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Magnesium in PDB 3dv0: Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex

Enzymatic activity of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex

All present enzymatic activity of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex:
1.2.4.1; 2.3.1.12;

Protein crystallography data

The structure of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex, PDB code: 3dv0 was solved by X.Y.Pei, C.M.Titman, R.A.W.Frank, F.J.Leeper, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.17 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.312, 232.820, 92.004, 90.00, 91.83, 90.00
R / Rfree (%) 17.3 / 24.1

Other elements in 3dv0:

The structure of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex (pdb code 3dv0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex, PDB code: 3dv0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3dv0

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Magnesium binding site 1 out of 6 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1368

b:12.7
occ:1.00
 O21 A:TPW1370 2.2 28.8 1.0
OD1 A:ASN202 2.2 21.7 1.0
O12 A:TPW1370 2.2 14.3 1.0
OD1 A:ASP173 2.3 17.3 1.0
O A:PHE204 2.3 25.8 1.0
CG A:ASN202 2.7 24.9 1.0
ND2 A:ASN202 2.7 38.1 1.0
P2 A:TPW1370 3.2 20.5 1.0
CG A:ASP173 3.3 25.7 1.0
O23 A:TPW1370 3.3 17.2 1.0
P1 A:TPW1370 3.3 26.2 1.0
O11 A:TPW1370 3.5 15.9 1.0
C A:PHE204 3.5 21.8 1.0
OD2 A:ASP173 3.7 20.6 1.0
NH1 A:ARG267 3.8 85.2 1.0
N A:ASP173 4.0 14.6 1.0
N A:ASN202 4.0 19.6 1.0
CB A:ASN202 4.1 22.6 1.0
N A:PHE204 4.1 21.0 1.0
O5G A:TPW1370 4.2 19.7 1.0
O A:GLN200 4.3 17.5 1.0
CA A:PHE204 4.3 17.8 1.0
CA A:ASN202 4.4 21.9 1.0
N A:ALA205 4.4 18.2 1.0
O A:HOH1489 4.5 17.9 1.0
CA A:GLY172 4.5 13.3 1.0
O22 A:TPW1370 4.5 32.0 1.0
O13 A:TPW1370 4.6 16.5 1.0
CB A:ASP173 4.6 21.6 1.0
C A:ASN202 4.6 21.3 1.0
CA A:ALA205 4.6 24.7 1.0
N A:ARG203 4.7 18.9 1.0
C A:GLY172 4.7 6.3 1.0
CZ A:ARG267 4.8 80.6 1.0
CA A:ASP173 4.9 13.7 1.0
NH2 A:ARG267 4.9 81.8 1.0
N A:GLY174 4.9 19.2 1.0
O A:ASN202 5.0 28.4 1.0

Magnesium binding site 2 out of 6 in 3dv0

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Magnesium binding site 2 out of 6 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1326

b:48.8
occ:1.00
 O A:HOH1436 2.4 6.0 1.0
O D:HOH1439 2.5 16.4 1.0
O B:HOH1436 2.6 25.0 1.0
O A:HOH1375 2.8 22.5 1.0
O C:HOH1421 2.9 13.3 1.0
O C:HOH1460 3.4 7.5 1.0
O B:GLU88 3.5 19.8 1.0
OE2 A:GLU183 3.5 22.9 1.0
CG B:GLU88 3.7 24.6 1.0
O C:HOH1440 3.7 24.7 1.0
CB B:GLU88 3.8 11.9 1.0
CA B:GLU88 3.9 14.1 1.0
CB B:SER60 3.9 16.4 1.0
C B:GLU88 4.1 11.5 1.0
OE1 C:GLN178 4.3 7.8 1.0
OG B:SER60 4.5 20.3 1.0
OD1 C:ASP180 4.6 21.8 1.0
CD A:GLU183 4.7 23.8 1.0
N C:GLY179 4.7 13.6 1.0
CA C:GLY179 4.8 6.7 1.0
CG C:ASP180 4.9 22.3 1.0
N C:ASP180 4.9 10.1 1.0
CD B:GLU88 5.0 16.2 1.0
OD2 C:ASP180 5.0 27.9 1.0

