Sodium in PDB 9fdj: Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak)

Protein crystallography data

The structure of Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak), PDB code: 9fdj 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) 47.93 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.241, 116.156, 189.026, 90, 90, 90
R / Rfree (%) 15.8 / 18.4

Other elements in 9fdj:

The structure of Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Iron (Fe) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak) (pdb code 9fdj). 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 the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak), PDB code: 9fdj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 9fdj

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Sodium binding site 1 out of 8 in the Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak)


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 the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:32.9
occ:1.00
 OD1 B:ASP94 2.6 23.1 1.0
O B:HOH758 2.6 20.2 1.0
O B:HOH807 2.7 23.6 1.0
O B:ALA179 2.8 24.2 1.0
O B:HOH818 3.2 33.7 1.0
OD2 B:ASP94 3.2 25.9 1.0
CG B:ASP94 3.3 23.2 1.0
N B:ALA179 3.6 25.0 1.0
C B:ALA179 3.6 22.7 1.0
CB B:CYS182 4.1 21.8 1.0
CA B:ALA179 4.1 25.1 1.0
CB B:ARG135 4.1 19.2 1.0
N B:GLY178 4.2 21.6 1.0
CA B:GLY176 4.3 20.6 1.0
CA B:ARG135 4.3 19.3 1.0
C B:GLY178 4.4 25.8 1.0
N B:ALA177 4.4 22.1 1.0
CE1 B:TYR133 4.5 20.1 1.0
N B:TYR180 4.5 21.2 1.0
OG B:SER96 4.6 25.4 1.0
CA B:GLY178 4.6 24.1 1.0
OH B:TYR133 4.7 22.7 1.0
C B:GLY176 4.8 21.0 1.0
CB B:ASP94 4.8 21.6 1.0
CB B:ALA179 4.8 25.6 1.0
N B:GLY136 4.8 19.8 1.0
OE1 B:GLU137 4.8 22.4 1.0
O B:ASP94 4.9 22.0 1.0
CA B:TYR180 4.9 21.1 1.0
SG B:CYS182 5.0 25.9 1.0

Sodium binding site 2 out of 8 in 9fdj

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Sodium binding site 2 out of 8 in the Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak)


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 the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na508

b:53.6
occ:1.00
 O B:HOH697 2.3 32.0 1.0
OE1 B:GLU108 2.3 33.9 1.0
O B:HOH784 2.4 29.0 1.0
CD B:GLU108 3.4 30.3 1.0
CB B:GLU108 3.5 23.8 1.0
NE B:ARG109 3.5 24.3 1.0
CG2 B:ILE7 3.7 29.1 0.5
CG2 B:ILE7 3.8 27.8 0.5
CG2 B:ILE105 3.8 25.1 1.0
NH2 B:ARG109 3.9 25.0 1.0
CA B:ILE105 4.0 23.3 1.0
CG B:GLU108 4.0 25.6 1.0
O B:ARG104 4.0 24.4 1.0
CZ B:ARG109 4.1 24.9 1.0
O B:HOH863 4.2 30.1 1.0
NE B:ARG104 4.2 24.1 1.0
CB B:ILE105 4.3 25.3 1.0
CD1 B:ILE7 4.4 25.7 0.5
CG B:ARG109 4.4 23.0 1.0
C B:ARG104 4.4 23.0 1.0
CG B:ARG104 4.5 22.6 1.0
N B:ILE105 4.5 22.6 1.0
OE2 B:GLU108 4.5 40.7 1.0
CD B:ARG109 4.5 23.6 1.0
O B:PRO8 4.7 26.2 1.0
CD B:ARG104 4.8 23.4 1.0
O B:HOH787 4.8 26.0 1.0
CA B:GLU108 4.9 21.6 1.0
CB B:ILE7 4.9 27.7 0.5
CD1 B:ILE10 4.9 24.5 1.0

Sodium binding site 3 out of 8 in 9fdj

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Sodium binding site 3 out of 8 in the Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak)


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 the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:56.3
occ:1.00
 O B:HOH848 2.3 41.6 1.0
O A:HOH367 2.6 43.2 1.0
O B:HOH664 3.0 21.4 1.0
O B:GLU345 3.5 21.1 1.0
O B:THR346 3.6 25.2 1.0
CZ A:PHE69 3.7 26.2 1.0
O B:HOH761 3.7 33.1 1.0
CE1 A:PHE69 3.8 28.9 1.0
CA B:CYS347 3.8 23.5 1.0
C B:THR346 4.0 23.5 1.0
CG2 B:ILE181 4.1 22.1 1.0
C B:GLU345 4.1 21.6 1.0
N B:CYS347 4.1 23.4 1.0
CB B:CYS347 4.3 22.1 1.0
CE2 A:PHE69 4.4 25.6 1.0
CB B:ALA179 4.5 25.6 1.0
O A:HOH368 4.5 33.8 1.0
CA B:GLU345 4.6 22.1 1.0
CD1 A:PHE69 4.6 29.4 1.0
OE1 B:GLU345 4.7 24.6 1.0
O B:HOH760 4.7 33.4 1.0
O B:HIS344 4.7 26.9 1.0
CB B:ILE181 4.9 20.7 1.0
O A:PHE69 4.9 29.7 1.0
N B:THR346 4.9 21.7 1.0
C B:CYS347 4.9 23.9 1.0

Sodium binding site 4 out of 8 in 9fdj

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Sodium binding site 4 out of 8 in the Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak)


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 the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na507

b:32.5
occ:1.00
 OD1 D:ASP94 2.6 21.1 1.0
O D:HOH752 2.6 21.0 1.0
O D:ALA179 2.8 22.7 1.0
O D:HOH798 2.8 23.9 1.0
OD2 D:ASP94 3.2 24.3 1.0
CG D:ASP94 3.2 22.4 1.0
O D:HOH840 3.3 34.6 1.0
N D:ALA179 3.5 23.8 1.0
C D:ALA179 3.6 22.7 1.0
CB D:CYS182 4.1 22.1 1.0
CA D:ALA179 4.1 23.6 1.0
CB D:ARG135 4.1 19.8 1.0
N D:GLY178 4.2 22.0 1.0
CA D:GLY176 4.3 21.6 1.0
CA D:ARG135 4.3 18.7 1.0
C D:GLY178 4.4 24.6 1.0
N D:ALA177 4.4 22.0 1.0
CE1 D:TYR133 4.5 21.5 1.0
N D:TYR180 4.5 20.9 1.0
CA D:GLY178 4.6 23.1 1.0
OG D:SER96 4.6 24.9 1.0
OH D:TYR133 4.7 23.9 1.0
CB D:ASP94 4.7 20.7 1.0
CB D:ALA179 4.8 25.3 1.0
C D:GLY176 4.8 21.8 1.0
N D:GLY136 4.8 19.9 1.0
OE1 D:GLU137 4.8 22.2 1.0
O D:ASP94 4.9 21.9 1.0
CA D:TYR180 4.9 20.0 1.0
SG D:CYS182 5.0 26.2 1.0
CA D:CYS182 5.0 21.3 1.0

Sodium binding site 5 out of 8 in 9fdj

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Sodium binding site 5 out of 8 in the Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak)


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 the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na508

b:36.7
occ:1.00
 O2B D:NAI503 2.1 35.5 1.0
O D:HOH834 3.0 26.4 1.0
N3A D:NAI503 3.2 40.6 1.0
C2B D:NAI503 3.2 36.3 1.0
C1B D:NAI503 3.4 39.0 1.0
O3B D:NAI503 3.7 28.0 1.0
CG1 D:VAL207 3.7 26.9 1.0
CD D:PRO206 3.7 26.7 1.0
CB D:TYR205 3.9 33.1 1.0
C4A D:NAI503 3.9 43.5 1.0
OE1 D:GLU185 3.9 30.9 1.0
OE2 D:GLU185 4.0 30.1 1.0
N9A D:NAI503 4.0 43.0 1.0
N D:VAL207 4.0 23.1 1.0
C3B D:NAI503 4.0 35.5 1.0
CG2 D:VAL207 4.1 28.0 1.0
C2A D:NAI503 4.1 42.7 1.0
N D:PRO206 4.2 26.8 1.0
CG D:PRO206 4.3 26.1 1.0
CD D:LYS76 4.3 24.5 1.0
CG D:LYS76 4.3 25.2 1.0
CB D:VAL207 4.3 27.2 1.0
CD D:GLU185 4.3 31.3 1.0
CD1 D:TYR205 4.4 38.5 1.0
CB D:PRO206 4.4 25.8 1.0
CG D:TYR205 4.5 36.3 1.0
O4B D:NAI503 4.7 39.2 1.0
C D:TYR205 4.7 25.9 1.0
CA D:PRO206 4.8 25.4 1.0
CA D:VAL207 4.8 25.2 1.0
CE D:LYS76 4.8 23.2 1.0
CA D:TYR205 4.8 29.2 1.0
C D:PRO206 4.9 24.5 1.0

Sodium binding site 6 out of 8 in 9fdj

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Sodium binding site 6 out of 8 in the Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak)


