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Sodium in PDB 7fi3: Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide

Protein crystallography data

The structure of Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide, PDB code: 7fi3 was solved by H.Yokoyama, N.Kamei, K.Konishi, K.Hara, H.Hashimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 122.661, 118.635, 112.718, 90, 105.32, 90
R / Rfree (%) 15.9 / 19.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide (pdb code 7fi3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide, PDB code: 7fi3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7fi3

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Sodium binding site 1 out of 8 in the Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:21.1
occ:1.00
 O A:THR159 2.3 31.7 1.0
OD2 A:ASP165 2.3 30.7 1.0
O A:TYR167 2.3 25.6 1.0
OE2 A:GLU156 2.4 40.7 1.0
O A:GLU156 2.4 24.6 1.0
OD2 A:ASP161 2.5 31.9 1.0
CG A:ASP165 3.3 30.9 1.0
C A:TYR167 3.4 26.4 1.0
C A:GLU156 3.5 26.5 1.0
C A:THR159 3.5 29.1 1.0
CD A:GLU156 3.6 41.2 1.0
CG A:ASP161 3.6 32.7 1.0
OD1 A:ASP165 3.8 27.7 1.0
CG A:GLU156 4.1 34.4 1.0
N A:ASP161 4.1 28.3 1.0
CB A:TYR167 4.2 26.9 1.0
CA A:GLU156 4.2 28.4 1.0
N A:TYR168 4.2 25.9 1.0
CA A:TYR167 4.3 27.4 1.0
CB A:TYR168 4.3 26.3 1.0
CA A:TYR168 4.3 25.6 1.0
CB A:ASP161 4.4 32.7 1.0
N A:TRP157 4.4 23.9 1.0
OD1 A:ASP161 4.4 33.0 1.0
OG1 A:THR159 4.4 34.0 1.0
N A:THR159 4.4 26.5 1.0
CA A:THR159 4.4 28.4 1.0
N A:GLN160 4.4 27.5 1.0
CA A:TRP157 4.5 24.4 1.0
CA A:GLN160 4.5 28.7 1.0
CB A:ASP165 4.6 33.9 1.0
CB A:SER109 4.6 34.0 1.0
OE1 A:GLU156 4.7 48.6 1.0
CB A:GLU156 4.8 31.3 1.0
C A:GLN160 4.8 28.5 1.0
OG A:SER109 4.9 39.0 1.0
C A:TRP157 4.9 24.5 1.0
CA A:ASP161 4.9 31.8 1.0
CB A:THR159 4.9 30.1 1.0
N A:TYR167 5.0 28.1 1.0

Sodium binding site 2 out of 8 in 7fi3

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Sodium binding site 2 out of 8 in the Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:34.3
occ:1.00
 O A:VAL235 2.4 25.0 1.0
O A:TYR241 2.5 23.9 1.0
O A:ASN238 2.5 32.4 1.0
O A:HOH1250 2.5 30.4 1.0
O A:HOH1234 2.6 29.0 1.0
C A:ASN238 3.4 32.0 1.0
CA A:PRO239 3.5 32.9 1.0
C A:VAL235 3.6 24.8 1.0
C A:TYR241 3.6 24.2 1.0
N A:PRO239 3.9 35.0 1.0
C A:PRO239 3.9 32.2 1.0
O A:PRO239 4.1 30.9 1.0
CA A:VAL235 4.2 23.5 1.0
N A:TYR241 4.2 27.9 1.0
CG1 A:VAL235 4.2 24.8 1.0
CA A:TYR241 4.4 25.6 1.0
N A:ASN238 4.5 30.3 1.0
CA A:ASN238 4.6 30.5 1.0
O A:HOH1138 4.6 32.0 1.0
N A:SER242 4.7 22.7 1.0
N A:LYS240 4.7 34.2 1.0
N A:ALA236 4.7 25.6 1.0
O A:ALA236 4.7 29.1 1.0
C A:ALA236 4.8 28.4 1.0
CB A:PRO239 4.8 34.3 1.0
CB A:VAL235 4.8 24.1 1.0
CA A:SER242 4.9 21.5 1.0
O A:LEU234 4.9 23.1 1.0
CA A:ALA236 5.0 26.6 1.0

Sodium binding site 3 out of 8 in 7fi3

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Sodium binding site 3 out of 8 in the Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na801

b:29.5
occ:1.00
 O B:THR159 2.2 38.2 1.0
OD2 B:ASP165 2.3 47.7 1.0
O B:TYR167 2.4 39.1 1.0
O B:GLU156 2.4 38.1 1.0
OD2 B:ASP161 2.5 73.7 1.0
OE1 B:GLU156 2.6 54.1 1.0
CG B:ASP165 3.4 45.1 1.0
C B:THR159 3.4 42.9 1.0
C B:GLU156 3.5 35.6 1.0
C B:TYR167 3.5 39.2 1.0
CG B:ASP161 3.6 67.8 1.0
CD B:GLU156 3.7 49.5 1.0
OD1 B:ASP165 3.8 40.9 1.0
N B:ASP161 4.1 52.1 1.0
CG B:GLU156 4.1 42.3 1.0
CB B:TYR167 4.2 37.8 1.0
CA B:GLU156 4.2 35.7 1.0
N B:TYR168 4.3 37.0 1.0
CA B:THR159 4.3 43.0 1.0
CB B:ASP161 4.3 61.4 1.0
CA B:TYR167 4.4 39.3 1.0
N B:GLN160 4.4 45.5 1.0
CB B:TYR168 4.4 36.0 1.0
CA B:TYR168 4.4 36.7 1.0
N B:TRP157 4.4 33.3 1.0
N B:THR159 4.4 39.8 1.0
OD1 B:ASP161 4.4 71.8 1.0
CB B:THR159 4.4 44.4 1.0
CA B:GLN160 4.5 47.6 1.0
CA B:TRP157 4.5 31.4 1.0
CB B:ASP165 4.6 46.5 1.0
CB B:SER109 4.7 51.4 1.0
OE2 B:GLU156 4.8 55.3 1.0
CB B:GLU156 4.8 39.7 1.0
C B:GLN160 4.8 50.5 1.0
CA B:ASP161 4.9 56.0 1.0
C B:TRP157 4.9 29.9 1.0

Sodium binding site 4 out of 8 in 7fi3

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Sodium binding site 4 out of 8 in the Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:36.5
occ:1.00
 O B:VAL235 2.2 37.6 1.0
O B:HOH1149 2.3 35.5 1.0
O B:TYR241 2.5 36.6 1.0
O B:ASN238 2.6 35.2 1.0
C B:VAL235 3.4 38.4 1.0
C B:ASN238 3.6 38.2 1.0
C B:TYR241 3.6 34.3 1.0
CA B:PRO239 3.8 40.0 1.0
CG1 B:VAL235 4.0 34.5 1.0
CA B:VAL235 4.0 36.1 1.0
N B:PRO239 4.0 39.5 1.0
C B:PRO239 4.1 40.1 1.0
O B:PRO239 4.2 38.0 1.0
N B:TYR241 4.3 34.6 1.0
CA B:TYR241 4.5 34.1 1.0
N B:ALA236 4.5 38.1 1.0
N B:ASN238 4.5 42.7 1.0
N B:SER242 4.6 33.7 1.0
CB B:VAL235 4.6 35.5 1.0
CA B:ASN238 4.7 39.3 1.0
O B:ALA236 4.7 40.0 1.0
C B:ALA236 4.7 41.9 1.0
CA B:SER242 4.8 33.5 1.0
O B:LEU234 4.8 35.3 1.0
CA B:ALA236 4.9 42.1 1.0
N B:LYS240 4.9 40.4 1.0

