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Sodium in PDB 7vz6: The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose

Protein crystallography data

The structure of The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose, PDB code: 7vz6 was solved by T.L.Li, R.Rajesh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.56 / 2.09
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.833, 104.941, 106.84, 74.87, 72.92, 68.08
R / Rfree (%) 20.1 / 22.8

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose (pdb code 7vz6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose, PDB code: 7vz6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 7vz6

Go back to Sodium Binding Sites List in 7vz6
Sodium binding site 1 out of 7 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:30.4
occ:1.00
 O A:PHE31 2.2 26.1 1.0
O A:ASP28 2.2 27.9 1.0
O A:HOH689 2.3 33.4 1.0
O A:HOH783 2.5 35.4 1.0
O A:LEU25 2.5 19.4 1.0
O A:ASP26 2.6 26.9 1.0
C A:ASP26 3.3 27.0 1.0
C A:PHE31 3.4 27.1 1.0
C A:ASP28 3.4 29.7 1.0
CA A:ASP26 3.6 30.1 1.0
C A:LEU25 3.6 21.7 1.0
N A:ASP28 4.0 28.0 1.0
O A:HOH603 4.0 49.5 1.0
N A:ASP26 4.0 24.3 1.0
N A:PHE31 4.2 26.9 1.0
N A:ALA27 4.2 26.8 1.0
CA A:PHE31 4.3 26.2 1.0
N A:PRO29 4.3 31.0 1.0
CA A:ASP28 4.3 27.7 1.0
CA A:PRO29 4.3 33.0 1.0
N A:GLU32 4.3 27.7 1.0
OE1 A:GLU32 4.3 41.3 1.0
C A:ALA27 4.3 30.3 1.0
CA A:GLU32 4.4 27.8 1.0
C A:PRO29 4.6 31.1 1.0
CB A:PHE31 4.6 26.4 1.0
CD A:PRO33 4.6 22.3 1.0
OD1 A:ASP26 4.6 45.6 1.0
O A:PRO29 4.7 31.2 1.0
CA A:ALA27 4.8 27.5 1.0
O A:ALA27 4.9 34.2 1.0
CA A:LEU25 4.9 18.5 1.0
CB A:ASP26 5.0 34.0 1.0

Sodium binding site 2 out of 7 in 7vz6

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Sodium binding site 2 out of 7 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:27.1
occ:1.00
 O C:ASP28 2.2 25.3 1.0
O C:PHE31 2.4 27.2 1.0
O C:ASP26 2.5 33.0 1.0
O C:LEU25 2.7 24.1 1.0
C C:ASP26 3.3 33.4 1.0
C C:ASP28 3.3 28.7 1.0
C C:PHE31 3.6 23.9 1.0
CA C:ASP26 3.7 33.5 1.0
C C:LEU25 3.7 24.9 1.0
N C:ASP28 3.9 29.7 1.0
CA C:PRO29 4.1 31.5 1.0
N C:PRO29 4.1 31.6 1.0
N C:ASP26 4.2 29.4 1.0
CA C:ASP28 4.2 30.0 1.0
N C:ALA27 4.2 30.3 1.0
C C:ALA27 4.2 35.6 1.0
N C:PHE31 4.3 27.4 1.0
CA C:PHE31 4.4 25.5 1.0
OE1 C:GLU32 4.4 30.9 1.0
C C:PRO29 4.4 29.0 1.0
N C:GLU32 4.5 22.3 1.0
O C:PRO29 4.6 30.0 1.0
CA C:GLU32 4.6 24.1 1.0
OD1 C:ASP26 4.7 50.1 1.0
CB C:PHE31 4.7 24.9 1.0
O C:ALA27 4.7 35.7 1.0
CA C:ALA27 4.8 31.9 1.0
CD C:PRO33 4.8 24.3 1.0

