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Sodium in PDB 5m2t: X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution

Enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution

All present enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution, PDB code: 5m2t was solved by I.I.Prokofev, A.A.Lashkov, A.G.Gabdulkhakov, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.46 / 1.03
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.323, 72.039, 89.193, 110.56, 107.53, 85.83
R / Rfree (%) 11.8 / 13.7

Other elements in 5m2t:

The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution (pdb code 5m2t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution, PDB code: 5m2t:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5m2t

Go back to Sodium Binding Sites List in 5m2t
Sodium binding site 1 out of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:10.5
occ:0.54
OE2 B:GLU48 2.7 11.2 1.0
OE2 A:GLU48 2.7 11.4 1.0
HB2 B:SER72 2.8 10.0 0.1
OG B:SER72 2.9 6.8 0.8
HB3 A:SER72 3.0 9.7 1.0
OG A:SER72 3.0 8.4 1.0
O B:ILE68 3.0 8.3 1.0
O A:ILE68 3.0 8.3 1.0
HB3 B:SER72 3.0 9.1 0.8
H B:ILE68 3.2 9.4 1.0
H A:ILE68 3.2 9.8 1.0
HB3 B:SER72 3.2 10.0 0.1
CB B:SER72 3.3 8.3 0.1
HA3 B:GLY67 3.4 10.2 1.0
HA3 A:GLY67 3.4 10.6 1.0
CB A:SER72 3.4 8.1 1.0
CB B:SER72 3.4 7.5 0.8
OG B:SER72 3.5 9.0 0.1
N B:ILE68 3.6 7.8 1.0
O A:HOH511 3.6 7.5 0.5
O A:HOH511 3.6 7.1 0.5
HG B:SER72 3.6 8.2 0.8
N A:ILE68 3.7 8.2 1.0
HG A:SER72 3.7 10.1 1.0
HB2 A:SER72 3.7 9.7 1.0
HG3 B:GLU48 3.8 13.2 1.0
HB2 B:SER72 3.8 9.1 0.8
CD B:GLU48 3.8 11.5 1.0
CD A:GLU48 3.9 11.9 1.0
HG3 A:GLU48 3.9 15.0 1.0
C B:ILE68 3.9 7.6 1.0
C A:ILE68 4.0 7.1 1.0
HB B:ILE68 4.1 9.7 1.0
HB A:ILE68 4.1 9.8 1.0
CA B:GLY67 4.1 8.5 1.0
HG B:SER72 4.1 10.8 0.1
C B:GLY67 4.2 8.2 1.0
CA A:GLY67 4.2 8.8 1.0
C A:GLY67 4.3 8.5 1.0
CA B:ILE68 4.3 7.1 1.0
CG B:GLU48 4.3 11.0 1.0
CA A:ILE68 4.3 7.5 1.0
CG A:GLU48 4.4 12.5 1.0
H B:SER72 4.4 8.1 0.8
H A:SER72 4.4 7.7 1.0
H B:SER72 4.4 8.1 0.1
HA2 B:GLY67 4.4 10.2 1.0
HA2 A:GLY67 4.5 10.6 1.0
HB3 B:GLU48 4.6 13.7 1.0
CB B:ILE68 4.7 8.1 1.0
CB A:ILE68 4.7 8.2 1.0
CA B:SER72 4.7 7.2 0.1
CA A:SER72 4.8 6.5 1.0
CA B:SER72 4.8 6.7 0.8
HB3 A:GLU48 4.8 14.6 1.0
O B:THR66 4.8 9.8 1.0
OE1 B:GLU48 4.8 12.8 1.0
OE1 A:GLU48 4.9 14.5 1.0
O A:THR66 4.9 9.6 1.0
CB B:GLU48 4.9 11.4 1.0
N A:SER72 5.0 6.4 1.0
N B:SER72 5.0 6.7 1.0
HB2 B:GLU48 5.0 13.7 1.0

