Atomistry » Sodium » PDB 8xxi-8zj7 » 8yec
Atomistry »
  Sodium »
    PDB 8xxi-8zj7 »
      8yec »

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

Go back to Sodium Binding Sites List in 8yec
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

Go back to Sodium Binding Sites List in 8yec
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

Go back to Sodium Binding Sites List in 8yec
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

Go back to Sodium Binding Sites List in 8yec
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

Go back to Sodium Binding Sites List in 8yec
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

Go back to Sodium Binding Sites List in 8yec
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

Go back to Sodium Binding Sites List in 8yec
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

Go back to Sodium Binding Sites List in 8yec
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

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy