Magnesium in PDB 5exd: Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate
Enzymatic activity of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate
All present enzymatic activity of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate:
1.2.7.10;
Protein crystallography data
The structure of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate, PDB code: 5exd
was solved by
M.I.Gibson,
P.Y.-T.Chen,
C.L.Drennan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.94 /
2.50
|
Space group
|
P 43
|
Cell size a, b, c (Å), α, β, γ (°)
|
138.430,
138.430,
217.069,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
22.9
|
Other elements in 5exd:
The structure of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate
(pdb code 5exd). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate, PDB code: 5exd:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5exd
Go back to
Magnesium Binding Sites List in 5exd
Magnesium binding site 1 out
of 4 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate
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 Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg403
b:19.8
occ:1.00
|
O1B
|
C:TPP402
|
2.0
|
23.1
|
1.0
|
O
|
C:HOH501
|
2.0
|
22.4
|
1.0
|
OD1
|
C:ASP110
|
2.0
|
23.2
|
1.0
|
OD1
|
C:ASN138
|
2.1
|
22.4
|
1.0
|
O
|
C:SER140
|
2.1
|
22.8
|
1.0
|
O1A
|
C:TPP402
|
2.1
|
21.6
|
1.0
|
CG
|
C:ASN138
|
3.0
|
23.0
|
1.0
|
CG
|
C:ASP110
|
3.1
|
22.6
|
1.0
|
PB
|
C:TPP402
|
3.2
|
24.5
|
1.0
|
PA
|
C:TPP402
|
3.2
|
22.9
|
1.0
|
ND2
|
C:ASN138
|
3.3
|
23.4
|
1.0
|
C
|
C:SER140
|
3.3
|
22.4
|
1.0
|
O3A
|
C:TPP402
|
3.3
|
21.1
|
1.0
|
OD2
|
C:ASP110
|
3.7
|
23.7
|
1.0
|
N
|
C:ASP110
|
3.8
|
21.5
|
1.0
|
N
|
C:SER140
|
4.1
|
22.3
|
1.0
|
O2B
|
C:TPP402
|
4.1
|
23.4
|
1.0
|
O7
|
C:TPP402
|
4.1
|
21.8
|
1.0
|
N
|
C:ALA142
|
4.2
|
22.3
|
1.0
|
N
|
C:TYR141
|
4.2
|
21.9
|
1.0
|
O3B
|
C:TPP402
|
4.3
|
22.3
|
1.0
|
CA
|
C:SER140
|
4.3
|
21.5
|
1.0
|
CB
|
C:ASP110
|
4.3
|
22.9
|
1.0
|
CA
|
C:TYR141
|
4.3
|
22.4
|
1.0
|
N
|
C:ASN138
|
4.4
|
22.7
|
1.0
|
CB
|
C:ASN138
|
4.4
|
23.2
|
1.0
|
O2A
|
C:TPP402
|
4.4
|
20.4
|
1.0
|
CA
|
C:GLY109
|
4.5
|
21.8
|
1.0
|
N
|
C:GLY111
|
4.5
|
20.9
|
1.0
|
CA
|
C:ASP110
|
4.6
|
22.0
|
1.0
|
C
|
C:GLY109
|
4.6
|
21.6
|
1.0
|
CB
|
C:ALA142
|
4.7
|
22.2
|
1.0
|
N
|
C:GLU139
|
4.7
|
22.0
|
1.0
|
CA
|
C:ASN138
|
4.8
|
22.7
|
1.0
|
C
|
C:ASN138
|
4.8
|
22.6
|
1.0
|
C
|
C:TYR141
|
4.8
|
22.3
|
1.0
|
OG
|
C:SER140
|
4.9
|
22.1
|
1.0
|
O
|
C:TYR136
|
4.9
|
22.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5exd
Go back to
Magnesium Binding Sites List in 5exd
Magnesium binding site 2 out
