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Magnesium in PDB 3ozf: Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine

Protein crystallography data

The structure of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine, PDB code: 3ozf was solved by M.Ho, K.Z.Hazleton, S.C.Almo, V.L.Schramm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.78 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.035, 88.907, 80.371, 90.00, 117.06, 90.00
R / Rfree (%) 18.9 / 23.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine (pdb code 3ozf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine, PDB code: 3ozf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3ozf

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Magnesium binding site 1 out of 6 in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg235

b:28.0
occ:1.00
 O5 A:POP233 2.0 27.1 1.0
O3 A:POP233 2.1 27.3 1.0
OD1 A:ASP204 2.1 19.1 1.0
O A:HOH238 2.1 24.5 1.0
O A:HOH237 2.3 23.6 1.0
O A:HOH298 2.5 29.5 1.0
CG A:ASP204 3.1 19.3 1.0
P2 A:POP233 3.2 27.6 1.0
P1 A:POP233 3.2 26.4 1.0
O A:POP233 3.3 26.8 1.0
OD2 A:ASP204 3.4 20.2 1.0
O A:HOH305 4.0 27.8 1.0
NH2 A:ARG210 4.0 18.3 1.0
O2 A:POP233 4.1 27.6 1.0
O4 A:POP233 4.2 27.5 1.0
O A:HOH418 4.2 33.1 1.0
O6 A:POP233 4.2 26.1 1.0
O A:ASP204 4.3 18.1 1.0
O A:HOH255 4.3 20.3 1.0
O1 A:POP233 4.3 25.8 1.0
NH1 A:ARG210 4.4 20.3 1.0
N3 A:HPA232 4.4 15.6 1.0
CB A:ASP204 4.4 17.5 1.0
O A:HOH236 4.6 31.3 1.0
N A:ASP204 4.6 18.2 1.0
CZ A:ARG210 4.6 20.6 1.0
CB A:TYR116 4.7 26.3 1.0
C A:ASP204 4.8 17.7 1.0
CA A:ASP204 4.9 18.2 1.0

Magnesium binding site 2 out of 6 in 3ozf

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Magnesium binding site 2 out of 6 in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg235

b:24.8
occ:1.00
 O2 B:POP233 1.9 30.0 1.0
O4 B:POP233 2.0 31.4 1.0
OD1 B:ASP204 2.1 20.1 1.0
O B:HOH236 2.2 23.8 1.0
O B:HOH240 2.3 25.8 1.0
O B:HOH299 2.5 30.3 1.0
P1 B:POP233 3.1 32.6 1.0
CG B:ASP204 3.1 20.4 1.0
P2 B:POP233 3.2 31.3 1.0
O B:POP233 3.3 30.9 1.0
OD2 B:ASP204 3.4 22.9 1.0
O B:HOH307 3.8 29.2 1.0
O5 B:POP233 4.1 30.2 1.0
O3 B:POP233 4.1 31.9 1.0
O1 B:POP233 4.1 30.5 1.0
NH2 B:ARG210 4.1 20.9 1.0
O B:ASP204 4.2 18.5 1.0
O6 B:POP233 4.3 28.5 1.0
O B:HOH263 4.4 17.0 1.0
NH1 B:ARG210 4.4 19.7 1.0
CB B:ASP204 4.5 18.8 1.0
N3 B:HPA232 4.5 17.1 1.0
N B:ASP204 4.7 18.4 1.0
O B:HOH370 4.7 45.5 1.0
CB B:TYR116 4.7 29.3 1.0
CZ B:ARG210 4.7 20.2 1.0
C B:ASP204 4.8 18.0 1.0
CA B:ASP204 4.9 18.4 1.0

Magnesium binding site 3 out of 6 in 3ozf

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Magnesium binding site 3 out of 6 in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg235

b:21.0
occ:1.00
 O C:HOH242 2.0 18.3 1.0
O3 C:POP233 2.0 18.3 1.0
O4 C:POP233 2.0 18.2 1.0
OD1 C:ASP204 2.0 15.5 1.0
O C:HOH240 2.2 17.5 1.0
O C:HOH241 2.3 19.5 1.0
CG C:ASP204 3.1 16.7 1.0
P1 C:POP233 3.2 19.5 1.0
P2 C:POP233 3.2 17.8 1.0
O C:POP233 3.4 18.6 1.0
OD2 C:ASP204 3.4 13.5 1.0
O C:HOH300 3.7 19.1 1.0
O C:HOH301 4.0 27.2 1.0
NH2 C:ARG210 4.0 18.4 1.0
O5 C:POP233 4.1 18.2 1.0
O2 C:POP233 4.2 19.6 1.0
O C:HOH305 4.2 26.4 1.0
O1 C:POP233 4.2 19.1 1.0
O C:ASP204 4.3 14.9 1.0
NH1 C:ARG210 4.3 15.7 1.0
O6 C:POP233 4.3 18.6 1.0
O C:HOH260 4.4 17.6 1.0
CB C:ASP204 4.4 13.9 1.0
N3 C:HPA232 4.4 13.7 1.0
N C:ASP204 4.5 15.0 1.0
CZ C:ARG210 4.6 18.8 1.0
CB C:TYR116 4.7 16.7 1.0
C C:ASP204 4.8 14.7 1.0
O C:HOH285 4.8 23.0 1.0
MG C:MG236 4.8 34.2 1.0
CA C:ASP204 4.8 15.4 1.0

