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Magnesium in PDB 5epu: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A.

Enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A.

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A.:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A., PDB code: 5epu 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) 46.46 / 1.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.848, 96.715, 92.890, 90.00, 119.96, 90.00
R / Rfree (%) 10.5 / 12.2

Other elements in 5epu:

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A. (pdb code 5epu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A., PDB code: 5epu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5epu

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Magnesium binding site 1 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:16.5
occ:0.30
 O A:HOH436 2.0 23.9 0.8
O A:HOH716 2.2 17.2 1.0
O A:HOH645 2.2 14.4 0.6
O A:HOH560 2.3 18.3 1.0
O A:HOH645 2.3 15.2 0.4
O A:HOH738 2.7 17.3 0.5
HA A:ALA206 3.5 5.1 1.0
O F:HOH559 4.1 10.4 0.6
O A:HOH544 4.1 6.8 1.0
O A:HOH738 4.2 22.8 0.5
O A:ALA206 4.3 7.4 1.0
O F:HOH605 4.3 9.4 1.0
CA A:ALA206 4.5 5.1 1.0
O A:LEU210 4.5 7.1 1.0
O A:HOH582 4.5 9.9 1.0
OD1 A:ASP132 4.5 9.6 1.0
HA A:ASP132 4.5 4.9 1.0
HB2 A:ASP132 4.6 5.8 1.0
O A:HOH572 4.6 24.5 1.0
HB2 A:ALA206 4.6 5.4 1.0
O A:HOH575 4.7 7.9 1.0
O F:HOH595 4.8 12.1 0.5
HG2 A:LYS211 4.8 9.8 0.4
O A:HOH614 4.8 10.1 1.0
HA2 A:GLY209 4.8 7.4 1.0
C A:ALA206 4.8 5.5 1.0
HA A:LYS211 4.9 5.8 0.4
HA A:LYS211 4.9 5.8 0.6
CB A:ALA206 5.0 5.7 1.0
HB1 A:ALA206 5.0 5.8 1.0

Magnesium binding site 2 out of 7 in 5epu

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Magnesium binding site 2 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:24.8
occ:0.49
 O A:HOH457 2.0 35.3 1.0
O A:HOH742 2.0 72.5 0.5
O A:HOH688 2.0 37.6 1.0
O B:HOH722 2.1 42.9 1.0
O A:HOH515 2.2 31.2 1.0
O A:HOH753 2.2 42.4 1.0
O A:SER45 3.8 11.8 1.0
O A:HOH421 4.2 39.1 1.0
HB1 B:ALA28 4.3 22.0 1.0
O B:HOH509 4.3 24.6 1.0
HA A:HIS46 4.4 9.5 0.5
HA A:HIS46 4.4 9.2 0.5
O A:HOH456 4.4 20.7 0.6
OG A:SER45 4.6 12.9 0.2
HG A:SER45 4.7 12.7 0.0
HB3 A:SER45 4.7 11.5 0.8
C A:SER45 4.8 10.2 1.0
HB2 B:ALA28 4.8 23.1 1.0
HD1 A:HIS46 4.8 12.2 0.5
O A:HOH618 4.9 37.3 1.0
CB B:ALA28 5.0 21.1 1.0

Magnesium binding site 3 out of 7 in 5epu

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Magnesium binding site 3 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:22.2
occ:0.56
 O B:HOH648 2.0 33.2 1.0
O B:HOH426 2.1 25.2 1.0
O F:HOH765 2.1 25.8 0.6
O F:HOH414 2.1 24.8 0.8
O F:HOH566 2.2 25.4 1.0
HG3 B:ARG177 3.8 7.0 0.6
HG3 B:ARG177 3.9 8.1 0.4
HE B:ARG177 4.0 7.6 0.6
HA3 F:GLY181 4.1 6.2 1.0
O B:HOH477 4.2 38.1 1.0
O F:HOH406 4.2 11.3 0.5
OE1 B:GLN180 4.2 9.6 0.2
NE B:ARG177 4.3 8.5 0.6
OE1 F:GLU185 4.3 12.3 0.5
O F:HOH507 4.3 12.6 1.0
O F:HOH431 4.4 20.4 1.0
OE1 B:GLN180 4.4 12.0 0.8
HE B:ARG177 4.4 11.2 0.4
HD2 B:ARG177 4.4 7.5 0.6
NE B:ARG177 4.4 10.2 0.4
O F:GLN180 4.5 7.3 1.0
CZ B:ARG177 4.5 11.7 0.4
O B:HOH443 4.5 49.7 1.0
O F:HOH526 4.6 38.9 1.0
CG B:ARG177 4.6 6.9 0.6
HH21 B:ARG177 4.6 14.0 0.4
NH2 B:ARG177 4.6 12.8 0.4
O D:HOH571 4.7 30.8 1.0
CD B:ARG177 4.7 7.2 0.6
HH21 B:ARG177 4.7 10.2 0.6
CZ B:ARG177 4.8 9.3 0.6
CG B:ARG177 4.8 8.3 0.4
O D:HOH411 4.9 18.4 0.5
HD3 B:ARG177 4.9 10.8 0.4
NH2 B:ARG177 4.9 11.3 0.6
CD B:ARG177 5.0 10.2 0.4
HH22 B:ARG177 5.0 12.8 0.4
HB2 B:ARG177 5.0 6.0 0.4

Magnesium binding site 4 out of 7 in 5epu

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Magnesium binding site 4 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:12.7
occ:0.75
 O B:HOH724 2.0 18.0 1.0
O B:HOH721 2.1 17.3 0.6
O B:HOH683 2.1 12.8 0.7
O B:HOH446 2.1 18.0 1.0
O B:HOH550 2.2 20.2 1.0
O B:HOH688 2.2 15.7 0.6
O B:PHE171 3.9 7.5 1.0
O B:THR170 4.2 6.8 1.0
O B:HOH601 4.5 27.1 1.0
O B:HOH650 4.5 20.1 0.5
O A:HOH715 4.5 28.4 1.0
O B:HOH650 4.8 30.2 0.5
HA B:PHE171 4.8 6.2 1.0
C B:PHE171 4.9 5.9 1.0

Magnesium binding site 5 out of 7 in 5epu

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Magnesium binding site 5 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:9.3
occ:0.30
 O E:HOH624 1.9 16.1 0.8
OD1 E:ASN102 2.0 19.4 1.0
O E:HOH703 2.2 16.8 1.0
O E:HOH414 2.3 16.3 0.4
CG E:ASN102 3.0 14.6 1.0
HE21 E:GLN224 3.3 9.7 0.5
HD21 E:ASN102 3.4 18.3 1.0
HE21 E:GLN224 3.5 8.6 0.5
ND2 E:ASN102 3.6 19.9 1.0
O E:HOH581 3.9 24.2 1.0
NE2 E:GLN224 4.1 9.2 0.5
O E:HOH572 4.1 18.2 1.0
HA E:ASN102 4.1 9.3 1.0
CB E:ASN102 4.2 11.5 1.0
HB3 E:ASN102 4.3 11.3 1.0
HE22 E:GLN224 4.3 8.7 0.5
O E:PRO99 4.3 13.9 1.0
NE2 E:GLN224 4.3 7.8 0.5
HD22 E:ASN102 4.6 19.6 1.0
HE22 E:GLN224 4.6 8.1 0.5
CA E:ASN102 4.7 9.3 1.0
O E:HOH681 5.0 54.1 1.0
HB2 E:ASN102 5.0 12.0 1.0

Magnesium binding site 6 out of 7 in 5epu

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Magnesium binding site 6 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:14.0
occ:0.74
 O F:HOH775 2.0 19.2 0.6
O F:HOH575 2.0 18.3 0.8
O F:HOH692 2.1 14.8 0.7
O F:HOH706 2.1 23.6 0.6
O F:HOH789 2.1 17.8 1.0
O F:HOH746 2.2 22.2 1.0
MG F:MG303 3.2 9.6 0.3
HD21 F:ASN102 3.4 19.6 1.0
HA F:HIS100 3.9 12.8 1.0
O F:HOH608 3.9 40.3 1.0
O F:HOH702 3.9 18.7 1.0
O F:HOH418 4.1 15.7 0.5
O F:HOH777 4.2 45.6 1.0
O F:HOH593 4.2 24.9 1.0
O F:PRO99 4.3 15.7 1.0
ND2 F:ASN102 4.3 17.1 1.0
O F:HOH688 4.4 43.2 1.0
OD1 F:ASN102 4.7 23.1 1.0
O F:HOH647 4.8 16.7 1.0
CA F:HIS100 4.8 12.9 1.0
HD22 F:ASN102 5.0 17.6 1.0
CG F:ASN102 5.0 16.0 1.0

Magnesium binding site 7 out of 7 in 5epu

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Magnesium binding site 7 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytosine at 1.06A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg303

b:9.6
occ:0.35
 HD21 F:ASN102 1.5 19.6 1.0
O F:HOH647 1.9 16.7 1.0
ND2 F:ASN102 1.9 17.1 1.0
HD22 F:ASN102 2.1 17.6 1.0
O F:HOH702 2.2 18.7 1.0
O F:HOH418 2.2 15.7 0.5
O F:HOH746 2.4 22.2 1.0
O F:HOH575 2.4 18.3 0.8
O F:HOH692 2.7 14.8 0.7
CG F:ASN102 3.0 16.0 1.0
MG F:MG302 3.2 14.0 0.7
HE21 F:GLN224 3.4 11.2 0.7
OD1 F:ASN102 3.5 23.1 1.0
HE21 F:GLN224 3.6 9.7 0.3
O F:HOH608 3.9 40.3 1.0
O F:HOH571 4.1 18.1 1.0
HA F:ASN102 4.1 10.7 1.0
NE2 F:GLN224 4.2 11.3 0.7
CB F:ASN102 4.2 12.6 1.0
O F:PRO99 4.3 15.7 1.0
HB3 F:ASN102 4.3 13.4 1.0
NE2 F:GLN224 4.4 8.2 0.3
HE22 F:GLN224 4.4 10.4 0.7
O F:HOH706 4.6 23.6 0.6
HE22 F:GLN224 4.7 8.7 0.3
CA F:ASN102 4.7 10.7 1.0
O F:HOH775 4.7 19.2 0.6
O F:HOH789 4.8 17.8 1.0
O F:HOH688 5.0 43.2 1.0
HB2 F:ASN102 5.0 12.9 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 Cytosine at 1.06A. To Be Published.
Page generated: Tue Aug 12 07:49:37 2025

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