Atomistry » Magnesium » PDB 4k6e-4kft » 4k6o
Atomistry »
  Magnesium »
    PDB 4k6e-4kft »
      4k6o »

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

Go back to Magnesium Binding Sites List in 4k6o
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

Go back to Magnesium Binding Sites List in 4k6o
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

Go back to Magnesium Binding Sites List in 4k6o
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

Go back to Magnesium Binding Sites List in 4k6o
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

Go back to Magnesium Binding Sites List in 4k6o
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

Go back to Magnesium Binding Sites List in 4k6o
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

Go back to Magnesium Binding Sites List in 4k6o
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

Go back to Magnesium Binding Sites List in 4k6o
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

Go back to Magnesium Binding Sites List in 4k6o
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

Go back to Magnesium Binding Sites List in 4k6o
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: Mon Dec 14 19:01:58 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy