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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:

Iron (Fe) 48 atoms

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

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