Magnesium binding site 3 out of 6 in 3dv0

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Magnesium binding site 3 out of 6 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1368

b:59.5
occ:1.00
 O C:PHE204 2.1 21.8 1.0
O21 C:TPW1370 2.2 15.6 1.0
OD1 C:ASN202 2.2 23.4 1.0
O12 C:TPW1370 2.4 42.0 1.0
CG C:ASN202 2.6 36.8 1.0
OD1 C:ASP173 2.7 35.0 1.0
ND2 C:ASN202 2.8 19.9 1.0
CG C:ASP173 3.2 22.9 1.0
C C:PHE204 3.3 26.6 1.0
OD2 C:ASP173 3.5 36.1 1.0
P2 C:TPW1370 3.5 18.6 1.0
N C:ASN202 3.6 20.0 1.0
P1 C:TPW1370 3.6 19.1 1.0
N C:PHE204 3.7 28.2 1.0
N C:ASP173 3.7 20.2 1.0
CB C:ASN202 3.8 19.5 1.0
O11 C:TPW1370 3.8 27.6 1.0
CA C:PHE204 4.0 25.9 1.0
O C:GLN200 4.0 18.2 1.0
CA C:ASN202 4.0 26.8 1.0
CB C:ASP173 4.1 23.6 1.0
O23 C:TPW1370 4.1 25.6 1.0
C C:ASN202 4.3 28.9 1.0
N C:ARG203 4.3 32.9 1.0
N C:ALA205 4.4 21.6 1.0
O5G C:TPW1370 4.4 13.6 1.0
CA C:ASP173 4.5 17.4 1.0
CA C:GLY172 4.5 16.7 1.0
C C:GLY172 4.6 19.4 1.0
C C:ASN201 4.7 19.0 1.0
O22 C:TPW1370 4.7 20.0 1.0
O13 C:TPW1370 4.8 30.7 1.0
CA C:ALA205 4.8 21.7 1.0
C C:ARG203 4.8 27.9 1.0
N C:GLY174 4.8 14.4 1.0
CA C:ASN201 4.8 15.9 1.0
CB C:PHE204 4.9 24.1 1.0
O C:ASN202 4.9 26.0 1.0

Magnesium binding site 4 out of 6 in 3dv0

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Magnesium binding site 4 out of 6 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1368

b:54.4
occ:1.00
 OD1 E:ASP173 2.6 40.2 1.0
O21 E:TPW1370 2.7 32.7 1.0
O E:GLN200 2.7 34.4 1.0
O23 E:TPW1370 2.9 19.9 1.0
O12 E:TPW1370 2.9 72.5 1.0
ND2 E:ASN202 3.0 54.9 1.0
OD1 E:ASN202 3.0 54.4 1.0
CA E:GLY172 3.0 43.5 1.0
N E:ASP173 3.1 38.0 1.0
P2 E:TPW1370 3.1 42.8 1.0
CG E:ASN202 3.2 54.4 1.0
O11 E:TPW1370 3.3 56.9 1.0
C E:GLY172 3.5 40.6 1.0
P1 E:TPW1370 3.6 55.3 1.0
C E:GLN200 3.8 36.6 1.0
CG E:ASP173 3.8 43.0 1.0
N E:ASN202 3.8 46.5 1.0
O E:PHE204 4.2 45.1 1.0
CA E:ASN201 4.3 41.1 1.0
CA E:ASP173 4.3 39.7 1.0
N E:GLY172 4.3 47.0 1.0
O13 E:TPW1370 4.3 60.9 1.0
CB E:ASP173 4.4 39.7 1.0
CB E:ASN202 4.4 45.5 1.0
N E:ASN201 4.5 37.5 1.0
C E:ASN201 4.6 43.3 1.0
O22 E:TPW1370 4.6 37.0 1.0
CA E:ASN202 4.7 45.1 1.0
O E:GLY172 4.8 40.6 1.0
CB E:GLN200 4.8 36.4 1.0
OD2 E:ASP173 4.8 31.8 1.0
CA E:GLN200 4.9 36.6 1.0
O5G E:TPW1370 5.0 59.5 1.0
N E:GLY174 5.0 33.9 1.0
O E:THR171 5.0 45.2 1.0

Magnesium binding site 5 out of 6 in 3dv0

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Magnesium binding site 5 out of 6 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1326

b:45.8
occ:1.00
 O H:HOH1372 2.4 25.9 1.0
O H:HOH1376 2.8 26.9 1.0
OE2 G:GLU183 3.0 35.7 1.0
OD1 G:ASP180 3.6 24.8 1.0
CA G:GLY179 3.7 25.2 1.0
O G:HOH1395 3.7 31.7 1.0
C G:GLY179 3.9 26.1 1.0
CA E:GLY179 3.9 27.1 1.0
OE2 E:GLU183 4.0 46.3 1.0
N G:ASP180 4.0 26.8 1.0
CD G:GLU183 4.2 35.2 1.0
OG H:SER60 4.4 24.4 1.0
O E:HOH1459 4.4 35.6 1.0
O G:HOH1441 4.4 31.6 1.0
CB H:SER60 4.4 25.5 1.0
C E:GLY179 4.4 28.1 1.0
N G:GLY179 4.4 27.9 1.0
O G:GLY179 4.5 27.6 1.0
OD1 E:ASP180 4.5 42.0 1.0
CG G:ASP180 4.5 36.2 1.0
N E:GLY179 4.6 26.1 1.0
N E:ASP180 4.7 25.7 1.0
O G:HOH1455 4.8 34.8 1.0
CA G:ASP180 4.8 26.4 1.0
OE1 G:GLU183 5.0 44.2 1.0

Magnesium binding site 6 out of 6 in 3dv0

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Magnesium binding site 6 out of 6 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1367

b:36.4
occ:1.00
 O G:PHE204 2.3 41.2 1.0
OD1 G:ASP173 2.3 35.7 1.0
O21 G:TPW1370 2.4 42.8 1.0
O12 G:TPW1370 2.4 49.2 1.0
OD1 G:ASN202 2.4 43.2 1.0
CG G:ASN202 2.8 38.2 1.0
ND2 G:ASN202 2.9 41.2 1.0
O23 G:TPW1370 3.3 45.8 1.0
P2 G:TPW1370 3.4 39.7 1.0
C G:PHE204 3.5 40.0 1.0
CG G:ASP173 3.6 39.0 1.0
P1 G:TPW1370 3.6 35.9 1.0
O11 G:TPW1370 3.8 52.3 1.0
N G:ASN202 3.8 38.0 1.0
N G:PHE204 4.0 42.3 1.0
N G:ASP173 4.0 27.5 1.0
CB G:ASN202 4.1 34.1 1.0
O G:GLN200 4.2 36.1 1.0
OD2 G:ASP173 4.2 41.3 1.0
CA G:PHE204 4.3 38.2 1.0
CA G:ASN202 4.3 40.0 1.0
O5G G:TPW1370 4.4 36.4 1.0
CA G:GLY172 4.4 33.1 1.0
C G:ASN202 4.5 42.2 1.0
N G:ALA205 4.6 36.0 1.0
N G:ARG203 4.6 41.4 1.0
CB G:ASP173 4.6 27.6 1.0
O22 G:TPW1370 4.7 41.7 1.0
C G:GLY172 4.7 30.9 1.0
O13 G:TPW1370 4.8 41.2 1.0
CA G:ALA205 4.8 33.6 1.0
CA G:ASP173 4.9 31.6 1.0
O G:ASN202 4.9 45.2 1.0
C G:ASN201 4.9 35.2 1.0

Reference:

X.Y.Pei, C.M.Titman, R.A.Frank, F.J.Leeper, B.F.Luisi. Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multienzyme Complex Structure V. 16 1860 2008.
ISSN: ISSN 0969-2126
PubMed: 19081062
DOI: 10.1016/J.STR.2008.10.009
Page generated: Wed Aug 14 12:43:45 2024

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