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Sodium in PDB 4lzw: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution

Enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution, PDB code: 4lzw was solved by I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 1.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.740, 95.850, 91.830, 90.00, 119.96, 90.00
R / Rfree (%) 17.8 / 21

Other elements in 4lzw:

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution (pdb code 4lzw). 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution, PDB code: 4lzw:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4lzw

Go back to Sodium Binding Sites List in 4lzw
Sodium binding site 1 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:5.6
occ:0.54
OE2 B:GLU48 2.6 7.7 1.0
OE2 A:GLU48 2.7 7.4 1.0
OG B:SER72 2.8 5.5 1.0
OG A:SER72 2.9 5.7 1.0
O B:ILE68 3.0 5.4 1.0
O A:ILE68 3.1 4.8 1.0
CB B:SER72 3.3 4.9 1.0
CB A:SER72 3.3 6.5 1.0
N B:ILE68 3.5 5.1 1.0
N A:ILE68 3.6 5.3 1.0
O B:HOH474 3.6 3.3 0.5
O B:HOH474 3.7 4.7 0.5
CD B:GLU48 3.7 8.5 1.0
CD A:GLU48 3.7 9.1 1.0
C B:ILE68 3.9 4.8 1.0
C A:ILE68 4.0 4.6 1.0
CA A:GLY67 4.0 6.6 1.0
CA B:GLY67 4.0 5.1 1.0
C B:GLY67 4.1 5.5 1.0
C A:GLY67 4.1 6.4 1.0
CG B:GLU48 4.2 8.8 1.0
CA B:ILE68 4.3 5.6 1.0
CG A:GLU48 4.3 9.7 1.0
CA A:ILE68 4.3 5.1 1.0
O B:THR66 4.6 6.5 1.0
CA B:SER72 4.7 5.5 1.0
O A:THR66 4.7 7.4 1.0
CA A:SER72 4.7 5.1 1.0
OE1 B:GLU48 4.7 10.0 1.0
OE1 A:GLU48 4.7 9.9 1.0
CB B:ILE68 4.7 5.3 1.0
CB A:ILE68 4.8 5.8 1.0
CB A:GLU48 4.9 9.7 1.0
CB B:GLU48 4.9 7.6 1.0
N A:SER72 4.9 5.2 1.0
N B:SER72 4.9 4.3 1.0

Sodium binding site 2 out of 3 in 4lzw

Go back to Sodium Binding Sites List in 4lzw
Sodium binding site 2 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:7.3
occ:0.71
OE2 D:GLU48 2.7 6.8 1.0
OE2 C:GLU48 2.7 7.3 1.0
OG C:SER72 2.8 4.9 1.0
OG D:SER72 2.8 4.5 1.0
O C:ILE68 3.0 5.1 1.0
O D:ILE68 3.0 4.8 1.0
CB C:SER72 3.3 5.0 1.0
CB D:SER72 3.3 4.5 1.0
N D:ILE68 3.6 4.9 1.0
N C:ILE68 3.6 4.8 1.0
O C:HOH470 3.6 5.6 0.6
O C:HOH470 3.6 3.7 0.4
CD D:GLU48 3.7 7.3 1.0
CD C:GLU48 3.8 8.4 1.0
C C:ILE68 3.9 4.4 1.0
C D:ILE68 3.9 4.2 1.0
CA D:GLY67 4.1 4.9 1.0
CA C:GLY67 4.1 5.7 1.0
C D:GLY67 4.1 5.6 1.0
C C:GLY67 4.1 4.8 1.0
CG D:GLU48 4.3 8.1 1.0
CA C:ILE68 4.3 5.5 1.0
CA D:ILE68 4.3 5.5 1.0
CG C:GLU48 4.3 8.2 1.0
CA C:SER72 4.7 4.5 1.0
O D:THR66 4.7 5.6 1.0
CA D:SER72 4.7 4.9 1.0
O C:THR66 4.7 5.6 1.0
OE1 D:GLU48 4.7 8.7 1.0
OE1 C:GLU48 4.8 9.6 1.0
CB C:ILE68 4.8 5.4 1.0
CB D:ILE68 4.8 5.5 1.0
CB C:GLU48 4.9 7.8 1.0
N C:SER72 4.9 4.1 1.0
CB D:GLU48 4.9 7.9 1.0
N D:SER72 4.9 4.5 1.0

Sodium binding site 3 out of 3 in 4lzw

Go back to Sodium Binding Sites List in 4lzw
Sodium binding site 3 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na304

b:7.5
occ:0.52
OE2 F:GLU48 2.6 9.2 1.0
OG F:SER72 2.7 5.8 1.0
OE2 E:GLU48 2.7 8.1 1.0
O F:ILE68 3.1 6.0 1.0
O E:ILE68 3.1 6.2 1.0
OG E:SER72 3.1 5.8 1.0
CB F:SER72 3.2 5.7 1.0
N F:ILE68 3.5 6.3 1.0
CB E:SER72 3.6 5.9 1.0
N E:ILE68 3.6 5.3 1.0
CD F:GLU48 3.6 10.2 1.0
O F:HOH453 3.7 8.2 0.5
CD E:GLU48 3.8 8.1 1.0
O F:HOH453 3.8 4.9 0.5
CA F:GLY67 3.9 6.9 1.0
C F:ILE68 4.0 5.6 1.0
C F:GLY67 4.0 6.6 1.0
C E:ILE68 4.0 6.3 1.0
CG F:GLU48 4.1 10.0 1.0
CA E:GLY67 4.2 6.4 1.0
C E:GLY67 4.2 5.5 1.0
CA F:ILE68 4.3 6.6 1.0
CA E:ILE68 4.3 6.5 1.0
CG E:GLU48 4.3 8.3 1.0
O F:THR66 4.5 7.4 1.0
CA F:SER72 4.6 6.1 1.0
OE1 F:GLU48 4.6 11.0 1.0
CB E:ILE68 4.7 6.7 1.0
OE1 E:GLU48 4.8 9.1 1.0
CB F:GLU48 4.8 9.2 1.0
O E:THR66 4.8 6.5 1.0
CB F:ILE68 4.8 6.0 1.0
N F:SER72 4.9 5.7 1.0
CA E:SER72 4.9 4.8 1.0
CB E:GLU48 4.9 8.3 1.0
O F:GLY67 5.0 8.5 1.0

Reference:

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution To Be Published.
Page generated: Tue Dec 15 06:53:02 2020

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