Magnesium binding site 4 out of 6 in 3ozf

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Magnesium binding site 4 out of 6 in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg236

b:34.2
occ:1.00
 O C:HOH300 1.9 19.1 1.0
O1 C:POP233 2.0 19.1 1.0
O C:HOH239 2.0 30.3 1.0
O C:HOH238 2.0 22.2 1.0
O C:HOH237 2.2 23.9 1.0
O C:HOH301 2.4 27.2 1.0
P1 C:POP233 3.1 19.5 1.0
O3 C:POP233 3.3 18.3 1.0
O C:HOH271 3.5 20.3 1.0
O C:HOH295 3.9 28.7 1.0
O2 C:POP233 4.1 19.6 1.0
O5 C:POP233 4.1 18.2 1.0
N9 C:HPA232 4.2 12.6 1.0
O1 C:PO4234 4.2 18.9 1.0
OE2 C:GLU144 4.2 29.1 1.0
O C:HOH242 4.3 18.3 1.0
O C:POP233 4.3 18.6 1.0
OD1 C:ASP145 4.3 23.2 1.0
CD1 C:TYR116 4.4 15.4 1.0
OD2 C:ASP145 4.5 29.7 1.0
OG1 C:THR152 4.5 20.4 1.0
O C:HOH287 4.6 26.2 1.0
OG C:SER115 4.6 19.6 1.0
O C:HOH310 4.7 25.8 1.0
P2 C:POP233 4.7 17.8 1.0
CE1 C:TYR116 4.8 17.4 1.0
MG C:MG235 4.8 21.0 1.0
CG C:ASP145 4.9 21.6 1.0
O4 C:POP233 5.0 18.2 1.0

Magnesium binding site 5 out of 6 in 3ozf

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Magnesium binding site 5 out of 6 in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg233

b:19.3
occ:1.00
 O5 D:POP236 1.9 16.5 1.0
O3 D:POP236 2.0 17.9 1.0
OD1 D:ASP204 2.1 15.9 1.0
O D:HOH238 2.1 19.1 1.0
O D:HOH237 2.2 21.8 1.0
O D:HOH239 2.2 20.0 1.0
CG D:ASP204 3.1 16.4 1.0
P2 D:POP236 3.2 17.1 1.0
P1 D:POP236 3.2 18.8 1.0
O D:POP236 3.3 18.1 1.0
OD2 D:ASP204 3.4 15.8 1.0
O D:HOH258 3.6 17.7 1.0
O D:HOH296 4.0 23.1 1.0
O2 D:POP236 4.0 19.2 1.0
NH2 D:ARG210 4.1 17.1 1.0
O4 D:POP236 4.2 17.2 1.0
O6 D:POP236 4.2 18.5 1.0
NH1 D:ARG210 4.2 15.7 1.0
O D:HOH289 4.3 23.5 1.0
O D:ASP204 4.3 13.3 1.0
O1 D:POP236 4.3 18.1 1.0
O D:HOH255 4.4 15.8 1.0
CB D:ASP204 4.4 14.1 1.0
N3 D:HPA235 4.4 13.8 1.0
N D:ASP204 4.5 15.4 1.0
CZ D:ARG210 4.6 18.0 1.0
CB D:TYR116 4.7 16.1 1.0
C D:ASP204 4.8 14.2 1.0
MG D:MG234 4.8 33.4 1.0
CA D:ASP204 4.8 14.8 1.0
O D:HOH253 4.9 20.5 1.0

Magnesium binding site 6 out of 6 in 3ozf

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Magnesium binding site 6 out of 6 in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg234

b:33.4
occ:1.00
 O6 D:POP236 1.9 18.5 1.0
O D:HOH258 2.1 17.7 1.0
O D:HOH296 2.2 23.1 1.0
O D:HOH247 2.2 21.9 1.0
O D:HOH252 2.2 16.7 1.0
O D:HOH294 2.2 33.4 1.0
P2 D:POP236 3.2 17.1 1.0
O5 D:POP236 3.4 16.5 1.0
O D:HOH311 3.5 23.3 1.0
O D:HOH288 3.8 26.3 1.0
O2 D:POP236 4.0 19.2 1.0
OE2 D:GLU144 4.2 22.8 1.0
O4 D:POP236 4.2 17.2 1.0
OD1 D:ASP145 4.2 25.3 1.0
O D:HOH238 4.2 19.1 1.0
O D:POP236 4.3 18.1 1.0
O D:HOH291 4.3 23.2 1.0
N9 D:HPA235 4.3 13.8 1.0
O2 D:PO4232 4.4 18.0 1.0
OD2 D:ASP145 4.4 28.4 1.0
OG1 D:THR152 4.6 19.1 1.0
CD1 D:TYR116 4.6 15.2 1.0
P1 D:POP236 4.6 18.8 1.0
CG D:ASP145 4.8 22.1 1.0
MG D:MG233 4.8 19.3 1.0
OG D:SER115 4.9 18.4 1.0
CD D:GLU144 4.9 21.0 1.0
OE1 D:GLU144 4.9 23.4 1.0
O3 D:POP236 4.9 17.9 1.0
CE1 D:TYR116 5.0 15.3 1.0

Reference:

K.Z.Hazleton, M.C.Ho, M.B.Cassera, K.Clinch, D.R.Crump, I.Rosario, E.F.Merino, S.C.Almo, P.C.Tyler, V.L.Schramm. Acyclic Immucillin Phosphonates: Second-Generation Inhibitors of Plasmodium Falciparum Hypoxanthine- Guanine-Xanthine Phosphoribosyltransferase. Chem.Biol. V. 19 721 2012.
ISSN: ISSN 1074-5521
PubMed: 22726686
DOI: 10.1016/J.CHEMBIOL.2012.04.012
Page generated: Thu Aug 15 08:59:50 2024

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