Sodium binding site 2 out of 3 in 5m2t

Go back to Sodium Binding Sites List in 5m2t
Sodium binding site 2 out of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:15.9
occ:0.58
HB2 C:SER72 2.6 12.6 0.3
HB2 D:SER72 2.7 11.3 0.3
OE2 C:GLU48 2.7 17.6 1.0
OE2 D:GLU48 2.7 17.2 1.0
O C:ILE68 2.9 11.6 1.0
HB3 C:SER72 2.9 11.2 0.7
O D:ILE68 2.9 10.5 1.0
OG C:SER72 3.0 9.4 0.7
HB3 D:SER72 3.0 10.5 0.7
OG D:SER72 3.0 9.0 0.7
HG C:SER72 3.1 14.0 0.3
H C:ILE68 3.1 12.8 1.0
H D:ILE68 3.2 12.5 1.0
HB3 C:SER72 3.2 12.6 0.3
CB C:SER72 3.2 10.5 0.3
CB D:SER72 3.3 9.4 0.3
HB3 D:SER72 3.3 11.3 0.3
CB C:SER72 3.4 9.3 0.7
HA3 C:GLY67 3.5 14.4 1.0
CB D:SER72 3.5 8.8 0.7
O D:HOH494 3.5 9.6 0.5
O D:HOH494 3.5 9.1 0.5
OG C:SER72 3.6 11.6 0.3
HA3 D:GLY67 3.6 13.9 1.0
OG D:SER72 3.6 10.4 0.3
N C:ILE68 3.6 10.7 1.0
N D:ILE68 3.7 10.4 1.0
HG C:SER72 3.7 11.3 0.7
HB2 C:SER72 3.7 11.2 0.7
HG D:SER72 3.8 10.8 0.7
HG3 C:GLU48 3.8 20.9 1.0
CD C:GLU48 3.8 17.3 1.0
C C:ILE68 3.9 10.0 1.0
CD D:GLU48 3.9 17.2 1.0
HB2 D:SER72 3.9 10.5 0.7
HB D:ILE68 3.9 13.2 1.0
C D:ILE68 3.9 9.3 1.0
HB C:ILE68 3.9 13.8 1.0
HG3 D:GLU48 3.9 21.0 1.0
CA C:ILE68 4.2 10.2 1.0
CA C:GLY67 4.2 12.0 1.0
C C:GLY67 4.2 11.2 1.0
CA D:ILE68 4.2 9.7 1.0
HG D:SER72 4.3 12.4 0.3
C D:GLY67 4.3 11.0 1.0
CA D:GLY67 4.3 11.6 1.0
CG C:GLU48 4.4 17.4 1.0
H C:SER72 4.4 10.2 0.3
H C:SER72 4.4 10.0 0.7
H D:SER72 4.4 9.6 0.7
H D:SER72 4.4 9.9 0.3
CG D:GLU48 4.4 17.5 1.0
HA2 C:GLY67 4.5 14.4 1.0
CB D:ILE68 4.6 11.0 1.0
CB C:ILE68 4.6 11.5 1.0
CA C:SER72 4.6 9.1 0.3
HA2 D:GLY67 4.6 13.9 1.0
CA D:SER72 4.7 8.7 0.3
CA C:SER72 4.7 8.8 0.7
CA D:SER72 4.8 8.3 0.7
HB3 C:GLU48 4.9 21.0 1.0
HB3 D:GLU48 4.9 21.0 1.0
OE1 C:GLU48 4.9 17.8 1.0
N C:SER72 4.9 8.5 0.3
OE1 D:GLU48 4.9 17.4 1.0
N C:SER72 4.9 8.3 0.7
HA C:SER72 4.9 11.0 0.3
O C:THR66 4.9 13.5 1.0
N D:SER72 5.0 8.2 0.3
N D:SER72 5.0 8.0 0.7
HA D:SER72 5.0 10.4 0.3

