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Magnesium in PDB 1qk5: Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions

Enzymatic activity of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions

All present enzymatic activity of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions:
2.4.2.8;

Protein crystallography data

The structure of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions, PDB code: 1qk5 was solved by A.Heroux, E.L.White, L.J.Ross, R.L.Davis, D.W.Borhani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.00 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 55.208, 112.255, 144.280, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 26.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions (pdb code 1qk5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions, PDB code: 1qk5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1qk5

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Magnesium binding site 1 out of 4 in the Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:29.4
occ:1.00
 O1 A:POP301 2.1 22.4 1.0
O4 A:POP301 2.1 20.4 1.0
O A:HOH2099 2.2 35.3 1.0
O A:HOH2065 2.3 19.4 1.0
O A:HOH2062 2.4 24.6 1.0
P2 A:POP301 3.2 19.0 1.0
P1 A:POP301 3.2 23.9 1.0
O2' A:XMP300 3.3 33.9 1.0
O A:POP301 3.3 20.5 1.0
O3' A:XMP300 3.4 35.3 1.0
O2 A:POP301 3.8 23.6 1.0
O5 A:POP301 3.9 20.4 1.0
OD1 A:ASP147 4.0 22.3 1.0
O A:HOH2102 4.0 30.6 1.0
O A:HOH2098 4.0 34.9 1.0
OD2 A:ASP147 4.0 22.1 1.0
N A:GLY80 4.2 13.4 1.0
OE2 A:GLU146 4.3 22.3 1.0
O6 A:POP301 4.3 17.1 1.0
C2' A:XMP300 4.3 33.1 1.0
C3' A:XMP300 4.4 34.1 1.0
CA A:GLY80 4.4 15.0 1.0
O3 A:POP301 4.4 22.3 1.0
CG A:ASP147 4.4 21.5 1.0
OE1 A:GLU146 4.4 23.4 1.0
O A:LEU115 4.7 30.9 1.0
O A:LEU78 4.7 16.9 1.0
MG A:MG303 4.8 21.4 1.0
CD A:GLU146 4.8 25.7 1.0
CG2 A:ILE77 4.9 14.2 1.0
C1' A:XMP300 4.9 29.9 1.0
N A:LYS79 4.9 15.0 1.0

Magnesium binding site 2 out of 4 in 1qk5

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Magnesium binding site 2 out of 4 in the Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:21.4
occ:1.00
 O A:HOH2084 2.0 32.5 1.0
O5 A:POP301 2.1 20.4 1.0
OD1 A:ASP206 2.1 19.3 1.0
O A:HOH2102 2.2 30.6 1.0
O A:HOH2083 2.2 40.2 1.0
O2 A:POP301 2.4 23.6 1.0
CG A:ASP206 3.2 23.9 1.0
P1 A:POP301 3.3 23.9 1.0
OD2 A:ASP206 3.3 23.4 1.0
P2 A:POP301 3.3 19.0 1.0
O A:POP301 3.4 20.5 1.0
NH2 A:ARG212 4.0 16.3 1.0
O A:HOH2082 4.0 26.2 1.0
O4 A:POP301 4.2 20.4 1.0
NH1 A:ARG212 4.3 16.0 1.0
O1 A:POP301 4.3 22.4 1.0
O3 A:POP301 4.3 22.3 1.0
O2 A:XMP300 4.4 27.4 1.0
O6 A:POP301 4.4 17.1 1.0
N3 A:XMP300 4.5 22.8 1.0
O A:HOH2085 4.5 25.0 1.0
CB A:ASP206 4.5 21.8 1.0
CZ A:ARG212 4.5 16.7 1.0
O A:ASP206 4.7 17.5 1.0
N A:ASP206 4.7 18.7 1.0
MG A:MG302 4.8 29.4 1.0
C2 A:XMP300 4.8 24.2 1.0
O A:HOH2086 4.9 24.4 1.0

Magnesium binding site 3 out of 4 in 1qk5

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Magnesium binding site 3 out of 4 in the Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:28.0
occ:1.00
 O B:HOH2077 2.1 29.0 1.0
O1 B:POP301 2.1 25.5 1.0
O B:HOH2049 2.1 26.0 1.0
O4 B:POP301 2.2 24.9 1.0
O B:HOH2054 2.2 29.0 1.0
O B:HOH2053 2.2 23.8 1.0
P1 B:POP301 3.2 25.1 1.0
P2 B:POP301 3.2 23.6 1.0
O B:POP301 3.4 22.8 1.0
O3' B:XMP300 3.7 35.9 1.0
O2' B:XMP300 3.9 36.9 1.0
O B:HOH2079 3.9 35.3 1.0
O2 B:POP301 4.2 27.9 1.0
OE2 B:GLU146 4.2 29.9 1.0
O B:HOH2078 4.2 35.2 1.0
OD1 B:ASP147 4.2 27.4 1.0
O5 B:POP301 4.2 22.3 1.0
N B:GLY80 4.3 19.3 1.0
O B:LEU78 4.3 17.5 1.0
O6 B:POP301 4.3 21.8 1.0
O3 B:POP301 4.3 27.0 1.0
OD2 B:ASP147 4.3 30.3 1.0
O B:LEU115 4.4 27.7 1.0
CA B:GLY80 4.5 19.5 1.0
CG2 B:ILE77 4.5 17.8 1.0
C3' B:XMP300 4.7 34.2 1.0
OE1 B:GLU146 4.7 30.9 1.0
O B:ILE77 4.7 20.2 1.0
CG B:ASP147 4.7 25.9 1.0
C B:LEU78 4.8 17.1 1.0
C2' B:XMP300 4.8 33.5 1.0
N B:LYS79 4.8 16.7 1.0
CD B:GLU146 4.8 29.0 1.0
MG B:MG303 4.9 31.9 1.0

Magnesium binding site 4 out of 4 in 1qk5

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Magnesium binding site 4 out of 4 in the Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:31.9
occ:1.00
 O5 B:POP301 2.0 22.3 1.0
OD1 B:ASP206 2.3 24.2 1.0
O B:HOH2078 2.3 35.2 1.0
O B:HOH2064 2.3 26.6 1.0
O2 B:POP301 2.3 27.9 1.0
O B:HOH2063 2.4 30.4 1.0
P2 B:POP301 3.1 23.6 1.0
P1 B:POP301 3.2 25.1 1.0
O B:POP301 3.2 22.8 1.0
CG B:ASP206 3.3 25.4 1.0
OD2 B:ASP206 3.5 25.3 1.0
O4 B:POP301 4.0 24.9 1.0
O1 B:POP301 4.1 25.5 1.0
NH2 B:ARG212 4.1 18.0 1.0
O B:HOH2055 4.1 27.6 1.0
O6 B:POP301 4.2 21.8 1.0
NH1 B:ARG212 4.2 16.3 1.0
O B:HOH2077 4.3 29.0 1.0
O3 B:POP301 4.3 27.0 1.0
N3 B:XMP300 4.4 29.7 1.0
O2 B:XMP300 4.5 31.2 1.0
CB B:ASP206 4.7 22.3 1.0
CZ B:ARG212 4.7 16.2 1.0
N B:ASP206 4.8 22.1 1.0
MG B:MG302 4.9 28.0 1.0
O B:ASP206 4.9 23.5 1.0
O B:HOH2080 4.9 26.9 1.0
C2 B:XMP300 4.9 29.2 1.0

Reference:

A.Heroux, E.L.White, L.J.Ross, R.L.Davis, D.W.Borhani. Crystal Structure of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two MG2+ Ions Bound: Insights Into the Catalytic Mechanism Biochemistry V. 38 14495 1999.
ISSN: ISSN 0006-2960
PubMed: 10545171
DOI: 10.1021/BI990508I
Page generated: Tue Aug 13 11:52:35 2024

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