Sodium binding site 3 out of 7 in 7vz6

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Sodium binding site 3 out of 7 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:30.3
occ:1.00
 O D:PHE31 2.1 35.8 1.0
O D:ASP28 2.2 33.4 1.0
O D:HOH608 2.3 30.2 1.0
O D:LEU25 2.6 28.4 1.0
O D:ASP26 2.7 34.8 1.0
C D:PHE31 3.3 30.7 1.0
C D:ASP28 3.4 34.8 1.0
C D:ASP26 3.4 32.9 1.0
C D:LEU25 3.7 29.1 1.0
CA D:ASP26 3.7 34.6 1.0
N D:ASP28 4.0 35.8 1.0
N D:PHE31 4.1 27.6 1.0
CA D:PHE31 4.2 30.2 1.0
N D:ASP26 4.2 30.3 1.0
N D:GLU32 4.2 31.6 1.0
N D:PRO29 4.2 35.2 1.0
CA D:PRO29 4.2 36.8 1.0
OE1 D:GLU32 4.3 42.5 1.0
CA D:ASP28 4.3 34.1 1.0
CA D:GLU32 4.4 29.7 1.0
N D:ALA27 4.4 29.4 1.0
C D:ALA27 4.4 37.4 1.0
C D:PRO29 4.5 33.3 1.0
CB D:PHE31 4.5 27.6 1.0
O D:PRO29 4.6 37.2 1.0
CD D:PRO33 4.6 30.2 1.0
OD1 D:ASP26 4.8 52.8 1.0
O D:ALA27 4.9 34.6 1.0
CA D:ALA27 4.9 32.4 1.0
CA D:LEU25 5.0 25.6 1.0

Sodium binding site 4 out of 7 in 7vz6

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Sodium binding site 4 out of 7 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na502

b:19.9
occ:1.00
 O E:ASP28 2.2 22.5 1.0
O E:PHE31 2.3 21.1 1.0
O E:HOH784 2.4 30.9 1.0
O E:HOH609 2.4 30.3 1.0
O E:ASP26 2.5 30.1 1.0
O E:LEU25 2.6 18.6 1.0
C E:ASP26 3.2 27.2 1.0
C E:ASP28 3.4 23.4 1.0
C E:PHE31 3.5 18.8 1.0
CA E:ASP26 3.6 26.1 1.0
C E:LEU25 3.6 21.3 1.0
N E:ASP28 3.9 22.9 1.0
N E:ASP26 4.0 22.6 1.0
N E:ALA27 4.2 26.3 1.0
N E:PRO29 4.2 26.4 1.0
CA E:PRO29 4.3 26.6 1.0
CA E:ASP28 4.3 23.1 1.0
C E:ALA27 4.3 24.2 1.0
OE1 E:GLU32 4.3 30.8 1.0
N E:PHE31 4.3 20.4 1.0
CA E:PHE31 4.4 20.3 1.0
N E:GLU32 4.4 20.6 1.0
CA E:GLU32 4.5 20.5 1.0
OD1 E:ASP26 4.5 36.8 1.0
C E:PRO29 4.6 23.3 1.0
CD E:PRO33 4.7 19.4 1.0
CB E:PHE31 4.7 19.9 1.0
O E:PRO29 4.7 26.0 1.0
CA E:ALA27 4.8 24.5 1.0
O E:ALA27 4.8 21.7 1.0
CB E:ASP26 4.9 29.7 1.0
CA E:LEU25 4.9 18.4 1.0

Sodium binding site 5 out of 7 in 7vz6

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Sodium binding site 5 out of 7 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na502

b:27.0
occ:1.00
 O F:HOH640 2.2 28.9 1.0
O F:ASP28 2.3 27.0 1.0
O F:PHE31 2.3 22.1 1.0
O F:ASP26 2.5 34.4 1.0
O F:LEU25 2.6 21.2 1.0
C F:ASP26 3.2 34.2 1.0
C F:ASP28 3.4 28.8 1.0
C F:PHE31 3.5 22.3 1.0
CA F:ASP26 3.6 31.0 1.0
C F:LEU25 3.7 24.2 1.0
N F:ASP28 3.9 30.0 1.0
N F:ASP26 4.1 27.3 1.0
N F:ALA27 4.2 30.2 1.0
N F:PRO29 4.2 28.7 1.0
CA F:PRO29 4.3 28.3 1.0
OE1 F:GLU32 4.3 41.5 1.0
CA F:ASP28 4.3 29.6 1.0
C F:ALA27 4.3 31.9 1.0
N F:PHE31 4.3 22.0 1.0
CA F:PHE31 4.4 20.0 1.0
N F:GLU32 4.4 23.1 1.0
CA F:GLU32 4.5 26.2 1.0
C F:PRO29 4.6 25.8 1.0
OD1 F:ASP26 4.6 49.8 1.0
CD F:PRO33 4.7 26.9 1.0
CB F:PHE31 4.7 20.1 1.0
O F:PRO29 4.7 25.8 1.0
CA F:ALA27 4.8 31.8 1.0
O F:ALA27 4.8 30.7 1.0
CB F:ASP26 5.0 37.3 1.0
CA F:LEU25 5.0 22.2 1.0

