Sodium in PDB 9fe0: Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+

Protein crystallography data

The structure of Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+, PDB code: 9fe0 was solved by D.Wohlwend, T.Friedrich, S.Goeppert-Asadollahpour, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.20 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.527, 116.5, 190.823, 90, 90, 90
R / Rfree (%) 18.6 / 22.9

Other elements in 9fe0:

The structure of Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ also contains other interesting chemical elements:

Iron (Fe) 12 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ (pdb code 9fe0). 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 Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+, PDB code: 9fe0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 9fe0

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Sodium binding site 1 out of 9 in the Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+


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 Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na508

b:47.7
occ:1.00
 O1N B:NAD503 2.5 30.9 1.0
O2A B:NAD503 3.5 32.9 1.0
O3 B:NAD503 3.6 28.3 1.0
PN B:NAD503 3.6 29.5 1.0
CA B:GLY394 3.9 23.9 1.0
O B:HOH668 4.0 20.5 1.0
PA B:NAD503 4.0 28.8 1.0
C5D B:NAD503 4.1 32.0 1.0
O B:HOH610 4.2 28.8 1.0
N B:GLY394 4.2 24.3 1.0
O5D B:NAD503 4.3 29.6 1.0
O1A B:NAD503 4.4 30.1 1.0
O2N B:NAD503 4.9 28.4 1.0
O B:HOH783 5.0 6.3 0.5

Sodium binding site 2 out of 9 in 9fe0

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Sodium binding site 2 out of 9 in the Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+


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 Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:38.3
occ:1.00
 O2B B:NAD503 2.5 27.1 1.0
O B:HOH758 2.8 25.7 1.0
N3A B:NAD503 3.0 31.8 1.0
CG1 B:VAL207 3.5 25.3 1.0
C2B B:NAD503 3.6 27.4 1.0
C1B B:NAD503 3.7 28.6 1.0
CD B:PRO206 3.7 25.6 1.0
CG2 B:VAL207 3.8 27.1 1.0
C2A B:NAD503 3.8 32.3 1.0
CB B:TYR205 3.9 31.7 1.0
N B:VAL207 3.9 25.0 1.0
C4A B:NAD503 3.9 31.5 1.0
O3B B:NAD503 4.0 25.5 1.0
CG B:LYS76 4.0 25.6 1.0
N B:PRO206 4.1 26.3 1.0
CB B:VAL207 4.1 26.4 1.0
CD B:LYS76 4.1 24.8 1.0
N9A B:NAD503 4.2 30.5 1.0
CB B:PRO206 4.3 24.4 1.0
OE1 B:GLU185 4.3 22.0 1.0
CG B:PRO206 4.3 24.2 1.0
C3B B:NAD503 4.4 26.5 1.0
OE2 B:GLU185 4.5 23.1 1.0
C B:TYR205 4.6 28.3 1.0
CA B:VAL207 4.6 25.9 1.0
CA B:PRO206 4.6 25.3 1.0
CE B:LYS76 4.6 24.1 1.0
CG B:TYR205 4.7 33.2 1.0
C B:PRO206 4.7 25.2 1.0
CA B:TYR205 4.8 30.4 1.0
CD1 B:TYR205 4.8 32.8 1.0
CD B:GLU185 4.8 22.6 1.0
O4B B:NAD503 4.9 28.2 1.0
O B:THR216 4.9 22.7 1.0

Sodium binding site 3 out of 9 in 9fe0

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Sodium binding site 3 out of 9 in the Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+


