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

Protein crystallography data

The structure of The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp, PDB code: 7vza 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) 19.90 / 2.58
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 81.82, 104.77, 106.314, 74.54, 73.05, 68.39
R / Rfree (%) 21 / 24.9

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp (pdb code 7vza). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp, PDB code: 7vza:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7vza

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Sodium binding site 1 out of 8 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:46.4
occ:1.00
 O A:ASP28 2.4 58.2 1.0
O A:ASP26 2.6 66.1 1.0
O A:PHE31 2.7 40.2 1.0
O A:LEU25 2.9 66.4 1.0
OE1 A:GLU32 3.3 66.6 1.0
C A:ASP26 3.3 60.4 1.0
C A:ASP28 3.4 56.3 1.0
CA A:ASP26 3.7 61.5 1.0
C A:LEU25 3.9 57.5 1.0
CA A:PRO29 3.9 50.7 1.0
C A:PHE31 4.0 42.3 1.0
N A:PRO29 4.0 55.9 1.0
N A:ASP28 4.1 56.4 1.0
N A:ASP26 4.3 60.5 1.0
N A:ALA27 4.3 63.8 1.0
C A:ALA27 4.3 61.2 1.0
CD A:GLU32 4.4 58.5 1.0
CA A:ASP28 4.4 52.3 1.0
C A:PRO29 4.4 46.9 1.0
O A:PRO29 4.6 51.9 1.0
O A:ALA27 4.6 68.5 1.0
OD1 A:ASP26 4.6 75.4 1.0
N A:PHE31 4.7 43.0 1.0
CA A:ALA27 4.8 60.8 1.0
CA A:PHE31 4.9 38.6 1.0
N A:GLU32 4.9 45.9 1.0
CA A:GLU32 4.9 46.9 1.0
CG A:GLU32 4.9 56.6 1.0

Sodium binding site 2 out of 8 in 7vza

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Sodium binding site 2 out of 8 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:59.9
occ:1.00
 O B:ASP28 2.5 56.0 1.0
O B:ASP26 2.7 48.2 1.0
O B:PHE31 2.7 45.7 1.0
O B:LEU25 3.0 38.1 1.0
OE1 B:GLU32 3.1 66.0 1.0
C B:ASP26 3.4 49.1 1.0
C B:ASP28 3.5 55.1 1.0
CA B:ASP26 3.8 46.7 1.0
CA B:PRO29 3.9 54.6 1.0
C B:PHE31 4.0 42.9 1.0
C B:LEU25 4.0 38.8 1.0
N B:PRO29 4.1 56.0 1.0
CD B:GLU32 4.2 58.7 1.0
N B:ASP28 4.2 54.0 1.0
N B:ASP26 4.4 44.1 1.0
N B:ALA27 4.4 50.4 1.0
C B:ALA27 4.4 52.5 1.0
C B:PRO29 4.4 50.4 1.0
CA B:ASP28 4.5 52.9 1.0
O B:PRO29 4.6 46.5 1.0
OD1 B:ASP26 4.6 55.6 1.0
O B:ALA27 4.6 58.9 1.0
N B:PHE31 4.7 37.8 1.0
CG B:GLU32 4.8 55.0 1.0
N B:GLU32 4.9 42.8 1.0
CA B:GLU32 4.9 43.6 1.0
CA B:PHE31 4.9 37.1 1.0
CA B:ALA27 4.9 49.7 1.0

Sodium binding site 3 out of 8 in 7vza

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Sodium binding site 3 out of 8 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:72.2
occ:1.00
 O C:ASP28 2.6 81.5 1.0
O C:ASP26 2.7 80.7 1.0
O C:PHE31 3.0 62.8 1.0
OE1 C:GLU32 3.1 92.8 1.0
O C:LEU25 3.4 76.9 1.0
C C:ASP28 3.4 83.2 1.0
C C:ASP26 3.5 79.4 1.0
CA C:PRO29 3.7 85.6 1.0
N C:PRO29 3.9 89.2 1.0
CA C:ASP26 4.1 77.1 1.0
C C:PHE31 4.3 57.7 1.0
CD C:GLU32 4.3 87.1 1.0
C C:PRO29 4.3 78.7 1.0
N C:ASP28 4.3 75.8 1.0
C C:ALA27 4.3 75.0 1.0
C C:LEU25 4.4 78.2 1.0
O C:PRO29 4.4 76.7 1.0
O C:ALA27 4.5 70.4 1.0
N C:ALA27 4.5 80.9 1.0
CA C:ASP28 4.5 74.8 1.0
N C:ASP26 4.7 76.8 1.0
CG C:GLU32 4.9 82.2 1.0
N C:PHE31 4.9 63.7 1.0
OD1 C:ASP26 4.9 105.9 1.0
CA C:ALA27 4.9 79.0 1.0
CB C:PRO29 5.0 85.2 1.0

Sodium binding site 4 out of 8 in 7vza

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Sodium binding site 4 out of 8 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:56.4
occ:1.00
 O D:PHE31 2.7 54.6 1.0
O D:ASP28 2.8 52.4 1.0
O D:ASP26 2.8 52.6 1.0
OE1 D:GLU32 2.8 68.5 1.0
O D:LEU25 3.2 47.5 1.0
C D:ASP26 3.6 50.6 1.0
C D:ASP28 3.7 57.1 1.0
CA D:ASP26 3.9 50.8 1.0
CD D:GLU32 4.0 65.3 1.0
C D:PHE31 4.0 47.5 1.0
CA D:PRO29 4.0 54.5 1.0
C D:LEU25 4.2 50.9 1.0
N D:PRO29 4.3 59.1 1.0
C D:PRO29 4.5 51.1 1.0
N D:ASP28 4.5 58.8 1.0
O D:PRO29 4.5 51.6 1.0
N D:ASP26 4.5 54.0 1.0
CG D:GLU32 4.6 58.0 1.0
N D:ALA27 4.6 52.9 1.0
OD1 D:ASP26 4.6 62.0 1.0
C D:ALA27 4.6 57.6 1.0
CA D:GLU32 4.8 45.1 1.0
CA D:ASP28 4.8 55.8 1.0
N D:PHE31 4.8 47.5 1.0
N D:GLU32 4.8 45.9 1.0
O D:ALA27 4.8 57.9 1.0
OE2 D:GLU32 5.0 55.3 1.0
CA D:PHE31 5.0 46.6 1.0

Sodium binding site 5 out of 8 in 7vza

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Sodium binding site 5 out of 8 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na402

b:57.5
occ:1.00
 O E:PHE31 2.7 41.1 1.0
O E:ASP28 2.7 46.3 1.0
OE1 E:GLU32 2.8 66.3 1.0
O E:ASP26 2.9 55.8 1.0
O E:LEU25 3.2 42.5 1.0
C E:ASP26 3.6 54.5 1.0
C E:ASP28 3.7 52.3 1.0
C E:PHE31 3.9 40.7 1.0
CA E:PRO29 3.9 56.4 1.0
CD E:GLU32 3.9 64.7 1.0
CA E:ASP26 4.0 49.6 1.0
N E:PRO29 4.2 56.8 1.0
C E:LEU25 4.2 43.0 1.0
C E:PRO29 4.3 57.5 1.0
O E:PRO29 4.4 61.1 1.0
CG E:GLU32 4.5 60.3 1.0
N E:ASP28 4.5 52.6 1.0
N E:ASP26 4.6 49.2 1.0
N E:ALA27 4.6 51.1 1.0
C E:ALA27 4.6 51.0 1.0
N E:PHE31 4.7 41.8 1.0
CA E:GLU32 4.7 46.6 1.0
OD1 E:ASP26 4.7 58.0 1.0
N E:GLU32 4.7 43.0 1.0
CA E:ASP28 4.7 49.1 1.0
O E:ALA27 4.9 61.7 1.0
CA E:PHE31 4.9 39.2 1.0
OE2 E:GLU32 4.9 70.1 1.0

Sodium binding site 6 out of 8 in 7vza

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Sodium binding site 6 out of 8 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na402

b:50.7
occ:1.00
 O F:ASP26 2.7 53.8 1.0
O F:ASP28 2.7 58.0 1.0
O F:PHE31 2.9 31.9 1.0
OE1 F:GLU32 2.9 64.0 1.0
O F:LEU25 3.2 41.7 1.0
C F:ASP26 3.5 52.7 1.0
C F:ASP28 3.6 57.0 1.0
CA F:ASP26 3.9 48.9 1.0
CA F:PRO29 4.0 56.0 1.0
CD F:GLU32 4.1 63.3 1.0
C F:PHE31 4.1 38.8 1.0
N F:PRO29 4.2 58.3 1.0
C F:LEU25 4.2 44.3 1.0
N F:ASP28 4.4 53.9 1.0
C F:ALA27 4.5 52.7 1.0
C F:PRO29 4.5 54.4 1.0
N F:ALA27 4.5 54.2 1.0
N F:ASP26 4.5 46.1 1.0
O F:PRO29 4.5 64.3 1.0
OD1 F:ASP26 4.6 69.7 1.0
CA F:ASP28 4.7 53.9 1.0
O F:ALA27 4.7 57.0 1.0
CG F:GLU32 4.7 58.4 1.0
N F:PHE31 4.9 41.2 1.0
CA F:GLU32 4.9 44.8 1.0
N F:GLU32 5.0 44.6 1.0
CA F:ALA27 5.0 52.5 1.0

Sodium binding site 7 out of 8 in 7vza

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Sodium binding site 7 out of 8 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na402

b:53.3
occ:1.00
 O G:PHE31 2.5 55.3 1.0
O G:ASP28 2.7 53.6 1.0
OE1 G:GLU32 2.8 58.5 1.0
O G:ASP26 2.9 58.1 1.0
O G:LEU25 3.0 55.3 1.0
C G:ASP26 3.6 53.4 1.0
C G:ASP28 3.7 58.1 1.0
C G:PHE31 3.8 51.7 1.0
CA G:ASP26 3.8 54.9 1.0
CD G:GLU32 3.9 68.1 1.0
C G:LEU25 4.1 57.8 1.0
CA G:PRO29 4.1 61.4 1.0
N G:PRO29 4.3 64.8 1.0
N G:ASP26 4.4 54.9 1.0
CG G:GLU32 4.5 66.7 1.0
C G:PRO29 4.5 59.0 1.0
O G:PRO29 4.5 64.0 1.0
N G:ASP28 4.5 57.6 1.0
OD1 G:ASP26 4.6 69.6 1.0
CA G:GLU32 4.6 55.9 1.0
N G:ALA27 4.6 52.9 1.0
N G:GLU32 4.6 55.0 1.0
N G:PHE31 4.7 48.5 1.0
C G:ALA27 4.7 54.7 1.0
CA G:PHE31 4.8 48.7 1.0
CA G:ASP28 4.8 53.0 1.0
OE2 G:GLU32 4.8 69.4 1.0
CD G:PRO33 4.9 52.0 1.0
O G:ALA27 5.0 64.6 1.0

Sodium binding site 8 out of 8 in 7vza

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Sodium binding site 8 out of 8 in the The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na402

b:48.5
occ:1.00
 O H:ASP28 2.4 63.4 1.0
O H:PHE31 2.5 54.3 1.0
O H:ASP26 3.0 51.9 1.0
OE1 H:GLU32 3.0 68.1 1.0
O H:LEU25 3.0 66.1 1.0
C H:ASP28 3.4 60.2 1.0
C H:ASP26 3.7 54.4 1.0
C H:PHE31 3.7 48.6 1.0
CA H:PRO29 3.8 57.7 1.0
CA H:ASP26 4.0 59.2 1.0
N H:PRO29 4.0 58.1 1.0
CD H:GLU32 4.1 77.6 1.0
C H:LEU25 4.1 57.8 1.0
C H:PRO29 4.2 59.1 1.0
N H:ASP28 4.3 57.0 1.0
O H:PRO29 4.3 59.4 1.0
N H:PHE31 4.4 45.8 1.0
N H:ASP26 4.5 57.5 1.0
CA H:ASP28 4.5 57.4 1.0
C H:ALA27 4.5 56.1 1.0
CG H:GLU32 4.6 72.6 1.0
N H:ALA27 4.6 53.8 1.0
N H:GLU32 4.6 53.4 1.0
CA H:PHE31 4.6 45.1 1.0
CA H:GLU32 4.7 59.7 1.0
O H:ALA27 4.8 58.1 1.0
OD1 H:ASP26 4.9 71.6 1.0
N H:GLY30 4.9 55.5 1.0

Reference:

T.L.Li, R.Rajesh. The Crystal Structure of Non-Hydrolyzing Udpglcnac 2-Epimerase in Complex with Udp To Be Published.
Page generated: Fri Apr 7 16:52:45 2023

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