Magnesium in PDB 3nm1: The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes
Enzymatic activity of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes
All present enzymatic activity of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes:
2.5.1.3;
2.7.1.50;
Protein crystallography data
The structure of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes, PDB code: 3nm1
was solved by
D.Paul,
A.Chatterjee,
T.P.Begley,
S.E.Ealick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.55 /
3.21
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.938,
154.212,
148.704,
90.00,
102.10,
90.00
|
R / Rfree (%)
|
20.1 /
23.2
|
Other elements in 3nm1:
The structure of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes
(pdb code 3nm1). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes, PDB code: 3nm1:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 3nm1
Go back to
Magnesium Binding Sites List in 3nm1
Magnesium binding site 1 out
of 6 in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg544
b:66.8
occ:1.00
|
OD2
|
A:ASP95
|
2.2
|
77.3
|
1.0
|
O6
|
A:POP543
|
2.4
|
84.8
|
1.0
|
O1
|
A:POP543
|
2.6
|
89.4
|
1.0
|
OD2
|
A:ASP76
|
2.7
|
89.7
|
1.0
|
O4
|
A:POP543
|
3.0
|
85.4
|
1.0
|
O3
|
A:POP543
|
3.0
|
80.7
|
1.0
|
CG
|
A:ASP95
|
3.1
|
80.9
|
1.0
|
P2
|
A:POP543
|
3.1
|
91.5
|
1.0
|
P1
|
A:POP543
|
3.2
|
76.2
|
1.0
|
CG
|
A:ASP76
|
3.2
|
90.7
|
1.0
|
OD1
|
A:ASP95
|
3.3
|
83.0
|
1.0
|
CB
|
A:ASP76
|
3.6
|
87.9
|
1.0
|
O
|
A:POP543
|
3.6
|
88.9
|
1.0
|
NZ
|
A:LYS47
|
3.8
|
81.8
|
1.0
|
ND2
|
A:ASN75
|
3.9
|
80.1
|
1.0
|
N
|
A:GLY92
|
4.1
|
74.8
|
1.0
|
OD1
|
A:ASP76
|
4.1
|
89.0
|
1.0
|
OD1
|
A:ASN75
|
4.4
|
84.2
|
1.0
|
CA
|
A:GLY92
|
4.4
|
71.2
|
1.0
|
CB
|
A:ASP95
|
4.5
|
77.3
|
1.0
|
CG
|
A:ASN75
|
4.5
|
80.3
|
1.0
|
O5
|
A:POP543
|
4.6
|
80.3
|
1.0
|
O2
|
A:POP543
|
4.6
|
64.3
|
1.0
|
C
|
A:VAL91
|
4.7
|
70.9
|
1.0
|
CA
|
A:ASP76
|
4.8
|
81.2
|
1.0
|
N
|
A:ASP76
|
4.8
|
78.0
|
1.0
|
CA
|
A:VAL91
|
4.9
|
67.8
|
1.0
|
O
|
A:HIS90
|
4.9
|
70.9
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 3nm1
Go back to
Magnesium Binding Sites List in 3nm1
Magnesium binding site 2 out
of 6 in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg544
b:60.4
occ:1.00
|
OD2
|
F:ASP95
|
2.3
|
76.3
|
1.0
|
OD2
|
F:ASP76
|
2.4
|
75.7
|
1.0
|
O4
|
F:POP543
|
2.7
|
80.8
|
1.0
|
O3
|
F:POP543
|
2.8
|
86.9
|
1.0
|
O6
|
F:POP543
|
2.9
|
81.3
|
1.0
|
CG
|
F:ASP95
|
3.0
|
83.5
|
1.0
|
OD1
|
F:ASP95
|
3.1
|
85.9
|
1.0
|
O2
|
F:POP543
|
3.1
|
78.2
|
1.0
|
P2
|
F:POP543
|
3.2
|
86.6
|
1.0
|
CG
|
F:ASP76
|
3.3
|
84.1
|
1.0
|
P1
|
F:POP543
|
3.3
|
