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
Go back to
Magnesium Binding Sites List in 1qk5
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 Sites List in 1qk5
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
Go back to
Magnesium Binding Sites List in 1qk5
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
Go back to
Magnesium Binding Sites List in 1qk5
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
|