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

Go back to Sodium Binding Sites List in 9fdj
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

Go back to Sodium Binding Sites List in 9fdj
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

Go back to Sodium Binding Sites List in 9fdj
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

Go back to Sodium Binding Sites List in 9fdj
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

Go back to Sodium Binding Sites List in 9fdj
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

Go back to Sodium Binding Sites List in 9fdj
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

Go back to Sodium Binding Sites List in 9fdj
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

Go back to Sodium Binding Sites List in 9fdj
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

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