81.1
|
1.0
|
O
|
F:POP543
|
3.5
|
79.7
|
1.0
|
NZ
|
F:LYS47
|
3.8
|
74.3
|
1.0
|
CB
|
F:ASP76
|
3.9
|
83.8
|
1.0
|
OD1
|
F:ASP76
|
4.2
|
84.5
|
1.0
|
N
|
F:GLY92
|
4.3
|
80.2
|
1.0
|
CB
|
F:ASP95
|
4.5
|
80.8
|
1.0
|
CA
|
F:GLY92
|
4.6
|
74.6
|
1.0
|
O5
|
F:POP543
|
4.6
|
68.8
|
1.0
|
ND2
|
F:ASN75
|
4.8
|
73.2
|
1.0
|
O1
|
F:POP543
|
4.8
|
69.5
|
1.0
|
CE
|
F:LYS47
|
4.9
|
78.6
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 3nm1
Go back to
Magnesium Binding Sites List in 3nm1
Magnesium binding site 3 out
of 6 in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg544
b:61.7
occ:1.00
|
OD2
|
E:ASP95
|
2.4
|
83.3
|
1.0
|
O6
|
E:POP543
|
2.5
|
84.0
|
1.0
|
O2
|
E:POP543
|
2.7
|
79.1
|
1.0
|
OD2
|
E:ASP76
|
2.7
|
87.5
|
1.0
|
O3
|
E:POP543
|
2.8
|
85.8
|
1.0
|
CB
|
E:ASP76
|
3.1
|
81.7
|
1.0
|
CG
|
E:ASP95
|
3.1
|
82.1
|
1.0
|
OD1
|
E:ASP95
|
3.2
|
83.3
|
1.0
|
CG
|
E:ASP76
|
3.2
|
84.8
|
1.0
|
P1
|
E:POP543
|
3.2
|
79.8
|
1.0
|
NZ
|
E:LYS47
|
3.6
|
75.9
|
1.0
|
P2
|
E:POP543
|
3.7
|
90.6
|
1.0
|
ND2
|
E:ASN75
|
3.8
|
69.6
|
1.0
|
O
|
E:POP543
|
3.9
|
84.4
|
1.0
|
OD1
|
E:ASN75
|
4.0
|
79.2
|
1.0
|
N
|
E:GLY92
|
4.2
|
76.2
|
1.0
|
OD1
|
E:ASP76
|
4.3
|
83.8
|
1.0
|
CG
|
E:ASN75
|
4.3
|
75.2
|
1.0
|
O4
|
E:POP543
|
4.4
|
73.8
|
1.0
|
CA
|
E:ASP76
|
4.4
|
79.1
|
1.0
|
O1
|
E:POP543
|
4.6
|
64.1
|
1.0
|
CB
|
E:ASP95
|
4.6
|
77.5
|
1.0
|
N
|
E:ASP76
|
4.7
|
78.5
|
1.0
|
CA
|
E:GLY92
|
4.8
|
74.3
|
1.0
|
CE
|
E:LYS47
|
4.8
|
74.0
|
1.0
|
O5
|
E:POP543
|
4.9
|
88.9
|
1.0
|
C
|
E:VAL91
|
5.0
|
76.4
|
1.0
|
CD
|
E:LYS47
|
5.0
|
72.8
|
1.0
|
CA
|
E:VAL91
|
5.0
|
71.7
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 3nm1
Go back to
Magnesium Binding Sites List in 3nm1
Magnesium binding site 4 out
of 6 in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg544
b:61.9
occ:1.00
|
OD2
|
D:ASP95
|
2.3
|
75.7
|
1.0
|
O6
|
D:POP543
|
2.4
|
72.6
|
1.0
|
OD1
|
D:ASP76
|
2.5
|
79.6
|
1.0
|
O3
|
D:POP543
|
2.6
|
72.3
|
1.0
|
CG
|
D:ASP76
|
3.1
|
85.1
|
1.0
|
O2
|
D:POP543
|
3.2
|
72.6
|
1.0
|
P1
|
D:POP543
|
3.3
|
70.3
|
1.0
|
CG
|
D:ASP95
|
3.3
|
79.4
|
1.0
|
P2
|
D:POP543
|
3.3
|
74.3
|
1.0
|
CB
|
D:ASP76
|
3.4
|
79.5
|
1.0
|
O4
|
D:POP543
|
3.5
|
67.6
|
1.0
|
ND2
|
D:ASN75
|
3.5
|
74.0
|
1.0
|
N
|
D:GLY92
|
3.7
|
75.8
|
1.0
|
OD1
|
D:ASP95
|
3.7
|
80.7
|
1.0
|
O
|
D:POP543
|
3.8
|
74.2
|
1.0
|
NZ
|
D:LYS47
|
4.0
|
78.7
|
1.0
|
OD2
|
D:ASP76
|
4.1
|
88.3
|
1.0
|
OD1
|
D:ASN75
|
4.1
|
77.9
|
1.0
|
CA
|
D:GLY92
|
4.1
|
73.2
|
1.0
|
CG
|
D:ASN75
|
4.2
|
74.6
|
1.0
|
C
|
D:VAL91
|
4.4
|
70.6
|
1.0
|
N
|
D:ASP76
|
4.4
|
74.7
|
1.0
|
CA
|
D:ASP76
|
4.4
