Atomistry » Sodium » PDB 8zj7-9fij » 9fe0
Atomistry »
  Sodium »
    PDB 8zj7-9fij »
      9fe0 »

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

Go back to Sodium Binding Sites List in 9fe0
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

Go back to Sodium Binding Sites List in 9fe0
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

Go back to Sodium Binding Sites List in 9fe0
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

Go back to Sodium Binding Sites List in 9fe0
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

Go back to Sodium Binding Sites List in 9fe0
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

Go back to Sodium Binding Sites List in 9fe0
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

Go back to Sodium Binding Sites List in 9fe0
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

Go back to Sodium Binding Sites List in 9fe0
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

Go back to Sodium Binding Sites List in 9fe0
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

Last articles

Zn in 2YRC
Zn in 2YQP
Zn in 2YR2
Zn in 2YQL
Zn in 2YPT
Zn in 2YPA
Zn in 2YPU
Zn in 2YNW
Zn in 2YNT
Zn in 2YNV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy