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Sodium in PDB 8yec: Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose

Protein crystallography data

The structure of Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose, PDB code: 8yec was solved by M.Watanabe, Y.Nakamichi, S.Mine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 130.425, 135.131, 151.131, 90, 90.06, 90
R / Rfree (%) 20.7 / 25.5

Other elements in 8yec:

The structure of Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose also contains other interesting chemical elements:

Magnesium (Mg) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose (pdb code 8yec). 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 L-Ribulose 3-Epimerase in Complex with D-Allulose, PDB code: 8yec:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8yec

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Sodium binding site 1 out of 8 in the Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose


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 L-Ribulose 3-Epimerase in Complex with D-Allulose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na304

b:34.8
occ:1.00
 O F:SER218 2.4 34.3 1.0
O E:SER218 2.4 46.4 1.0
OD1 F:ASN184 2.5 32.4 1.0
OD1 E:ASN184 2.5 32.1 1.0
O F:HOH424 2.7 32.8 1.0
C F:SER218 3.5 33.5 1.0
C E:SER218 3.5 40.8 1.0
CG F:ASN184 3.6 34.9 1.0
CG E:ASN184 3.6 31.4 1.0
CB F:SER218 3.6 39.2 1.0
O E:HOH403 3.6 31.1 1.0
CB E:SER218 3.8 43.2 1.0
ND2 F:ASN184 4.1 34.8 1.0
ND2 E:ASN184 4.1 31.1 1.0
CA F:SER218 4.1 33.9 1.0
O F:HOH422 4.2 37.7 1.0
CA E:SER218 4.3 41.3 1.0
N E:VAL219 4.5 37.4 1.0
N F:VAL219 4.6 34.2 1.0
CA E:VAL219 4.6 35.0 1.0
OG F:SER218 4.7 45.4 1.0
CA F:VAL219 4.7 34.2 1.0
O E:ASN184 4.9 35.6 1.0
O F:ASN184 4.9 36.8 1.0
CB F:ASN184 4.9 34.9 1.0
CB E:ASN184 4.9 32.4 1.0
OG E:SER218 5.0 50.2 1.0

Sodium binding site 2 out of 8 in 8yec

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Sodium binding site 2 out of 8 in the Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose


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 L-Ribulose 3-Epimerase in Complex with D-Allulose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:36.4
occ:1.00
 O A:SER218 2.2 44.4 1.0
O B:SER218 2.5 30.6 1.0
OD1 A:ASN184 2.8 29.1 1.0
OD1 B:ASN184 2.9 30.1 1.0
C A:SER218 3.4 38.3 1.0
C B:SER218 3.7 30.7 1.0
CB A:SER218 3.7 43.1 1.0
O A:HOH407 3.7 33.0 1.0
CB B:SER218 3.8 34.0 1.0
O B:HOH420 3.9 26.4 1.0
CG A:ASN184 3.9 29.2 1.0
CG B:ASN184 4.0 31.7 1.0
CA A:SER218 4.1 37.7 1.0
CA B:SER218 4.3 31.1 1.0
N A:VAL219 4.4 34.2 1.0
ND2 A:ASN184 4.4 26.5 1.0
ND2 B:ASN184 4.5 31.9 1.0
CA A:VAL219 4.6 34.8 1.0
OG A:SER218 4.7 50.9 1.0
N B:VAL219 4.7 30.4 1.0
CA B:VAL219 4.8 29.9 1.0
OG B:SER218 4.9 38.6 1.0
C A:VAL219 4.9 34.2 1.0
N A:ASP220 5.0 35.1 1.0

Sodium binding site 3 out of 8 in 8yec

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Sodium binding site 3 out of 8 in the Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose


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 L-Ribulose 3-Epimerase in Complex with D-Allulose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:42.6
occ:1.00
 O C:SER218 2.3 39.3 1.0
O D:SER218 2.4 38.0 1.0
OD1 D:ASN184 2.8 32.1 1.0
OD1 C:ASN184 2.9 28.8 1.0
C C:SER218 3.4 36.9 1.0
CB C:SER218 3.5 40.5 1.0
C D:SER218 3.6 35.8 1.0
O D:HOH427 3.8 26.0 1.0
CB D:SER218 4.0 34.9 1.0
CG C:ASN184 4.0 28.8 1.0
CG D:ASN184 4.0 31.9 1.0
CA C:SER218 4.0 39.6 1.0
CA D:SER218 4.3 34.2 1.0
ND2 C:ASN184 4.4 30.9 1.0
N C:VAL219 4.5 35.1 1.0
ND2 D:ASN184 4.5 32.4 1.0
N D:VAL219 4.6 38.1 1.0
CA C:VAL219 4.6 35.4 1.0
OG C:SER218 4.7 47.4 1.0
CA D:VAL219 4.7 35.1 1.0
OG D:SER218 4.9 38.1 1.0
N C:ASP220 4.9 32.0 1.0
N D:ASP220 4.9 33.0 1.0

Sodium binding site 4 out of 8 in 8yec

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Sodium binding site 4 out of 8 in the Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose


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 L-Ribulose 3-Epimerase in Complex with D-Allulose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na304

b:47.7
occ:1.00
 O G:SER218 2.3 39.6 1.0
O H:SER218 2.4 37.8 1.0
OD1 H:ASN184 2.8 34.3 1.0
OD1 G:ASN184 3.0 30.6 1.0
C G:SER218 3.4 38.6 1.0
CB G:SER218 3.6 38.8 1.0
C H:SER218 3.6 36.5 1.0
O H:HOH418 3.7 30.2 1.0
O G:HOH410 3.9 49.4 1.0
CB H:SER218 4.0 40.6 1.0
CA G:SER218 4.0 37.9 1.0
CG H:ASN184 4.0 37.5 1.0
CG G:ASN184 4.0 31.2 1.0
ND2 G:ASN184 4.3 30.6 1.0
CA H:SER218 4.3 36.8 1.0
N G:VAL219 4.4 37.7 1.0
N H:VAL219 4.6 41.2 1.0
CA G:VAL219 4.6 36.6 1.0
ND2 H:ASN184 4.6 39.3 1.0
CA H:VAL219 4.7 39.4 1.0
OG G:SER218 4.8 46.9 1.0
N H:ASP220 4.9 38.0 1.0
OG H:SER218 4.9 42.2 1.0
N G:ASP220 4.9 35.0 1.0

Sodium binding site 5 out of 8 in 8yec

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Sodium binding site 5 out of 8 in the Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose


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 L-Ribulose 3-Epimerase in Complex with D-Allulose within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na301

b:43.0
occ:1.00
 OD1 I:ASN184 2.4 33.5 1.0
O J:SER218 2.4 36.4 1.0
O I:SER218 2.5 47.9 1.0
OD1 J:ASN184 2.7 37.5 1.0
O J:HOH421 2.8 39.0 1.0
C J:SER218 3.4 34.8 1.0
CB J:SER218 3.4 39.9 1.0
CG I:ASN184 3.5 33.8 1.0
C I:SER218 3.6 39.6 1.0
O I:HOH417 3.7 30.1 1.0
CG J:ASN184 3.7 36.9 1.0
ND2 I:ASN184 4.0 33.8 1.0
CA J:SER218 4.0 35.5 1.0
CB I:SER218 4.0 44.7 1.0
ND2 J:ASN184 4.1 35.9 1.0
O J:HOH414 4.3 36.7 1.0
CA I:SER218 4.4 41.6 1.0
N I:VAL219 4.5 38.2 1.0
N J:VAL219 4.5 34.9 1.0
CA I:VAL219 4.6 36.3 1.0
OG J:SER218 4.6 46.1 1.0
O I:ASN184 4.7 33.2 1.0
CB I:ASN184 4.7 33.9 1.0
CA J:VAL219 4.8 35.9 1.0
N I:ASP220 5.0 40.5 1.0

Sodium binding site 6 out of 8 in 8yec

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Sodium binding site 6 out of 8 in the Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose