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 Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na510

b:32.5
occ:1.00
 O B:HOH684 2.5 16.2 1.0
OD1 B:ASP94 2.7 21.3 1.0
O B:HOH742 2.8 21.0 1.0
O B:ALA179 3.0 22.9 1.0
O B:HOH694 3.0 32.2 1.0
CG B:ASP94 3.5 20.9 1.0
OD2 B:ASP94 3.6 21.2 1.0
N B:ALA179 3.6 25.9 1.0
C B:ALA179 3.7 23.4 1.0
N B:GLY178 4.0 25.7 1.0
CB B:ARG135 4.0 20.3 1.0
CA B:ARG135 4.2 20.3 1.0
CA B:ALA179 4.2 25.0 1.0
N B:ALA177 4.3 25.4 1.0
C B:GLY178 4.3 26.2 1.0
CB B:CYS182 4.3 23.7 1.0
CA B:GLY176 4.4 24.1 1.0
CA B:GLY178 4.5 26.1 1.0
OE1 B:GLU137 4.5 25.7 1.0
N B:TYR180 4.6 23.2 1.0
OG B:SER96 4.6 19.5 1.0
C B:GLY176 4.7 24.8 1.0
N B:GLY136 4.7 21.5 1.0
CE1 B:TYR133 4.7 20.0 1.0
CB B:ALA179 4.9 25.9 1.0
OH B:TYR133 4.9 21.1 1.0
CB B:ASP94 4.9 20.5 1.0

Sodium binding site 4 out of 9 in 9fe0

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Sodium binding site 4 out of 9 in the Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+


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 Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na511

b:45.4
occ:1.00
 O B:HOH620 2.3 20.8 1.0
OE1 B:GLU108 2.4 29.6 1.0
O B:HOH749 2.4 29.2 1.0
NE B:ARG109 3.5 26.5 1.0
CD B:GLU108 3.6 28.1 1.0
NH2 B:ARG109 3.8 27.8 1.0
CG2 B:ILE7 3.8 31.4 1.0
CB B:GLU108 3.9 25.5 1.0
CG2 B:ILE105 4.0 25.6 1.0
CZ B:ARG109 4.0 27.6 1.0
O B:HOH800 4.0 29.6 1.0
CA B:ILE105 4.1 24.1 1.0
O B:PRO8 4.3 28.9 1.0
O B:ARG104 4.3 22.0 1.0
CG B:GLU108 4.3 25.9 1.0
NE B:ARG104 4.3 21.6 1.0
CB B:ILE105 4.5 24.8 1.0
CD B:ARG109 4.5 25.6 1.0
OE2 B:GLU108 4.5 30.5 1.0
CG B:ARG109 4.6 25.1 1.0
N B:ILE105 4.7 22.4 1.0
C B:ARG104 4.7 22.0 1.0
CG B:ARG104 4.7 20.9 1.0
CD1 B:ILE10 4.7 23.5 1.0
O B:HOH774 4.7 24.3 1.0
CB B:ILE7 4.8 32.4 1.0
CD1 B:ILE7 4.8 33.6 1.0
CD B:ARG104 4.9 21.3 1.0

Sodium binding site 5 out of 9 in 9fe0

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Sodium binding site 5 out of 9 in the Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+


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 Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na208

b:38.1
occ:1.00
 OE2 C:GLU133 2.3 29.3 1.0
O D:PRO261 2.8 23.2 1.0
N D:TYR11 3.1 25.2 1.0
OG C:SER132 3.5 22.7 1.0
CD C:GLU133 3.5 27.5 1.0
CB D:TYR11 3.6 26.0 1.0
C D:PRO261 3.7 22.7 1.0
O D:HOH683 3.7 22.8 1.0
CB C:SER132 3.8 23.2 1.0
CA D:ILE10 3.9 24.5 1.0
CA D:TYR11 4.0 25.6 1.0
C D:ILE10 4.0 24.6 1.0
O C:SER132 4.0 23.7 1.0
O C:HOH354 4.1 54.2 1.0
CA D:GLY262 4.1 21.5 1.0
N D:GLY262 4.3 21.8 1.0
C C:SER132 4.3 23.0 1.0
CG C:GLU133 4.3 25.2 1.0
OE1 C:GLU133 4.4 29.7 1.0
CG2 D:ILE10 4.4 23.0 1.0
O D:ARG9 4.5 26.6 1.0
CG D:PRO261 4.5 24.3 1.0
CB D:ILE10 4.6 23.1 1.0
CA C:SER132 4.7 23.1 1.0
O D:TYR11 4.7 24.4 1.0
CA D:PRO261 4.8 23.1 1.0
CB D:PRO261 4.8 23.3 1.0
C D:TYR11 4.9 25.1 1.0
N C:GLU133 4.9 23.0 1.0
N D:ILE10 5.0 25.2 1.0

Sodium binding site 6 out of 9 in 9fe0

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Sodium binding site 6 out of 9 in the Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+


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 Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na508

b:41.2
occ:1.00
 OD1 D:ASP94 2.5 20.5 1.0
O D:HOH718 2.5 16.5 1.0
O D:HOH717 2.9 25.9 1.0
O D:ALA179 3.1 22.4 1.0
O D:HOH733 3.2 41.7 1.0
CG D:ASP94 3.3 20.0 1.0
OD2 D:ASP94 3.4 20.6 1.0
N D:ALA179 3.8 25.4 1.0
C D:ALA179 3.8 23.1 1.0
CB D:ARG135 4.0 19.4 1.0
CB D:CYS182 4.3 23.5 1.0
CA D:ARG135 4.3 19.2 1.0
N D:GLY178 4.3 24.8 1.0
CA D:ALA179 4.3 25.4 1.0
CA D:GLY176 4.4 21.9 1.0
C D:GLY178 4.5 26.2 1.0
N D:ALA177 4.5 23.6 1.0
OE1 D:GLU137 4.5 22.6 1.0
OG D:SER96 4.6 21.0 1.0
N D:TYR180 4.6 22.5 1.0
CE1 D:TYR133 4.7 21.6 1.0
CB D:ASP94 4.8 19.0 1.0
CA D:GLY178 4.8 25.4 1.0
O D:ASP94 4.9 18.8 1.0
C D:GLY176 4.9 23.0 1.0
N D:GLY136 4.9 20.6 1.0
OH D:TYR133 4.9 23.1 1.0
CA D:TYR180 4.9 21.8 1.0

Sodium binding site 7 out of 9 in 9fe0

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Sodium binding site 7 out of 9 in the Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+


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 Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na509

b:33.2
occ:1.00
 O2B D:NAD503 2.5 23.3 1.0
O D:HOH729 2.9 21.8 1.0
N3A D:NAD503 3.3 26.0 1.0
CG1 D:VAL207 3.5 24.8 1.0
C2B D:NAD503 3.5 23.2 1.0
C1B D:NAD503 3.6 23.8 1.0
CG2 D:VAL207 3.7 26.0 1.0
CD D:PRO206 3.8 24.2 1.0
O3B D:NAD503 3.8 21.4 1.0
CG D:LYS76 3.9 24.7 1.0
N D:VAL207 4.0 25.0 1.0
CB D:TYR205 4.0 28.9 1.0
CD D:LYS76 4.0 23.8 1.0
CB D:VAL207 4.1 25.8 1.0
C4A D:NAD503 4.1 25.7 1.0
C2A D:NAD503 4.2 27.5 1.0
N9A D:NAD503 4.2 24.6 1.0
N D:PRO206 4.2 25.0 1.0
C3B D:NAD503 4.3 22.2 1.0
OE1 D:GLU185 4.4 21.2 1.0
OE2 D:GLU185 4.4 21.1 1.0
CB D:PRO206 4.5 24.1 1.0
CG D:PRO206 4.6 23.7 1.0
CE D:LYS76 4.6 23.0 1.0
CA D:VAL207 4.6 25.8 1.0
CG D:TYR205 4.7 30.1 1.0
O4B D:NAD503 4.8 23.3 1.0
CD1 D:TYR205 4.8 29.7 1.0
C D:TYR205 4.8 26.6 1.0
CD D:GLU185 4.8 21.3 1.0
CA D:PRO206 4.8 24.9 1.0
C D:PRO206 4.9 25.2 1.0
CA D:TYR205 4.9 27.8 1.0
O D:THR216 5.0 21.8 1.0