Sodium binding site 6 out of 7 in 7vz6

Go back to Sodium Binding Sites List in 7vz6
Sodium binding site 6 out of 7 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na502

b:45.4
occ:1.00
 O G:PHE31 2.4 30.7 1.0
O G:ASP28 2.4 37.4 1.0
O G:ASP26 2.6 35.5 1.0
O G:LEU25 2.9 37.9 1.0
C G:ASP26 3.3 40.9 1.0
C G:ASP28 3.5 36.7 1.0
C G:PHE31 3.6 28.5 1.0
CA G:ASP26 3.7 40.3 1.0
C G:LEU25 3.9 33.8 1.0
OE1 G:GLU32 4.1 37.4 1.0
N G:ASP28 4.1 37.7 1.0
CA G:PRO29 4.2 38.7 1.0
N G:PRO29 4.3 38.1 1.0
N G:ASP26 4.3 33.5 1.0
N G:ALA27 4.4 41.1 1.0
N G:PHE31 4.4 29.4 1.0
C G:ALA27 4.4 44.4 1.0
CA G:ASP28 4.4 35.6 1.0
N G:GLU32 4.5 29.9 1.0
CA G:PHE31 4.5 27.2 1.0
CA G:GLU32 4.5 32.9 1.0
C G:PRO29 4.5 33.7 1.0
OD1 G:ASP26 4.6 52.5 1.0
O G:PRO29 4.6 37.4 1.0
CD G:PRO33 4.8 36.7 1.0
CB G:PHE31 4.9 25.8 1.0
O G:ALA27 4.9 39.0 1.0
CA G:ALA27 4.9 41.3 1.0

Sodium binding site 7 out of 7 in 7vz6

Go back to Sodium Binding Sites List in 7vz6
Sodium binding site 7 out of 7 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na502

b:33.0
occ:1.00
 O H:ASP28 2.1 35.7 1.0
O H:PHE31 2.4 34.2 1.0
O H:ASP26 2.5 38.6 1.0
O H:HOH611 2.6 34.7 1.0
O H:LEU25 2.7 29.3 1.0
C H:ASP28 3.2 32.9 1.0
C H:ASP26 3.3 36.6 1.0
C H:PHE31 3.6 34.4 1.0
CA H:ASP26 3.7 37.0 1.0
C H:LEU25 3.8 29.8 1.0
N H:ASP28 3.8 35.0 1.0
N H:PRO29 4.0 37.8 1.0
CA H:PRO29 4.0 39.4 1.0
CA H:ASP28 4.2 32.2 1.0
N H:ASP26 4.2 31.8 1.0
C H:ALA27 4.2 36.8 1.0
N H:ALA27 4.2 36.8 1.0
N H:PHE31 4.3 34.0 1.0
C H:PRO29 4.4 35.1 1.0
OE1 H:GLU32 4.4 51.6 1.0
CA H:PHE31 4.4 32.8 1.0
N H:GLU32 4.5 36.5 1.0
O H:PRO29 4.5 35.1 1.0
CA H:GLU32 4.7 39.4 1.0
O H:ALA27 4.7 34.5 1.0
OD1 H:ASP26 4.7 47.5 1.0
CB H:PHE31 4.7 27.7 1.0
CA H:ALA27 4.8 37.5 1.0
CD H:PRO33 4.9 37.2 1.0
CB H:ASP28 5.0 33.6 1.0
N H:GLY30 5.0 35.1 1.0

Reference:

T.L.Li, R.Rajesh. The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp-Glucose To Be Published.
Page generated: Mon Aug 18 12:22:00 2025

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