 in the Crystal Structure of Oxidized 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 Oxidized 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:51.1
occ:1.00
 O D:HOH972 2.6 41.8 1.0
O D:HOH946 3.0 34.9 1.0
CB C:PRO124 3.9 20.9 1.0
CG2 C:VAL87 3.9 17.8 1.0
CG1 C:VAL87 4.1 18.2 1.0
CB C:VAL87 4.3 17.9 1.0
CG C:PRO124 4.3 22.6 1.0
O C:HOH415 4.4 28.1 1.0
O C:HOH457 4.4 49.7 1.0

Sodium binding site 3 out of 8 in 8qgw

Go back to Sodium Binding Sites List in 8qgw
Sodium binding site 3 out of 8 in the Crystal Structure of Oxidized 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 Oxidized 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:37.9
occ:1.00
 OE1 D:GLU108 2.5 24.5 1.0
O D:HOH811 2.5 20.9 1.0
O D:HOH667 2.5 24.0 1.0
NE D:ARG109 3.4 17.4 1.0
CB D:GLU108 3.6 17.8 1.0
CD D:GLU108 3.6 22.3 1.0
CG2 D:ILE105 3.8 22.4 1.0
CA D:ILE105 3.9 17.8 1.0
NH1 D:ARG109 3.9 18.5 1.0
CG2 D:ILE7 3.9 22.4 1.0
O D:ARG104 3.9 17.8 1.0
CZ D:ARG109 4.0 18.4 1.0
CG D:GLU108 4.1 19.2 1.0
CB D:ILE105 4.2 22.2 1.0
CG D:ARG109 4.2 16.4 1.0
CD D:ARG109 4.3 16.9 1.0
C D:ARG104 4.3 16.5 1.0
NE D:ARG104 4.4 18.8 1.0
N D:ILE105 4.4 16.8 1.0
CG D:ARG104 4.4 16.9 1.0
O D:HOH928 4.5 21.1 1.0
OE2 D:GLU108 4.7 25.9 1.0
CD D:ARG104 4.8 17.3 1.0
O D:HOH840 4.8 18.8 1.0
O D:PRO8 4.8 20.1 1.0
CA D:GLU108 4.8 16.4 1.0
O D:ILE105 4.9 16.9 1.0
CD1 D:ILE7 4.9 24.4 1.0
C D:ILE105 4.9 16.1 1.0
CD1 D:ILE10 4.9 18.1 1.0

Sodium binding site 4 out of 8 in 8qgw

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Sodium binding site 4 out of 8 in the Crystal Structure of Oxidized 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 Oxidized 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:Na509

b:47.9
occ:1.00
 OE1 D:GLU129 2.3 23.5 1.0
O D:HOH627 2.3 36.5 1.0
O D:HOH1017 3.0 31.9 1.0
CD D:GLU129 3.3 25.1 1.0
CB D:GLU129 3.7 20.5 1.0
O D:HOH630 3.7 36.2 1.0
CG D:GLU129 3.8 22.5 1.0
CG C:PRO24 4.0 24.3 1.0
OH D:TYR172 4.2 25.6 1.0
OE2 D:GLU129 4.3 27.1 1.0
O D:HOH641 4.3 34.6 1.0
O D:HOH1004 4.4 29.0 1.0
CE2 D:TYR172 4.6 22.4 1.0
O D:HOH1006 4.6 39.8 1.0
CB C:PRO24 4.6 25.2 1.0
O D:HOH787 4.7 32.9 1.0
O D:HOH1034 4.7 45.6 1.0
CA D:GLU129 4.8 18.0 1.0
CZ D:TYR172 4.8 23.1 1.0

Sodium binding site 5 out of 8 in 8qgw

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Sodium binding site 5 out of 8 in the Crystal Structure of Oxidized 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 Oxidized 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:Na510

b:51.3
occ:1.00
 OE1 D:GLU151 2.3 32.9 1.0
O D:HOH876 3.2 32.6 1.0
CD D:GLU151 3.3 26.5 1.0
O D:HOH1019 3.4 43.2 1.0
CG D:GLU151 3.7 23.4 1.0
O D:HOH845 3.9 44.9 1.0
O D:HOH993 4.4 39.6 1.0
OE2 D:GLU151 4.4 25.5 1.0
CB D:SER30 4.5 26.8 1.0
CG2 D:ILE31 4.5 22.4 1.0
OG D:SER30 4.8 28.9 1.0
CB D:GLU151 4.8 21.8 1.0
O D:HOH896 4.9 32.3 1.0
O D:HOH913 4.9 32.3 1.0

