Sodium in PDB 9fil: Crystal Structure of Reduced Nuoef Variant E222K(Nuof) From Aquifex Aeolicus Bound to Nad+

Protein crystallography data

The structure of Crystal Structure of Reduced Nuoef Variant E222K(Nuof) From Aquifex Aeolicus Bound to Nad+, PDB code: 9fil 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) 49.40 / 2.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.136, 115.539, 189.92, 90, 90, 90
R / Rfree (%) 20.1 / 24.8

Other elements in 9fil:

The structure of Crystal Structure of Reduced Nuoef Variant E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ also contains other interesting chemical elements:

Iron (Fe) 12 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Reduced Nuoef Variant E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ (pdb code 9fil). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Reduced Nuoef Variant E222K(Nuof) From Aquifex Aeolicus Bound to Nad+, PDB code: 9fil:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 9fil

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Sodium binding site 1 out of 10 in the Crystal Structure of Reduced Nuoef Variant E222K(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 E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:22.3
occ:1.00
 OE2 A:GLU143 2.3 13.1 1.0
O A:LEU128 2.4 11.7 1.0
O B:GLU137 2.8 12.5 1.0
CD A:GLU143 3.2 12.8 1.0
O B:HOH700 3.2 25.4 1.0
OE1 A:GLU143 3.3 12.6 1.0
NH1 B:ARG104 3.5 13.2 1.0
C A:LEU128 3.5 11.5 1.0
CD1 B:TYR138 3.6 10.9 1.0
CE1 B:TYR138 3.7 10.7 1.0
CB A:LEU128 3.8 11.9 1.0
C B:GLU137 3.9 12.4 1.0
CA A:LEU128 4.0 11.7 1.0
CZ B:ARG104 4.1 13.2 1.0
NH2 B:ARG104 4.1 13.6 1.0
CB B:GLU137 4.3 12.9 1.0
CD2 A:LEU128 4.4 12.5 1.0
SD A:MET138 4.5 15.3 1.0
CG A:GLU143 4.5 13.0 1.0
N A:GLY129 4.6 11.4 1.0
CE A:MET138 4.6 15.2 1.0
CG A:LEU128 4.7 12.4 1.0
CA B:GLU137 4.7 12.8 1.0
N B:TYR138 4.8 12.0 1.0
CA B:TYR138 4.9 11.8 1.0
CG B:TYR138 4.9 10.8 1.0

Sodium binding site 2 out of 10 in 9fil

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Sodium binding site 2 out of 10 in the Crystal Structure of Reduced Nuoef Variant E222K(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 E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:19.6
occ:1.00
 OE1 B:GLU33 2.7 20.1 1.0
O B:HOH730 3.0 17.4 1.0
N B:SER30 3.2 16.4 1.0
O B:HOH632 3.4 17.2 1.0
O B:VAL28 3.4 15.9 1.0
CB B:SER30 3.8 17.8 1.0
CD B:GLU33 3.9 20.4 1.0
CA B:HIS29 3.9 15.3 1.0
CB B:GLU33 4.0 20.0 1.0
OG B:SER30 4.0 18.1 1.0
C B:HIS29 4.0 15.3 1.0
CA B:SER30 4.0 16.7 1.0
NH2 B:ARG27 4.1 18.3 1.0
C B:VAL28 4.4 15.0 1.0
CG B:GLU33 4.6 20.2 1.0
N B:HIS29 4.6 14.7 1.0
C B:SER30 4.8 16.8 1.0
O B:SER30 4.8 16.7 1.0
OE2 B:GLU33 4.9 20.5 1.0
CB B:HIS29 5.0 15.0 1.0

Sodium binding site 3 out of 10 in 9fil

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Sodium binding site 3 out of 10 in the Crystal Structure of Reduced Nuoef Variant E222K(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 E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na508

b:24.2
occ:1.00
 OD1 B:ASP94 2.5 11.5 1.0
O B:ALA179 2.8 14.9 1.0
O B:HOH706 2.8 10.5 1.0
O B:HOH658 2.8 8.8 1.0
OD2 B:ASP94 3.2 12.1 1.0
CG B:ASP94 3.2 11.7 1.0
O B:HOH688 3.4 18.4 1.0
C B:ALA179 3.7 14.5 1.0
N B:ALA179 3.8 15.6 1.0
CB B:ARG135 4.0 10.8 1.0
CA B:ARG135 4.1 10.7 1.0
CB B:CYS182 4.2 12.2 1.0
CA B:ALA179 4.3 15.3 1.0
OG B:SER96 4.3 11.0 1.0
CA B:GLY176 4.4 13.0 1.0
N B:GLY178 4.4 15.4 1.0
CE1 B:TYR133 4.5 10.3 1.0
N B:ALA177 4.6 14.4 1.0
CB B:ASP94 4.7 11.3 1.0
N B:TYR180 4.7 13.4 1.0
CB B:ALA179 4.7 15.8 1.0
C B:GLY178 4.8 16.2 1.0
OE1 B:GLU137 4.8 12.4 1.0
N B:GLY136 4.8 11.6 1.0
OH B:TYR133 4.8 11.1 1.0
O B:ASP94 4.9 11.1 1.0
CA B:GLY178 4.9 15.7 1.0
C B:GLY176 4.9 13.8 1.0

Sodium binding site 4 out of 10 in 9fil

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Sodium binding site 4 out of 10 in the Crystal Structure of Reduced Nuoef Variant E222K(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 E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:37.3
occ:1.00
 OD2 B:ASP376 2.5 24.2 1.0
CG B:ASP376 3.5 24.3 1.0
O B:HOH709 3.5 23.7 1.0
CD B:LYS366 3.7 30.5 1.0
OD1 B:ASP376 3.7 24.0 1.0
CG2 B:THR373 3.8 27.1 1.0
NZ B:LYS366 3.8 34.2 1.0
CE B:LYS366 4.0 32.4 1.0
O B:GLU371 4.1 31.3 1.0
O B:HOH666 4.1 16.5 1.0
N B:THR373 4.7 26.9 1.0
CG B:LYS366 4.7 28.3 1.0
OG1 B:THR373 4.8 26.5 1.0
CB B:ASP376 4.9 24.4 1.0
CB B:THR373 4.9 27.4 1.0

Sodium binding site 5 out of 10 in 9fil

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Sodium binding site 5 out of 10 in the Crystal Structure of Reduced Nuoef Variant E222K(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 E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na510

b:35.2
occ:1.00
 OE2 B:GLU365 2.7 27.0 1.0
O B:HOH685 2.7 28.6 1.0
CE B:LYS369 3.6 36.7 1.0
CD B:GLU365 3.7 25.2 1.0
NZ B:LYS369 3.9 37.6 1.0
CG B:GLU365 4.1 23.9 1.0
CD2 B:LEU336 4.5 18.4 1.0
OE2 B:GLU340 4.6 16.9 1.0
OE1 B:GLU365 4.8 25.7 1.0
CD B:LYS369 4.9 35.2 1.0
CB B:GLU365 5.0 22.3 1.0

Sodium binding site 6 out of 10 in 9fil

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Sodium binding site 6 out of 10 in the Crystal Structure of Reduced Nuoef Variant E222K(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 E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na511

b:26.7
occ:1.00
 OD2 A:ASP71 2.3 33.4 1.0
CB B:HIS344 3.1 20.5 1.0
CD2 B:HIS344 3.3 28.2 1.0
CG B:HIS344 3.4 25.2 1.0
O A:HOH347 3.5 23.3 1.0
CG A:ASP71 3.6 29.1 1.0
O B:HIS344 3.7 15.8 1.0
O A:HOH348 4.0 25.1 1.0
CA B:HIS344 4.1 18.4 1.0
CG A:GLN126 4.2 15.8 1.0
OD1 A:ASP71 4.2 29.8 1.0
C B:HIS344 4.3 16.0 1.0
NE2 A:GLN126 4.5 17.4 1.0
NE2 B:HIS344 4.6 29.9 1.0
CB A:ASP71 4.6 25.7 1.0
ND1 B:HIS344 4.7 28.3 1.0
CD A:GLN126 4.8 16.6 1.0
OE2 B:GLU345 4.8 12.9 1.0

Sodium binding site 7 out of 10 in 9fil

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Sodium binding site 7 out of 10 in the Crystal Structure of Reduced Nuoef Variant E222K(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 E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:35.2
occ:1.00
 OD1 C:ASP54 2.7 42.9 1.0
O C:LEU58 2.9 34.4 1.0
N C:ASP54 3.9 37.5 1.0
C C:ALA53 3.9 35.6 1.0
CB C:ALA53 3.9 35.5 1.0
CG C:ASP54 3.9 43.3 1.0
C C:LEU58 4.0 33.3 1.0
O C:ALA53 4.0 34.9 1.0
CA C:ASP54 4.1 39.1 1.0
CA C:PRO59 4.4 35.1 1.0
CE C:LYS50 4.4 47.6 1.0
N C:LEU60 4.5 36.2 1.0
NZ C:LYS50 4.5 48.4 1.0
CA C:ALA53 4.5 34.5 1.0
CB C:ASP54 4.6 41.5 1.0
N C:PRO59 4.6 33.6 1.0
C C:PRO59 4.7 34.4 1.0
CD C:LYS50 4.8 45.4 1.0
N C:LEU58 4.8 32.3 1.0
O C:LYS50 4.9 40.1 1.0
OD2 C:ASP54 4.9 45.1 1.0

Sodium binding site 8 out of 10 in 9fil

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Sodium binding site 8 out of 10 in the Crystal Structure of Reduced Nuoef Variant E222K(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 E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na203

b:12.3
occ:1.00
 OE2 C:GLU143 2.3 12.8 1.0
O C:LEU128 2.5 10.7 1.0
O D:GLU137 2.9 11.7 1.0
CD C:GLU143 3.1 12.6 1.0
OE1 C:GLU143 3.4 12.4 1.0
NH1 D:ARG104 3.4 12.3 1.0
C C:LEU128 3.5 10.7 1.0
CD1 D:TYR138 3.6 10.4 1.0
CE1 D:TYR138 3.7 10.3 1.0
C D:GLU137 3.8 11.4 1.0
CB C:LEU128 3.8 11.1 1.0
CA C:LEU128 4.0 10.8 1.0
NH2 D:ARG104 4.1 12.6 1.0
CZ D:ARG104 4.1 12.4 1.0
CB D:GLU137 4.1 11.7 1.0
SD C:MET138 4.3 13.6 1.0
CD2 C:LEU128 4.5 11.6 1.0
CG C:GLU143 4.5 12.7 1.0
CA D:GLU137 4.6 11.6 1.0
N D:TYR138 4.6 11.1 1.0
CE C:MET138 4.7 13.8 1.0
N C:GLY129 4.7 10.7 1.0
CG C:LEU128 4.7 11.5 1.0
CA D:TYR138 4.8 11.1 1.0
CG D:TYR138 4.9 10.3 1.0
CG C:MET138 5.0 13.6 1.0

Sodium binding site 9 out of 10 in 9fil

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Sodium binding site 9 out of 10 in the Crystal Structure of Reduced Nuoef Variant E222K(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 E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na507

b:25.3
occ:1.00
 OD1 D:ASP94 2.6 11.6 1.0
O D:HOH661 2.7 2.9 1.0
O D:ALA179 2.8 15.2 1.0
O D:HOH673 2.8 15.2 1.0
OD2 D:ASP94 3.2 12.6 1.0
CG D:ASP94 3.3 12.0 1.0
O D:HOH660 3.4 16.9 1.0
C D:ALA179 3.7 14.5 1.0
N D:ALA179 3.7 16.6 1.0
CB D:ARG135 4.0 9.8 1.0
CA D:ARG135 4.1 9.7 1.0
CB D:CYS182 4.1 12.6 1.0
CA D:ALA179 4.2 15.8 1.0
N D:GLY178 4.3 16.3 1.0
CA D:GLY176 4.3 12.7 1.0
N D:ALA177 4.4 14.3 1.0
OG D:SER96 4.4 12.6 1.0
CE1 D:TYR133 4.5 9.4 1.0
C D:GLY178 4.6 17.3 1.0
N D:TYR180 4.7 13.3 1.0
OH D:TYR133 4.7 10.1 1.0
N D:GLY136 4.7 10.3 1.0
OE1 D:GLU137 4.7 11.1 1.0
C D:GLY176 4.7 13.4 1.0
CB D:ASP94 4.7 11.4 1.0
CA D:GLY178 4.8 16.7 1.0
CB D:ALA179 4.8 16.6 1.0
O D:ASP94 5.0 12.1 1.0
C D:ARG135 5.0 10.0 1.0

Sodium binding site 10 out of 10 in 9fil

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Sodium binding site 10 out of 10 in the Crystal Structure of Reduced Nuoef Variant E222K(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 10 of Crystal Structure of Reduced Nuoef Variant E222K(Nuof) From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na508

b:30.4
occ:1.00
 OE1 D:GLU185 3.3 14.2 1.0
O3B D:NAD503 3.4 16.5 1.0
CD D:LYS76 3.6 15.2 1.0
O2B D:NAD503 3.6 18.3 1.0
N D:VAL218 3.6 11.6 1.0
CB D:PRO206 3.8 16.3 1.0
CE D:LYS76 3.9 15.3 1.0
CG1 D:VAL207 3.9 17.4 1.0
CG D:LYS76 4.0 15.9 1.0
CG D:PRO206 4.0 16.1 1.0
O D:VAL218 4.0 11.0 1.0
NZ D:LYS76 4.0 14.5 1.0
O D:THR216 4.1 13.7 1.0
CD D:PRO206 4.1 16.9 1.0
CD D:GLU185 4.2 14.4 1.0
CA D:VAL217 4.3 12.5 1.0
CB D:VAL218 4.4 11.0 1.0
C3B D:NAD503 4.4 17.7 1.0
CA D:VAL218 4.5 11.0 1.0
N D:VAL207 4.5 17.8 1.0
C2B D:NAD503 4.5 18.4 1.0
C D:VAL217 4.5 11.7 1.0
OE2 D:GLU185 4.6 14.9 1.0
C D:VAL218 4.7 10.9 1.0
CG2 D:VAL218 4.7 11.2 1.0
C1B D:NAD503 4.8 19.1 1.0
N D:PRO206 4.8 17.4 1.0
CA D:PRO206 4.8 17.1 1.0
C D:PRO206 5.0 17.5 1.0
CB D:VAL207 5.0 18.4 1.0
C D:THR216 5.0 13.5 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 14:41:16 2024

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