Sodium binding site 3 out of 3 in 5m2t

Go back to Sodium Binding Sites List in 5m2t
Sodium binding site 3 out of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:13.2
occ:0.53
HB2 E:SER72 2.6 10.0 0.2
HB2 F:SER72 2.6 9.9 0.2
OE2 E:GLU48 2.6 15.5 1.0
OE2 F:GLU48 2.8 13.9 1.0
O F:ILE68 2.9 9.3 1.0
HB3 E:SER72 2.9 10.0 0.8
OG E:SER72 3.0 8.8 0.8
OG F:SER72 3.0 7.8 0.8
HB3 F:SER72 3.1 9.7 0.8
O E:ILE68 3.1 9.6 1.0
H F:ILE68 3.1 11.3 1.0
H E:ILE68 3.1 11.0 1.0
CB E:SER72 3.2 8.3 0.2
CB F:SER72 3.3 8.3 0.2
HB3 E:SER72 3.3 10.0 0.2
HB3 F:SER72 3.3 9.9 0.2
OG E:SER72 3.3 9.0 0.2
CB E:SER72 3.4 8.4 0.8
HA3 F:GLY67 3.4 13.0 1.0
HA3 E:GLY67 3.4 12.6 1.0
OG F:SER72 3.5 8.8 0.2
CB F:SER72 3.5 8.1 0.8
N F:ILE68 3.6 9.4 1.0
O E:HOH498 3.6 8.7 0.5
O E:HOH498 3.6 8.4 0.5
N E:ILE68 3.7 9.2 1.0
HG E:SER72 3.7 10.6 0.8
HB2 E:SER72 3.7 10.0 0.8
HG F:SER72 3.7 9.4 0.8
HG3 E:GLU48 3.7 19.6 1.0
CD E:GLU48 3.8 15.5 1.0
C F:ILE68 3.8 7.9 1.0
HB F:ILE68 3.9 11.5 1.0
HB2 F:SER72 3.9 9.7 0.8
CD F:GLU48 3.9 13.9 1.0
HG3 F:GLU48 3.9 16.6 1.0
C E:ILE68 4.0 8.2 1.0
HB E:ILE68 4.0 11.6 1.0
HG E:SER72 4.1 10.8 0.2
HG F:SER72 4.2 10.6 0.2
CA F:ILE68 4.2 8.4 1.0
CA F:GLY67 4.2 10.9 1.0
C F:GLY67 4.2 9.7 1.0
CA E:GLY67 4.2 10.5 1.0
CG E:GLU48 4.3 16.3 1.0
C E:GLY67 4.3 9.6 1.0
CA E:ILE68 4.3 8.5 1.0
H E:SER72 4.4 8.9 0.8
CG F:GLU48 4.4 13.8 1.0
H F:SER72 4.5 8.4 0.8
H E:SER72 4.5 9.1 0.2
HA2 F:GLY67 4.5 13.0 1.0
H F:SER72 4.5 8.5 0.2
HA2 E:GLY67 4.5 12.6 1.0
CB F:ILE68 4.5 9.6 1.0
CA E:SER72 4.6 7.8 0.2
CA F:SER72 4.7 7.5 0.2
CB E:ILE68 4.7 9.7 1.0
HB3 F:GLU48 4.7 17.4 1.0
CA E:SER72 4.8 7.9 0.8
HB3 E:GLU48 4.8 19.8 1.0
OE1 E:GLU48 4.8 16.4 1.0
CA F:SER72 4.8 7.7 0.8
HA E:SER72 4.8 9.4 0.2
OE1 F:GLU48 4.9 15.6 1.0
O E:THR66 4.9 12.2 1.0
HA F:SER72 4.9 9.0 0.2
N E:SER72 4.9 7.5 0.2
N E:SER72 5.0 7.4 0.8
O F:THR66 5.0 11.2 1.0

Reference:

I.I.Prokofev, A.A.Lashkov, A.G.Gabdulkhakov, M.V.Dontsova, C.Betzel, A.M.Mikhailov. X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution To Be Published.
Page generated: Tue Dec 15 11:15:20 2020

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