Sodium binding site 5 out of 8 in 7fi3

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Sodium binding site 5 out of 8 in the Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na801

b:25.7
occ:1.00
 O C:THR159 2.1 31.5 1.0
OD2 C:ASP165 2.3 32.3 1.0
O C:GLU156 2.3 29.0 1.0
O C:TYR167 2.4 28.7 1.0
OE2 C:GLU156 2.6 47.2 1.0
OD2 C:ASP161 2.6 46.4 1.0
CG C:ASP165 3.3 36.0 1.0
C C:THR159 3.4 34.6 1.0
C C:GLU156 3.4 28.1 1.0
C C:TYR167 3.4 26.3 1.0
CG C:ASP161 3.6 49.4 1.0
CD C:GLU156 3.7 43.6 1.0
OD1 C:ASP165 3.8 34.3 1.0
N C:ASP161 4.1 39.1 1.0
CG C:GLU156 4.2 37.4 1.0
CA C:GLU156 4.2 28.5 1.0
N C:TYR168 4.2 27.0 1.0
CB C:TYR167 4.2 27.4 1.0
CB C:TYR168 4.3 26.5 1.0
CA C:TYR168 4.3 26.6 1.0
N C:GLN160 4.3 37.0 1.0
OG1 C:THR159 4.3 34.1 1.0
CA C:THR159 4.3 31.8 1.0
N C:TRP157 4.3 28.1 1.0
N C:THR159 4.3 29.7 1.0
CA C:TYR167 4.4 27.3 1.0
OD1 C:ASP161 4.4 54.8 1.0
CA C:GLN160 4.4 38.0 1.0
CB C:ASP161 4.4 45.7 1.0
CA C:TRP157 4.4 26.6 1.0
CB C:ASP165 4.5 38.2 1.0
CB C:SER109 4.7 39.6 1.0
C C:GLN160 4.7 37.0 1.0
OE1 C:GLU156 4.8 48.7 1.0
CB C:GLU156 4.8 31.9 1.0
C C:TRP157 4.8 26.4 1.0
CB C:THR159 4.8 34.5 1.0
CA C:ASP161 4.9 43.6 1.0
CD1 C:TYR168 4.9 27.3 1.0
N C:TYR167 5.0 28.7 1.0

Sodium binding site 6 out of 8 in 7fi3

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Sodium binding site 6 out of 8 in the Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na802

b:47.5
occ:1.00
 O C:HOH1202 2.3 32.3 1.0
O C:VAL235 2.6 31.1 1.0
O C:TYR241 2.7 29.5 1.0
O C:ASN238 3.1 32.9 1.0
C C:VAL235 3.7 29.1 1.0
CA C:PRO239 3.9 39.5 1.0
C C:TYR241 3.9 30.4 1.0
C C:ASN238 4.0 34.6 1.0
CG1 C:VAL235 4.2 28.1 1.0
N C:PRO239 4.3 38.2 1.0
C C:PRO239 4.3 40.2 1.0
O C:PRO239 4.4 40.5 1.0
CA C:VAL235 4.4 28.4 1.0
N C:TYR241 4.7 33.1 1.0
O C:ALA236 4.7 35.3 1.0
N C:ALA236 4.8 31.7 1.0
C C:ALA236 4.8 35.6 1.0
N C:SER242 4.8 28.2 1.0
CA C:TYR241 4.9 32.6 1.0
N C:ASN238 4.9 37.0 1.0
CA C:SER242 4.9 26.8 1.0
CB C:VAL235 5.0 27.9 1.0
CA C:ALA236 5.0 32.8 1.0