of 4 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate
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 Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg403
b:26.0
occ:1.00
|
OD1
|
F:ASP110
|
1.9
|
26.6
|
1.0
|
O
|
F:SER140
|
1.9
|
28.4
|
1.0
|
O28
|
F:O2T402
|
2.0
|
26.9
|
1.0
|
O25
|
F:O2T402
|
2.1
|
26.2
|
1.0
|
OD1
|
F:ASN138
|
2.1
|
26.8
|
1.0
|
O
|
F:HOH501
|
2.2
|
26.0
|
1.0
|
CG
|
F:ASP110
|
3.0
|
27.3
|
1.0
|
C
|
F:SER140
|
3.2
|
29.0
|
1.0
|
CG
|
F:ASN138
|
3.2
|
26.8
|
1.0
|
P24
|
F:O2T402
|
3.2
|
27.2
|
1.0
|
P22
|
F:O2T402
|
3.3
|
28.4
|
1.0
|
OD2
|
F:ASP110
|
3.5
|
28.7
|
1.0
|
O23
|
F:O2T402
|
3.6
|
26.6
|
1.0
|
ND2
|
F:ASN138
|
3.6
|
27.6
|
1.0
|
O30
|
F:O2T402
|
3.8
|
28.8
|
1.0
|
N
|
F:SER140
|
3.8
|
28.2
|
1.0
|
O21
|
F:O2T402
|
3.8
|
28.6
|
1.0
|
N
|
F:ASP110
|
3.9
|
24.9
|
1.0
|
CA
|
F:SER140
|
4.1
|
28.4
|
1.0
|
N
|
F:TYR141
|
4.1
|
29.2
|
1.0
|
N
|
F:ALA142
|
4.2
|
30.0
|
1.0
|
CB
|
F:ASP110
|
4.2
|
26.5
|
1.0
|
CA
|
F:TYR141
|
4.2
|
28.8
|
1.0
|
N
|
F:ASN138
|
4.4
|
26.0
|
1.0
|
O29
|
F:O2T402
|
4.5
|
27.6
|
1.0
|
CB
|
F:ASN138
|
4.5
|
27.6
|
1.0
|
N
|
F:GLY111
|
4.5
|
24.9
|
1.0
|
N
|
F:GLU139
|
4.6
|
26.6
|
1.0
|
O27
|
F:O2T402
|
4.6
|
27.3
|
1.0
|
CA
|
F:ASP110
|
4.6
|
25.2
|
1.0
|
C
|
F:ASN138
|
4.7
|
27.5
|
1.0
|
CA
|
F:GLY109
|
4.7
|
25.2
|
1.0
|
OG
|
F:SER140
|
4.7
|
28.5
|
1.0
|
CA
|
F:ASN138
|
4.7
|
27.3
|
1.0
|
C
|
F:GLY109
|
4.7
|
24.2
|
1.0
|
C
|
F:TYR141
|
4.8
|
29.8
|
1.0
|
CB
|
F:ALA142
|
4.8
|
27.8
|
1.0
|
O
|
F:TYR136
|
4.9
|
23.6
|
1.0
|
C
|
F:GLU139
|
5.0
|
27.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5exd
Go back to
Magnesium Binding Sites List in 5exd
Magnesium binding site 3 out
of 4 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate
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 Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg403
b:26.5
occ:1.00
|
O
|
I:HOH504
|
2.0
|
27.3
|
1.0
|
OD1
|
I:ASP110
|
2.0
|
27.7
|
1.0
|
O3B
|
I:TPP402
|
2.0
|
26.6
|
1.0
|
O2A
|
I:TPP402
|
2.1
|
27.2
|
1.0
|
OD1
|
I:ASN138
|
2.2
|
27.5
|
1.0
|
O
|
I:SER140
|
2.2
|
28.1
|
1.0
|
CG
|
I:ASN138
|
3.1
|
27.6
|
1.0
|
PB
|
I:TPP402
|
3.1
|
28.8
|
1.0
|
CG
|
I:ASP110
|
3.2
|
27.6
|
1.0
|
PA
|
I:TPP402
|
3.2
|
27.7
|
1.0
|
O3A
|
I:TPP402
|
3.3
|
26.5
|
1.0
|
ND2
|
I:ASN138
|
3.3
|
28.2
|
1.0
|
C
|
I:SER140
|
3.4
|
27.6
|
1.0
|
OD2
|
I:ASP110
|
3.8
|
27.5
|
1.0
|
N
|
I:ASP110
|
3.8
|
26.6
|
1.0
|
O1B
|
I:TPP402
|
3.9
|
27.1
|
1.0
|
N
|
I:ALA142
|
4.0
|
26.3
|
1.0
|
N
|
I:SER140
|
4.2
|
27.9
|
1.0
|
O7
|
I:TPP402
|
4.2
|
25.9
|
1.0
|
N
|
I:TYR141
|
4.3
|
27.2
|
1.0
|
CA
|
I:TYR141
|
4.3
|
27.0
|
1.0
|
O1A
|
I:TPP402
|
4.3
|
26.8
|
1.0
|
CB