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 L-Ribulose 3-Epimerase in Complex with D-Allulose within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na304

b:39.3
occ:1.00
 O K:SER218 2.3 44.6 1.0
O L:SER218 2.4 30.3 1.0
OD1 K:ASN184 2.7 27.9 1.0
OD1 L:ASN184 2.9 32.2 1.0
C K:SER218 3.4 37.3 1.0
C L:SER218 3.6 30.3 1.0
O K:HOH422 3.6 37.5 1.0
CB K:SER218 3.6 41.9 1.0
CB L:SER218 3.7 34.4 1.0
CG K:ASN184 3.8 30.5 1.0
O L:HOH429 4.0 29.3 1.0
CG L:ASN184 4.0 33.5 1.0
CA K:SER218 4.1 37.3 1.0
CA L:SER218 4.2 29.9 1.0
N K:VAL219 4.4 35.4 1.0
ND2 K:ASN184 4.4 28.9 1.0
ND2 L:ASN184 4.4 33.9 1.0
CA K:VAL219 4.5 34.5 1.0
OG K:SER218 4.6 49.7 1.0
N L:VAL219 4.6 30.0 1.0
CA L:VAL219 4.8 29.5 1.0
OG L:SER218 4.9 38.9 1.0
N K:ASP220 4.9 37.0 1.0
C K:VAL219 4.9 34.4 1.0
O K:HOH419 5.0 37.6 1.0

Sodium binding site 7 out of 8 in 8yec

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Sodium binding site 7 out of 8 in the Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose


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 L-Ribulose 3-Epimerase in Complex with D-Allulose within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na301

b:43.8
occ:1.00
 O N:SER218 2.2 38.1 1.0
O M:SER218 2.4 33.7 1.0
O M:HOH437 2.5 35.5 1.0
OD1 M:ASN184 2.7 27.5 1.0
OD1 N:ASN184 2.8 32.4 1.0
C N:SER218 3.4 37.0 1.0
C M:SER218 3.5 34.8 1.0
O N:HOH420 3.7 31.9 1.0
CB N:SER218 3.7 41.4 1.0
CG M:ASN184 3.8 28.0 1.0
O M:HOH417 3.9 40.9 1.0
CB M:SER218 3.9 37.1 1.0
CG N:ASN184 3.9 37.3 1.0
CA N:SER218 4.1 37.5 1.0
ND2 M:ASN184 4.2 25.4 1.0
CA M:SER218 4.3 35.1 1.0
N N:VAL219 4.5 38.9 1.0
ND2 N:ASN184 4.5 39.0 1.0
N M:VAL219 4.5 34.0 1.0
CA M:VAL219 4.6 34.8 1.0
CA N:VAL219 4.6 37.7 1.0
OG N:SER218 4.8 45.4 1.0
N N:ASP220 5.0 37.6 1.0

Sodium binding site 8 out of 8 in 8yec

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Sodium binding site 8 out of 8 in the Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose


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 L-Ribulose 3-Epimerase in Complex with D-Allulose within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na304

b:43.0
occ:1.00
 O O:SER218 2.2 36.2 1.0
O P:SER218 2.4 37.3 1.0
OD1 O:ASN184 2.9 29.8 1.0
OD1 P:ASN184 2.9 28.7 1.0
C O:SER218 3.4 34.2 1.0
C P:SER218 3.6 35.9 1.0
CB O:SER218 3.6 39.8 1.0
O P:HOH423 3.8 25.8 1.0
CB P:SER218 3.9 34.6 1.0
CG O:ASN184 4.0 30.1 1.0
CG P:ASN184 4.0 29.5 1.0
CA O:SER218 4.0 37.7 1.0
CA P:SER218 4.3 33.7 1.0
N O:VAL219 4.4 31.6 1.0
ND2 O:ASN184 4.4 31.0 1.0
ND2 P:ASN184 4.5 27.8 1.0
N P:VAL219 4.6 37.5 1.0
CA O:VAL219 4.6 32.1 1.0
OG O:SER218 4.7 48.5 1.0
CA P:VAL219 4.7 36.2 1.0
OG P:SER218 4.9 37.3 1.0
N O:ASP220 4.9 31.4 1.0
C O:VAL219 5.0 31.3 1.0

Reference:

M.Watanabe, Y.Nakamichi, S.Mine. Crystal Structure of L-Ribulose 3-Epimerase in Complex with D-Allulose To Be Published.
Page generated: Mon Aug 18 16:28:45 2025

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