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Magnesium in PDB 4k6o: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution

Enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution, PDB code: 4k6o 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) 40.28 / 1.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.012, 97.100, 93.017, 90.00, 119.99, 90.00
R / Rfree (%) 10.8 / 12.8

Other elements in 4k6o:

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms
Sodium (Na) 4 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution (pdb code 4k6o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution, PDB code: 4k6o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 4k6o

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Magnesium binding site 1 out of 16 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution


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 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:16.0
occ:0.79
 OE1 A:GLN180 2.0 14.0 0.7
O A:HOH499 2.0 17.6 1.0
O A:HOH535 2.1 17.6 1.0
O A:HOH496 2.1 14.8 0.8
O A:HOH543 2.1 18.3 1.0
O A:HOH600 2.1 19.2 1.0
NE2 A:GLN180 2.1 9.1 0.3
CD A:GLN180 2.8 9.3 0.3
OE1 A:GLN180 2.9 9.3 0.3
CD A:GLN180 3.1 13.3 0.7
HE22 A:GLN180 3.2 17.2 0.7
NE2 A:GLN180 3.5 14.4 0.7
HA A:ARG177 4.0 10.2 1.0
O A:HOH440 4.1 13.3 0.7
O A:HOH730 4.2 41.0 1.0
HG3 A:ARG177 4.2 16.6 1.0
O C:HOH464 4.3 13.5 1.0
CG A:GLN180 4.3 9.2 0.3
OE1 C:GLU185 4.3 13.0 1.0
HE21 A:GLN180 4.4 17.2 0.7
HB2 A:GLN180 4.4 13.0 0.7
CG A:GLN180 4.4 11.8 0.7
O A:HOH495 4.4 16.9 1.0
HB2 A:GLN180 4.4 11.2 0.3
O C:HOH458 4.4 13.6 1.0
O C:HOH610 4.4 35.2 1.0
HB2 A:ARG177 4.5 14.1 1.0
HB3 A:GLN180 4.7 11.2 0.3
HB3 A:GLN180 4.7 13.0 0.7
HG3 A:GLN180 4.7 14.2 0.7
HG3 A:GLN180 4.7 11.1 0.3
CB A:GLN180 4.7 9.3 0.3
O C:HOH590 4.7 39.6 1.0
CB A:GLN180 4.8 10.8 0.7
HG2 A:GLN180 4.8 11.1 0.3
CA A:ARG177 4.9 8.5 1.0
CB A:ARG177 5.0 11.8 1.0

Magnesium binding site 2 out of 16 in 4k6o

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Magnesium binding site 2 out of 16 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution


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 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:13.7
occ:0.70
 O A:HOH493 2.0 17.4 1.0
O A:HOH519 2.1 15.8 1.0
O A:HOH546 2.1 12.5 0.5
O A:HOH474 2.1 14.9 1.0
O A:HOH461 2.1 12.4 1.0
O A:HOH457 2.1 13.7 1.0
HA A:ALA206 3.5 6.6 1.0
O A:HOH433 4.1 7.2 1.0
O F:HOH821 4.2 39.0 1.0
O F:HOH440 4.2 14.3 0.4
O F:HOH456 4.2 13.1 1.0
O A:ALA206 4.3 7.4 1.0
O A:LEU210 4.3 7.3 1.0
O F:HOH415 4.3 7.6 1.0
O A:HOH520 4.3 23.0 1.0
CA A:ALA206 4.4 5.5 1.0
O A:HOH518 4.4 17.7 0.7
O A:HOH451 4.4 10.2 1.0
HB2 A:ASP132 4.4 7.8 1.0
OD1 A:ASP132 4.5 8.2 1.0
HA A:ASP132 4.5 6.0 1.0
HB1 A:ALA206 4.6 7.6 1.0
O F:HOH440 4.7 5.3 0.6
HA2 A:GLY209 4.8 9.5 1.0
C A:ALA206 4.8 6.3 1.0
CL A:CL309 4.8 21.4 1.0
HA A:LYS211 4.9 7.5 1.0
HG2 A:LYS211 4.9 13.2 1.0
CB A:ALA206 5.0 6.4 1.0

Magnesium binding site 3 out of 16 in 4k6o

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Magnesium binding site 3 out of 16 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution


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 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:16.5
occ:0.80
 OE1 B:GLN180 2.0 12.0 0.4
O B:HOH510 2.0 18.2 1.0
O B:HOH598 2.1 19.5 1.0
O B:HOH563 2.1 17.6 1.0
O B:HOH500 2.1 15.6 0.8
O B:HOH471 2.1 15.9 1.0
OE1 B:GLN180 2.2 15.4 0.6
HE22 B:GLN180 2.8 17.8 0.6
CD B:GLN180 3.0 12.0 0.4
CD B:GLN180 3.0 14.5 0.6
NE2 B:GLN180 3.2 14.8 0.6
NE2 B:GLN180 3.4 12.4 0.4
HA B:ARG177 3.9 8.8 1.0
HE21 B:GLN180 4.0 17.8 0.6
HG3 B:ARG177 4.1 13.5 1.0
O F:HOH457 4.2 13.3 1.0
O B:HOH474 4.2 9.4 0.6
O B:HOH473 4.3 16.4 1.0
OE2 F:GLU185 4.3 12.3 1.0
O B:HOH592 4.3 27.7 1.0
CG B:GLN180 4.3 11.5 0.4
O F:HOH458 4.4 13.4 1.0
CG B:GLN180 4.4 12.9 0.6
HB2 B:ARG177 4.4 11.3 1.0
HB2 B:GLN180 4.4 13.6 0.6
HB2 B:GLN180 4.5 12.7 0.4
O F:HOH651 4.6 30.2 1.0
HG3 B:GLN180 4.6 13.8 0.4
HB3 B:GLN180 4.7 12.7 0.4
HB3 B:GLN180 4.7 13.6 0.6
HG3 B:GLN180 4.8 15.5 0.6
CB B:GLN180 4.8 10.6 0.4
CA B:ARG177 4.8 7.4 1.0
CB B:GLN180 4.8 11.3 0.6
CG B:ARG177 4.9 11.2 1.0
CB B:ARG177 4.9 9.4 1.0

Magnesium binding site 4 out of 16 in 4k6o

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Magnesium binding site 4 out of 16 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution


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 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:13.7
occ:0.40
 O B:HOH506 2.1 16.4 1.0
O B:HOH727 2.1 13.8 0.4
O B:HOH446 2.1 12.2 1.0
O B:HOH444 2.1 14.2 1.0
O B:HOH727 2.2 13.3 0.6
O B:HOH518 3.0 27.0 1.0
HA B:ALA206 3.5 6.7 1.0
O B:HOH424 4.0 7.7 1.0
O C:HOH485 4.2 17.8 1.0
O C:HOH415 4.3 8.3 1.0
O C:HOH775 4.3 45.6 1.0
O B:LEU210 4.3 8.0 1.0
O B:ALA206 4.3 7.2 1.0
CA B:ALA206 4.4 5.6 1.0
O B:HOH556 4.5 25.0 1.0
O B:HOH437 4.5 10.0 1.0
HB2 B:ASP132 4.6 8.5 1.0
O B:HOH436 4.6 9.7 1.0
HA B:ASP132 4.6 7.4 1.0
HB1 B:ALA206 4.6 8.0 1.0
OD1 B:ASP132 4.6 9.9 1.0
HA2 B:GLY209 4.8 10.2 1.0
C B:ALA206 4.8 5.8 1.0
HA B:LYS211 4.8 8.7 0.4
HA B:LYS211 4.8 8.5 0.6
HG2 B:LYS211 4.9 12.7 0.6
O B:HOH758 4.9 13.0 1.0
HG2 B:LYS211 4.9 12.1 0.4
CB B:ALA206 4.9 6.7 1.0
HB2 B:ALA206 5.0 8.0 1.0
O B:HOH694 5.0 40.3 1.0

Magnesium binding site 5 out of 16 in 4k6o

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Magnesium binding site 5 out of 16 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution


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 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:12.8
occ:0.80
 O B:HOH456 2.1 14.3 1.0
O B:HOH463 2.1 14.9 1.0
O B:HOH492 3.9 18.6 1.0
O B:PHE171 4.0 7.9 1.0
O B:THR170 4.2 7.2 1.0
O B:HOH539 4.3 30.6 1.0
O B:HOH546 4.4 25.0 1.0
O A:HOH510 4.5 24.4 1.0
HA B:PHE171 4.8 8.1 1.0
C B:PHE171 4.9 6.7 1.0

Magnesium binding site 6 out of 16 in 4k6o

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Magnesium binding site 6 out of 16 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution


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 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg305

b:17.9
occ:0.30
 O C:HOH591 2.0 19.5 1.0
OE1 C:GLN180 2.1 17.7 1.0
O E:HOH543 2.1 18.3 1.0
O C:HOH579 2.1 18.7 1.0
O C:HOH601 2.1 20.3 1.0
O C:HOH525 2.1 19.3 1.0
HE22 C:GLN180 2.9 21.9 1.0
CD C:GLN180 3.0 16.7 1.0
NE2 C:GLN180 3.3 18.3 1.0
HA C:ARG177 3.9 8.8 1.0
HG3 C:ARG177 4.0 14.1 1.0
O E:HOH479 4.1 15.0 1.0
HE21 C:GLN180 4.1 21.9 1.0
OE2 E:GLU185 4.2 13.3 1.0
O C:HOH626 4.2 33.7 1.0
O C:HOH783 4.2 61.5 1.0
O E:HOH502 4.3 16.0 1.0
O C:HOH547 4.3 18.8 1.0
CG C:GLN180 4.4 14.3 1.0
HB2 C:GLN180 4.4 14.7 1.0
HB2 C:ARG177 4.4 11.1 1.0
O E:HOH833 4.6 30.6 1.0
HB3 C:GLN180 4.7 14.7 1.0
CB C:GLN180 4.8 12.2 1.0
HG3 C:GLN180 4.8 17.2 1.0
CA C:ARG177 4.8 7.4 1.0
CG C:ARG177 4.9 11.7 1.0
CB C:ARG177 4.9 9.3 1.0
HG2 C:GLN180 5.0 17.2 1.0
HE C:ARG177 5.0 16.2 1.0

Magnesium binding site 7 out of 16 in 4k6o

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Magnesium binding site 7 out of 16 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution


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 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg306

b:29.9
occ:0.57
 O C:HOH758 2.1 30.4 1.0
O C:HOH754 2.1 30.2 1.0
O C:HOH603 2.1 29.4 0.7
O C:HOH789 2.1 29.7 1.0
O C:HOH692 2.1 30.6 1.0
O C:HOH624 2.1 30.1 1.0
O C:HOH603 3.8 12.7 0.3
HA C:LYS250 3.9 12.5 1.0
O C:ARG249 4.3 11.9 1.0
O C:HOH724 4.3 47.2 1.0
O C:HOH554 4.4 26.2 1.0
HG2 C:ARG249 4.6 18.9 0.7
O C:LEU252 4.7 20.7 1.0
O C:HOH511 4.8 20.1 1.0
CA C:LYS250 4.8 10.4 1.0
O C:LYS250 4.9 12.6 1.0
O C:HOH657 4.9 30.9 1.0

Magnesium binding site 8 out of 16 in 4k6o

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Magnesium binding site 8 out of 16 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg307

b:12.7
occ:0.63
 O C:HOH533 2.1 12.9 0.6
O B:HOH493 2.1 10.8 0.5
O B:HOH527 2.1 16.3 1.0
O C:HOH450 2.1 14.2 1.0
O C:HOH444 2.1 12.6 1.0
O C:HOH439 2.1 13.4 1.0
HA C:ALA206 3.5 7.1 1.0
O C:HOH412 4.1 7.7 1.0
O B:HOH460 4.2 14.4 1.0
O B:HOH520 4.3 26.5 1.0
O B:HOH429 4.3 8.8 1.0
O C:HOH541 4.3 22.7 1.0
O C:LEU210 4.3 7.9 1.0
O C:ALA206 4.3 7.6 1.0
O C:HOH431 4.4 11.1 1.0
OD1 C:ASP132 4.4 9.8 1.0
HB2 C:ASP132 4.5 8.4 1.0
CA C:ALA206 4.5 6.0 1.0
HA C:ASP132 4.5 7.2 1.0
HG2 C:LYS211 4.7 10.7 0.2
O C:HOH446 4.7 13.5 1.0
HA2 C:GLY209 4.7 9.6 1.0
HB1 C:ALA206 4.7 8.4 1.0
CL C:CL303 4.8 23.4 1.0
HA C:LYS211 4.8 8.7 0.2
C C:ALA206 4.8 6.2 1.0
HA C:LYS211 4.8 8.6 0.8
O B:HOH729 5.0 29.3 1.0
HG2 C:LYS211 5.0 14.0 0.8