|
73.2
|
1.0
|
CB
|
D:ASP95
|
4.6
|
76.2
|
1.0
|
CA
|
D:VAL91
|
4.6
|
64.8
|
1.0
|
O5
|
D:POP543
|
4.7
|
73.1
|
1.0
|
O
|
D:HIS90
|
4.7
|
71.8
|
1.0
|
O1
|
D:POP543
|
4.7
|
61.6
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 3nm1
Go back to
Magnesium Binding Sites List in 3nm1
Magnesium binding site 5 out
of 6 in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg544
b:57.0
occ:1.00
|
O6
|
C:POP543
|
2.2
|
72.9
|
1.0
|
OD1
|
C:ASP76
|
2.4
|
76.4
|
1.0
|
OD2
|
C:ASP95
|
2.5
|
73.2
|
1.0
|
O3
|
C:POP543
|
3.1
|
76.4
|
1.0
|
CG
|
C:ASP76
|
3.1
|
79.9
|
1.0
|
OD1
|
C:ASP95
|
3.1
|
84.8
|
1.0
|
CG
|
C:ASP95
|
3.2
|
76.4
|
1.0
|
P2
|
C:POP543
|
3.2
|
82.4
|
1.0
|
O2
|
C:POP543
|
3.4
|
66.7
|
1.0
|
O5
|
C:POP543
|
3.4
|
80.5
|
1.0
|
CB
|
C:ASP76
|
3.5
|
77.3
|
1.0
|
P1
|
C:POP543
|
3.6
|
68.6
|
1.0
|
NZ
|
C:LYS47
|
3.6
|
70.8
|
1.0
|
O
|
C:POP543
|
3.7
|
75.3
|
1.0
|
OD2
|
C:ASP76
|
3.9
|
81.2
|
1.0
|
OD1
|
C:ASN75
|
4.2
|
65.6
|
1.0
|
N
|
C:GLY92
|
4.3
|
69.6
|
1.0
|
ND2
|
C:ASN75
|
4.5
|
74.3
|
1.0
|
O4
|
C:POP543
|
4.5
|
72.1
|
1.0
|
CA
|
C:GLY92
|
4.7
|
69.5
|
1.0
|
CB
|
C:ASP95
|
4.7
|
68.1
|
1.0
|
CG
|
C:ASN75
|
4.8
|
72.1
|
1.0
|
CA
|
C:ASP76
|
4.9
|
68.5
|
1.0
|
CE
|
C:LYS47
|
5.0
|
70.8
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 3nm1
Go back to
Magnesium Binding Sites List in 3nm1
Magnesium binding site 6 out
of 6 in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg544
b:56.1
occ:1.00
|
O3
|
B:POP543
|
2.5
|
81.9
|
1.0
|
O4
|
B:POP543
|
2.5
|
78.1
|
1.0
|
OD2
|
B:ASP95
|
2.8
|
87.7
|
1.0
|
OD1
|
B:ASP95
|
3.0
|
86.7
|
1.0
|
OD1
|
B:ASN75
|
3.1
|
80.6
|
1.0
|
CG
|
B:ASP95
|
3.1
|
86.4
|
1.0
|
CG
|
B:ASP76
|
3.2
|
91.7
|
1.0
|
CB
|
B:ASP76
|
3.3
|
89.2
|
1.0
|
NZ
|
B:LYS47
|
3.3
|
75.3
|
1.0
|
OD1
|
B:ASP76
|
3.4
|
88.7
|
1.0
|
OD2
|
B:ASP76
|
3.6
|
91.4
|
1.0
|
P2
|
B:POP543
|
3.6
|
81.6
|
1.0
|
P1
|
B:POP543
|
3.6
|
79.0
|
1.0
|
O6
|
B:POP543
|
3.7
|
87.5
|
1.0
|
O2
|
B:POP543
|
3.9
|
75.6
|
1.0
|
O
|
B:POP543
|
4.1
|
81.0
|
1.0
|
CG
|
B:ASN75
|
4.3
|
80.5
|
1.0
|
N
|
B:GLY92
|
4.4
|
80.5
|
1.0
|
CB
|
B:ASP95
|
4.5
|
80.8
|
1.0
|
CA
|
B:ASP76
|
4.7
|
82.8
|
1.0
|
CE
|
B:LYS47
|
4.8
|
79.7
|
1.0
|
O1
|
B:POP543
|
4.8
|
70.8
|
1.0
|
O5
|
B:POP543
|
4.9
|
75.9
|
1.0
|
CA
|
B:GLY92
|
5.0
|
74.6
|
1.0
|
|
Reference:
D.Paul,
A.Chatterjee,
T.P.Begley,
S.E.Ealick.
Domain Organization in Candida Glabrata THI6, A Bifunctional Enzyme Required For Thiamin Biosynthesis in Eukaryotes . Biochemistry V. 49 9922 2010.
ISSN: ISSN 0006-2960
PubMed: 20968298
DOI: 10.1021/BI101008U
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