Sodium binding site 8 out of 9 in 9fe0

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Sodium binding site 8 out of 9 in the Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+


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 Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na510

b:33.8
occ:1.00
 OE1 D:GLU190 2.8 27.7 1.0
O D:HOH795 2.9 40.2 1.0
O D:ARG196 2.9 26.4 1.0
CD D:GLU190 3.7 26.6 1.0
CB D:HIS198 3.8 26.4 1.0
C D:ARG196 3.8 26.3 1.0
CB D:LYS195 3.9 29.4 1.0
CG D:GLU190 3.9 25.0 1.0
CB D:GLU190 4.0 24.1 1.0
N D:HIS198 4.0 24.8 1.0
ND1 D:HIS198 4.0 29.2 1.0
O D:HOH668 4.0 39.5 1.0
N D:ARG196 4.0 28.5 1.0
CG D:HIS198 4.1 27.4 1.0
CE D:LYS195 4.2 33.3 1.0
CA D:ARG196 4.3 27.9 1.0
CB D:ARG196 4.4 29.1 1.0
CA D:HIS198 4.4 25.1 1.0
O D:HIS198 4.4 24.6 1.0
O D:HOH735 4.5 42.6 1.0
CD D:LYS195 4.5 32.9 1.0
O D:HOH776 4.5 24.9 1.0
C D:LYS195 4.7 28.1 1.0
CG D:LYS195 4.8 31.3 1.0
N D:GLY197 4.9 25.0 1.0
OE2 D:GLU190 4.9 27.3 1.0
C D:HIS198 4.9 24.6 1.0
CA D:LYS195 5.0 28.8 1.0

Sodium binding site 9 out of 9 in 9fe0

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Sodium binding site 9 out of 9 in the Crystal Structure of Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+


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 Reduced Nuoef Variant R66G(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na511

b:53.4
occ:1.00
 O D:HOH619 2.2 32.0 1.0
OE1 D:GLU108 2.3 27.8 1.0
O D:HOH749 2.3 36.2 1.0
CD D:GLU108 3.5 27.4 1.0
NE D:ARG109 3.6 23.8 1.0
CG2 D:ILE7 3.7 27.8 1.0
CB D:GLU108 3.7 25.0 1.0
NH2 D:ARG109 3.9 24.6 1.0
CG2 D:ILE105 3.9 22.8 1.0
O D:HOH743 4.0 23.1 1.0
CA D:ILE105 4.1 21.7 1.0
CZ D:ARG109 4.1 24.6 1.0
CG D:GLU108 4.1 26.1 1.0
NE D:ARG104 4.3 20.9 1.0
O D:PRO8 4.4 24.4 1.0
OE2 D:GLU108 4.4 29.8 1.0
O D:ARG104 4.5 20.1 1.0
CB D:ILE105 4.5 22.3 1.0
CD D:ARG109 4.5 22.9 1.0
CG D:ARG109 4.5 22.9 1.0
CG D:ARG104 4.5 19.9 1.0
N D:ILE105 4.6 20.7 1.0
C D:ARG104 4.7 20.1 1.0
O D:HOH725 4.7 16.6 1.0
CB D:ILE7 4.7 28.3 1.0
CD1 D:ILE7 4.8 28.9 1.0
CD D:ARG104 4.9 20.4 1.0
CD1 D:ILE10 4.9 22.2 1.0

Reference:

S.Goppert-Asadollahpour, D.Wohlwend, T.Friedrich. Structural Robustness of the Nadh Binding Site in Nadh:Ubiquinone Oxidoreductase (Complex I). Biochim Biophys Acta V.1865 49491 2024BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 38960077
DOI: 10.1016/J.BBABIO.2024.149491
Page generated: Wed Oct 9 14:31:41 2024

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