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 the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na509

b:50.6
occ:1.00
 OE1 D:GLU108 2.1 33.5 1.0
O D:HOH761 2.2 34.3 1.0
O D:HOH847 2.3 27.5 1.0
CD D:GLU108 3.3 29.1 1.0
CB D:GLU108 3.5 22.9 1.0
NE D:ARG109 3.6 21.9 1.0
CG2 D:ILE7 3.8 31.7 1.0
CG2 D:ILE105 3.8 25.6 1.0
NH2 D:ARG109 3.8 23.1 1.0
CA D:ILE105 3.9 22.5 1.0
CG D:GLU108 3.9 25.1 1.0
O D:ARG104 4.0 20.3 1.0
CZ D:ARG109 4.1 22.8 1.0
O D:HOH856 4.2 25.9 1.0
OE2 D:GLU108 4.3 37.0 1.0
CB D:ILE105 4.3 25.1 1.0
NE D:ARG104 4.3 22.2 1.0
CG D:ARG109 4.3 20.8 1.0
C D:ARG104 4.4 21.2 1.0
N D:ILE105 4.4 20.8 1.0
CD D:ARG109 4.5 20.7 1.0
CG D:ARG104 4.5 21.9 1.0
O D:HOH809 4.7 21.4 1.0
O D:PRO8 4.7 22.7 1.0
CD1 D:ILE7 4.7 34.2 1.0
CA D:GLU108 4.8 20.9 1.0
CD D:ARG104 4.9 21.8 1.0
CB D:ILE7 4.9 29.6 1.0
O D:ILE105 4.9 21.0 1.0
C D:ILE105 4.9 21.7 1.0

Sodium binding site 7 out of 8 in 9fdj

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Sodium binding site 7 out of 8 in the Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak)


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 the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na510

b:47.9
occ:1.00
 O D:HOH899 2.2 18.1 0.5
O4 D:FMN502 2.8 23.8 1.0
O D:HOH778 3.0 37.1 1.0
N D:SER96 3.1 19.1 1.0
N D:GLU97 3.2 20.1 0.5
N D:GLU97 3.2 19.5 0.5
C4 D:FMN502 3.2 22.5 1.0
O D:HOH734 3.4 35.0 1.0
CB D:GLU97 3.4 24.1 0.5
CB D:GLU97 3.6 22.1 0.5
N5 D:FMN502 3.7 22.7 1.0
CA D:GLU95 3.7 20.2 1.0
C4A D:FMN502 3.7 21.2 1.0
C D:GLU95 3.9 19.4 1.0
CA D:GLU97 3.9 22.4 0.5
CA D:GLU97 3.9 21.3 0.5
O D:HOH732 4.0 18.6 0.4
O D:HOH666 4.0 25.9 1.0
C D:SER96 4.0 20.5 1.0
N3 D:FMN502 4.1 20.8 1.0
CA D:SER96 4.1 20.6 1.0
CE1 D:TYR180 4.3 24.0 1.0
N D:GLU95 4.4 19.5 1.0
O D:HOH677 4.6 23.3 1.0
OE1 D:GLU97 4.7 23.8 0.5
CG D:GLU97 4.7 26.0 0.5
CB D:GLU95 4.8 21.2 1.0
C5A D:FMN502 4.8 22.2 1.0
C10 D:FMN502 4.8 20.3 1.0
OE1 D:GLU97 4.8 29.7 0.5
CG D:GLU95 4.8 21.3 1.0
CD1 D:TYR180 4.9 21.0 1.0
CB D:SER96 4.9 21.9 1.0
CG D:GLU97 5.0 22.4 0.5

Sodium binding site 8 out of 8 in 9fdj

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Sodium binding site 8 out of 8 in the Crystal Structure of the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak)


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 the Nuoef Variant R66G (Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na511

b:56.1
occ:1.00
 OE1 D:GLU129 2.3 32.3 1.0
O D:HOH624 2.4 45.3 1.0
O D:HOH920 3.3 46.1 1.0
CD D:GLU129 3.4 34.3 1.0
O D:HOH656 3.7 43.2 1.0
CB D:GLU129 4.0 29.6 1.0
CG C:PRO24 4.0 32.5 1.0
O D:HOH618 4.0 45.6 1.0
CG D:GLU129 4.0 31.2 1.0
O D:HOH913 4.2 38.7 1.0
OH D:TYR172 4.3 31.7 1.0
OE2 D:GLU129 4.4 34.6 1.0
CB C:PRO24 4.5 33.3 1.0
O D:HOH799 4.6 43.3 1.0
CE2 D:TYR172 4.8 30.3 1.0
CZ D:TYR172 5.0 30.6 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 14:31:08 2024

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