|
I:ASP110
|
4.3
|
27.5
|
1.0
|
O2B
|
I:TPP402
|
4.3
|
26.3
|
1.0
|
CA
|
I:GLY109
|
4.4
|
27.3
|
1.0
|
N
|
I:ASN138
|
4.4
|
28.1
|
1.0
|
CA
|
I:SER140
|
4.4
|
27.4
|
1.0
|
CB
|
I:ASN138
|
4.5
|
27.6
|
1.0
|
C
|
I:GLY109
|
4.6
|
26.6
|
1.0
|
CB
|
I:ALA142
|
4.6
|
27.1
|
1.0
|
CA
|
I:ASP110
|
4.6
|
26.7
|
1.0
|
N
|
I:GLY111
|
4.6
|
27.4
|
1.0
|
C
|
I:TYR141
|
4.7
|
26.4
|
1.0
|
O
|
I:TYR136
|
4.8
|
27.5
|
1.0
|
CA
|
I:ASN138
|
4.8
|
28.7
|
1.0
|
N
|
I:GLU139
|
4.9
|
28.0
|
1.0
|
CE2
|
I:TYR136
|
4.9
|
26.5
|
1.0
|
C
|
I:ASN138
|
4.9
|
28.3
|
1.0
|
OG
|
I:SER140
|
4.9
|
27.8
|
1.0
|
CA
|
I:ALA142
|
5.0
|
26.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5exd
Go back to
Magnesium Binding Sites List in 5exd
Magnesium binding site 4 out
of 4 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate
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 Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg403
b:32.6
occ:1.00
|
O1B
|
L:TPP402
|
2.0
|
32.7
|
1.0
|
OD1
|
L:ASP110
|
2.0
|
33.4
|
1.0
|
OD1
|
L:ASN138
|
2.0
|
33.9
|
1.0
|
O
|
L:SER140
|
2.0
|
33.8
|
1.0
|
O
|
L:HOH501
|
2.2
|
31.9
|
1.0
|
O1A
|
L:TPP402
|
2.5
|
31.5
|
1.0
|
CG
|
L:ASN138
|
2.9
|
33.5
|
1.0
|
CG
|
L:ASP110
|
3.1
|
33.7
|
1.0
|
PB
|
L:TPP402
|
3.1
|
33.2
|
1.0
|
C
|
L:SER140
|
3.3
|
33.7
|
1.0
|
ND2
|
L:ASN138
|
3.3
|
33.7
|
1.0
|
O3A
|
L:TPP402
|
3.4
|
32.0
|
1.0
|
PA
|
L:TPP402
|
3.5
|
32.5
|
1.0
|
OD2
|
L:ASP110
|
3.6
|
34.4
|
1.0
|
O2B
|
L:TPP402
|
3.8
|
33.5
|
1.0
|
N
|
L:SER140
|
4.0
|
34.6
|
1.0
|
N
|
L:ASP110
|
4.0
|
31.8
|
1.0
|
N
|
L:ALA142
|
4.0
|
32.3
|
1.0
|
N
|
L:TYR141
|
4.2
|
32.9
|
1.0
|
CA
|
L:SER140
|
4.2
|
33.3
|
1.0
|
N
|
L:ASN138
|
4.3
|
34.3
|
1.0
|
O7
|
L:TPP402
|
4.3
|
33.1
|
1.0
|
CA
|
L:TYR141
|
4.3
|
32.7
|
1.0
|
CB
|
L:ASN138
|
4.3
|
33.6
|
1.0
|
CB
|
L:ASP110
|
4.3
|
32.3
|
1.0
|
O3B
|
L:TPP402
|
4.4
|
31.5
|
1.0
|
CB
|
L:ALA142
|
4.6
|
32.6
|
1.0
|
CA
|
L:ASN138
|
4.6
|
34.1
|
1.0
|
N
|
L:GLU139
|
4.6
|
34.5
|
1.0
|
N
|
L:GLY111
|
4.7
|
31.0
|
1.0
|
C
|
L:ASN138
|
4.7
|
34.5
|
1.0
|
CA
|
L:ASP110
|
4.7
|
32.4
|
1.0
|
C
|
L:TYR141
|
4.7
|
32.3
|
1.0
|
CA
|
L:GLY109
|
4.7
|
31.2
|
1.0
|
O2A
|
L:TPP402
|
4.7
|
30.6
|
1.0
|
OG
|
L:SER140
|
4.8
|
33.2
|
1.0
|
C
|
L:GLY109
|
4.8
|
30.5
|
1.0
|
O
|
L:TYR136
|
4.9
|
32.4
|
1.0
|
CA
|
L:ALA142
|
5.0
|
32.0
|
1.0
|
|
Reference:
M.I.Gibson,
P.Y.Chen,
A.C.Johnson,
E.Pierce,
M.Can,
S.W.Ragsdale,
C.L.Drennan.
One-Carbon Chemistry of Oxalate Oxidoreductase Captured By X-Ray Crystallography. Proc.Natl.Acad.Sci.Usa V. 113 320 2016.
ISSN: ESSN 1091-6490
PubMed: 26712008
DOI: 10.1073/PNAS.1518537113
Page generated: Sun Sep 29 03:59:42 2024
|