Sodium binding site 6 out of 8 in 8qgw

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Sodium binding site 6 out of 8 in the Crystal Structure of Oxidized 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 Oxidized 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:Na511

b:49.1
occ:1.00
 OE2 D:GLU170 2.2 39.6 1.0
CD D:GLU170 2.6 33.0 1.0
O D:HOH839 2.8 21.5 1.0
OE1 D:GLU170 2.8 38.2 1.0
O D:LEU169 3.2 18.6 1.0
N D:GLY159 3.2 20.3 1.0
NZ D:LYS153 3.3 42.0 1.0
CA D:GLY159 3.5 21.6 1.0
CE D:LYS153 3.6 38.8 1.0
CB D:LEU158 3.6 20.2 1.0
CG D:GLU170 3.7 27.4 1.0
CA D:GLU170 3.7 19.9 1.0
O D:HOH848 3.8 41.9 1.0
C D:LEU158 3.8 20.9 1.0
CG D:LYS153 3.9 28.9 1.0
CB D:GLU170 4.0 23.4 1.0
C D:LEU169 4.1 18.2 1.0
CA D:LEU158 4.3 19.5 1.0
CD D:LYS153 4.3 33.9 1.0
N D:GLU170 4.4 19.0 1.0
CG D:LEU158 4.5 19.5 1.0
O D:LEU158 4.6 23.2 1.0
CD1 D:LEU158 4.6 19.3 1.0
N D:ILE171 4.8 16.9 1.0
NA D:NA512 4.8 48.5 1.0
C D:GLY159 4.8 21.7 1.0
CD2 D:LEU158 4.8 20.0 1.0
C D:GLU170 4.8 17.9 1.0
O D:HOH917 5.0 46.7 1.0

Sodium binding site 7 out of 8 in 8qgw

Go back to Sodium Binding Sites List in 8qgw
Sodium binding site 7 out of 8 in the Crystal Structure of Oxidized 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 Oxidized 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:Na512

b:48.5
occ:1.00
 OE1 D:GLU170 2.3 38.2 1.0
O3 D:SO4507 2.5 39.6 1.0
O D:HOH935 2.7 38.0 1.0
CD D:GLU170 3.4 33.0 1.0
CG D:LYS160 3.6 27.4 1.0
CG D:GLU170 3.8 27.4 1.0
S D:SO4507 3.9 39.0 1.0
CA D:GLY159 4.0 21.6 1.0
N D:LYS160 4.0 22.5 1.0
C D:GLY159 4.0 21.7 1.0
CE D:LYS160 4.1 32.6 1.0
CD D:LYS160 4.3 30.6 1.0
O4 D:SO4507 4.3 42.8 1.0
OE2 D:GLU170 4.5 39.6 1.0
O1 D:SO4507 4.6 24.6 1.0
O D:GLY159 4.7 22.1 1.0
O D:HOH1034 4.7 45.6 1.0
CB D:LYS160 4.7 25.3 1.0
O2 D:SO4507 4.7 37.3 1.0
CA D:LYS160 4.8 22.9 1.0
NA D:NA511 4.8 49.1 1.0

Sodium binding site 8 out of 8 in 8qgw

Go back to Sodium Binding Sites List in 8qgw
Sodium binding site 8 out of 8 in the Crystal Structure of Oxidized 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 Oxidized 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:Na513

b:43.0
occ:1.00
 OE1 D:GLU44 2.2 27.3 0.5
O D:HOH939 2.3 31.7 1.0
OE1 D:GLU44 2.8 26.5 0.5
NE2 D:GLN41 3.0 20.5 0.5
CD D:GLU44 3.0 25.9 0.5
OE2 D:GLU44 3.2 26.7 0.5
CD D:GLU44 3.5 26.8 0.5
O D:HOH755 3.7 36.5 1.0
OE2 D:GLU44 3.8 28.5 0.5
CD D:GLN41 3.8 21.2 0.5
OE1 D:GLN41 3.9 22.5 0.5
O D:HOH665 4.2 33.4 1.0
CG D:GLU44 4.4 23.8 0.5
CG D:GLU44 4.7 25.5 0.5

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 13:10:31 2024

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