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Magnesium in PDB 5exe: Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct

Enzymatic activity of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct

All present enzymatic activity of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct:
1.2.7.10;

Protein crystallography data

The structure of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct, PDB code: 5exe 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) 48.70 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.653, 144.131, 161.715, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.3

Other elements in 5exe:

The structure of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct also contains other interesting chemical elements:

Iron (Fe) 24 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct (pdb code 5exe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct, PDB code: 5exe:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5exe

Go back to Magnesium Binding Sites List in 5exe
Magnesium binding site 1 out of 3 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct


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-Tpp Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:13.2
occ:1.00
OD1 C:ASN138 2.0 19.2 1.0
O28 C:5SR402 2.1 16.0 1.0
OD1 C:ASP110 2.1 19.6 1.0
O27 C:5SR402 2.1 17.2 1.0
O C:SER140 2.1 15.0 1.0
O C:HOH608 2.3 16.2 1.0
CG C:ASN138 3.0 15.7 1.0
CG C:ASP110 3.0 19.2 1.0
P24 C:5SR402 3.2 16.1 1.0
P22 C:5SR402 3.3 18.1 1.0
C C:SER140 3.3 19.9 1.0
OD2 C:ASP110 3.4 15.8 1.0
ND2 C:ASN138 3.4 16.8 1.0
O23 C:5SR402 3.5 13.0 1.0
O30 C:5SR402 3.8 16.1 1.0
N C:ASP110 3.8 18.5 1.0
N C:SER140 3.9 17.1 1.0
O21 C:5SR402 4.0 16.9 1.0
N C:ALA142 4.1 16.9 1.0
N C:TYR141 4.3 13.5 1.0
N C:ASN138 4.3 16.2 1.0
CA C:SER140 4.3 17.6 1.0
CB C:ASP110 4.3 18.1 1.0
CB C:ASN138 4.3 17.4 1.0
CA C:TYR141 4.4 13.7 1.0
N C:GLU139 4.5 16.6 1.0
C C:ASN138 4.5 19.8 1.0
O29 C:5SR402 4.5 14.3 1.0
O25 C:5SR402 4.6 17.5 1.0
N C:GLY111 4.6 15.0 1.0
CA C:ASP110 4.6 16.2 1.0
CA C:ASN138 4.6 18.4 1.0
CB C:ALA142 4.6 17.5 1.0
CA C:GLY109 4.6 14.2 1.0
C C:GLY109 4.7 18.6 1.0
C C:TYR141 4.8 16.2 1.0
OG C:SER140 4.8 17.7 1.0
O C:TYR136 4.9 14.8 1.0

Magnesium binding site 2 out of 3 in 5exe

Go back to Magnesium Binding Sites List in 5exe
Magnesium binding site 2 out of 3 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct


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-Tpp Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:33.7
occ:0.97
O C:GLN213 2.1 27.7 1.0
O C:HOH707 2.3 41.2 1.0
O C:LEU211 2.3 22.7 1.0
OD1 C:ASP130 2.5 24.4 1.0
O C:HOH566 2.5 34.9 1.0
O C:HOH562 2.6 26.4 1.0
C C:LEU211 3.3 24.9 1.0
C C:GLN213 3.3 28.6 1.0
CG C:ASP130 3.5 27.2 1.0
OD2 C:ASP130 3.8 31.7 1.0
CA C:LEU211 3.9 24.2 1.0
O C:GLY210 4.0 21.5 1.0
N C:GLN213 4.0 25.0 1.0
CA C:GLN213 4.2 25.1 1.0
O C:GLY215 4.2 23.7 1.0
C C:ASN212 4.3 27.9 1.0
N C:GLU214 4.3 29.6 1.0
N C:ASN212 4.3 22.5 1.0
CA C:GLU214 4.4 33.8 1.0
N C:GLY215 4.4 28.5 1.0
O C:HOH811 4.5 55.5 1.0
O C:HOH537 4.7 22.1 1.0
CA C:ASN212 4.7 24.9 1.0
O C:ASN212 4.7 28.9 1.0
CB C:GLN213 4.7 27.0 1.0
C C:GLY210 4.8 22.4 1.0
N C:LEU211 4.9 19.8 1.0
CB C:ASP130 4.9 24.8 1.0
CB C:LEU211 4.9 22.9 1.0
C C:ASP130 5.0 22.2 1.0

Magnesium binding site 3 out of 3 in 5exe

Go back to Magnesium Binding Sites List in 5exe
Magnesium binding site 3 out of 3 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct


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-Tpp Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg403

b:15.1
occ:1.00
O28 F:5SR402 1.9 19.8 1.0
OD1 F:ASP110 2.0 18.9 1.0
OD1 F:ASN138 2.1 17.6 1.0
O F:SER140 2.1 19.6 1.0
O27 F:5SR402 2.1 16.4 1.0
O F:HOH628 2.3 14.5 1.0
CG F:ASN138 3.0 18.4 1.0
CG F:ASP110 3.1 20.8 1.0
P24 F:5SR402 3.1 16.5 1.0
P22 F:5SR402 3.2 18.4 1.0
O23 F:5SR402 3.2 18.1 1.0
C F:SER140 3.4 19.5 1.0
ND2 F:ASN138 3.4 13.6 1.0
OD2 F:ASP110 3.5 21.9 1.0
O30 F:5SR402 3.7 19.1 1.0
N F:ASP110 3.9 17.0 1.0
O21 F:5SR402 4.0 20.3 1.0
N F:SER140 4.0 17.2 1.0
N F:ALA142 4.1 19.7 1.0
N F:TYR141 4.2 20.0 1.0
N F:ASN138 4.3 17.2 1.0
CA F:TYR141 4.3 18.8 1.0
CB F:ASP110 4.3 15.8 1.0
O29 F:5SR402 4.3 17.3 1.0
CA F:SER140 4.3 18.8 1.0
CB F:ASN138 4.4 15.4 1.0
O25 F:5SR402 4.5 19.1 1.0
N F:GLY111 4.5 18.2 1.0
CB F:ALA142 4.5 19.6 1.0
N F:GLU139 4.5 17.9 1.0
CA F:ASP110 4.6 22.2 1.0
C F:ASN138 4.6 16.3 1.0
CA F:GLY109 4.6 16.6 1.0
CA F:ASN138 4.7 16.7 1.0
C F:GLY109 4.7 19.9 1.0
C F:TYR141 4.7 22.2 1.0
O F:TYR136 4.8 17.7 1.0
OG F:SER140 4.9 17.1 1.0
CA F:ALA142 5.0 18.6 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: Mon Dec 14 20:16:51 2020

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