Magnesium binding site 9 out of 16 in 4k6o

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Magnesium binding site 9 out of 16 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:16.7
occ:0.86
 O D:HOH464 2.0 17.8 1.0
OE1 D:GLN180 2.1 10.7 0.6
O D:HOH499 2.1 17.4 1.0
O D:HOH631 2.1 19.6 1.0
O D:HOH498 2.1 18.0 1.0
O D:HOH544 2.1 18.9 1.0
OE1 D:GLN180 2.2 15.1 0.4
HE22 D:GLN180 2.4 16.0 0.4
CD D:GLN180 2.8 13.3 0.4
NE2 D:GLN180 2.9 13.3 0.4
CD D:GLN180 3.1 10.2 0.6
NE2 D:GLN180 3.5 11.2 0.6
HE21 D:GLN180 3.7 16.0 0.4
HA D:ARG177 4.0 10.3 1.0
O D:HOH457 4.1 10.4 0.5
HG3 D:ARG177 4.2 16.3 1.0
O B:HOH462 4.3 13.2 1.0
CG D:GLN180 4.3 11.8 0.4
O B:HOH692 4.3 32.1 1.0
O D:HOH690 4.3 36.7 1.0
OE1 B:GLU185 4.3 12.2 1.0
O D:HOH461 4.3 16.9 1.0
CG D:GLN180 4.4 9.4 0.6
HB2 D:GLN180 4.4 11.0 0.6
O B:HOH451 4.5 13.5 1.0
HB2 D:ARG177 4.5 13.7 1.0
HB2 D:GLN180 4.5 12.5 0.4
O B:HOH572 4.6 29.4 1.0
HG3 D:GLN180 4.7 14.2 0.4
HG3 D:GLN180 4.7 11.3 0.6
HB3 D:GLN180 4.7 12.5 0.4
HB3 D:GLN180 4.8 11.0 0.6
CB D:GLN180 4.8 10.4 0.4
CB D:GLN180 4.8 9.2 0.6
CA D:ARG177 4.8 8.6 1.0
HG2 D:GLN180 4.8 14.2 0.4
CB D:ARG177 5.0 11.4 1.0

Magnesium binding site 10 out of 16 in 4k6o

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Magnesium binding site 10 out of 16 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:22.6
occ:0.55
 HE2 D:HIS46 1.3 22.9 1.0
O D:HOH814 1.9 25.5 0.6
NE2 D:HIS46 2.0 19.1 1.0
O D:HOH652 2.1 24.9 1.0
O D:HOH814 2.1 23.1 0.5
O D:HOH797 2.1 24.6 1.0
CE1 D:HIS46 2.8 16.6 1.0
HE1 D:HIS46 2.9 19.9 1.0
O D:HOH518 3.0 25.7 1.0
CD2 D:HIS46 3.1 16.5 1.0
HD2 D:HIS46 3.4 19.8 1.0
O D:HOH762 3.5 47.1 1.0
ND1 D:HIS46 3.9 15.5 1.0
HA3 D:GLY9 3.9 13.6 1.0
O D:HOH644 4.0 41.2 1.0
CG D:HIS46 4.1 14.4 1.0
HA2 D:GLY9 4.6 13.6 1.0
HD1 D:HIS46 4.7 18.6 1.0
CA D:GLY9 4.7 11.4 1.0

Reference:

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, M.V.Dontsova, T.A.Seregina, A.S.Mironov, C.Betzel, A.M.Mikhailov. Crystallization and Preliminary X-Ray Study of Vibrio Cholerae Uridine Phosphorylase in Complex with 6-Methyluracil Acta Crystallogr.,Sect.F V. 70 60 2014.
ISSN: ESSN 1744-3091
DOI: 10.1107/S2053230X13031877
Page generated: Sat Aug 17 03:27:27 2024

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