Sodium binding site 7 out of 8 in 7fi3

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Sodium binding site 7 out of 8 in the Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na801

b:23.4
occ:1.00
 O D:THR159 2.3 30.9 1.0
O D:GLU156 2.3 26.1 1.0
O D:TYR167 2.3 26.3 1.0
OD2 D:ASP165 2.4 38.8 1.0
OD2 D:ASP161 2.4 45.9 1.0
OE1 D:GLU156 2.4 41.9 1.0
CG D:ASP165 3.4 39.2 1.0
C D:GLU156 3.4 27.6 1.0
C D:TYR167 3.5 29.3 1.0
C D:THR159 3.5 34.7 1.0
CG D:ASP161 3.6 45.7 1.0
CD D:GLU156 3.6 41.1 1.0
OD1 D:ASP165 3.8 37.6 1.0
CG D:GLU156 4.1 38.1 1.0
CB D:TYR167 4.2 29.5 1.0
CA D:GLU156 4.2 30.3 1.0
N D:ASP161 4.2 41.4 1.0
N D:TYR168 4.3 30.0 1.0
CA D:TYR167 4.4 29.3 1.0
CA D:THR159 4.4 35.7 1.0
N D:TRP157 4.4 25.7 1.0
OD1 D:ASP161 4.4 49.2 1.0
CB D:ASP161 4.4 44.7 1.0
CA D:TYR168 4.4 30.7 1.0
CB D:TYR168 4.4 30.1 1.0
N D:THR159 4.4 31.9 1.0
N D:GLN160 4.5 35.8 1.0
CB D:THR159 4.5 39.5 1.0
CB D:SER109 4.5 48.3 1.0
CA D:TRP157 4.5 26.7 1.0
CA D:GLN160 4.6 36.2 1.0
OE2 D:GLU156 4.7 44.1 1.0
CB D:ASP165 4.7 40.5 1.0
CB D:GLU156 4.7 34.2 1.0
OG D:SER109 4.9 51.6 1.0
C D:GLN160 4.9 37.9 1.0
C D:TRP157 4.9 26.7 1.0
CA D:ASP161 5.0 43.7 1.0

Sodium binding site 8 out of 8 in 7fi3

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Sodium binding site 8 out of 8 in the Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Archaeal Oligopeptide Permease A (Oppa) From Thermococcus Kodakaraensis in Complex with An Endogenous Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na802

b:38.5
occ:1.00
 O D:VAL235 2.3 29.3 1.0
O D:HOH1175 2.4 40.4 1.0
O D:TYR241 2.4 24.9 1.0
O D:ASN238 2.6 35.1 1.0
C D:VAL235 3.5 31.0 1.0
C D:ASN238 3.6 36.7 1.0
C D:TYR241 3.6 25.1 1.0
CA D:PRO239 3.8 36.0 1.0
N D:PRO239 4.1 37.5 1.0
CG1 D:VAL235 4.1 29.3 1.0
CA D:VAL235 4.1 30.4 1.0
C D:PRO239 4.1 35.2 1.0
O D:PRO239 4.2 37.2 1.0
N D:TYR241 4.2 28.7 1.0
CA D:TYR241 4.4 26.7 1.0
N D:ASN238 4.5 36.4 1.0
N D:ALA236 4.6 29.6 1.0
N D:SER242 4.6 24.4 1.0
O D:ALA236 4.7 35.8 1.0
CA D:ASN238 4.7 34.5 1.0
C D:ALA236 4.7 33.8 1.0
CB D:VAL235 4.7 29.1 1.0
N D:LYS240 4.8 34.2 1.0
CA D:SER242 4.8 23.5 1.0
CA D:ALA236 4.9 32.1 1.0
O D:LEU234 4.9 31.9 1.0

Reference:

H.Yokoyama, N.Kamei, K.Konishi, K.Hara, Y.Ishikawa, I.Matsui, P.Forterre, H.Hashimoto. Structural Basis For Peptide Recognition By Archaeal Oligopeptide Permease A. Proteins V. 90 1434 2022.
ISSN: ESSN 1097-0134
PubMed: 35170084
DOI: 10.1002/PROT.26324
Page generated: Tue Oct 8 16:50:59 2024

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