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Magnesium in PDB 3dva: 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: 3dva 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 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.673, 232.294, 91.936, 90.00, 91.20, 90.00
R / Rfree (%) 19 / 24.7

Other elements in 3dva:

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) 2 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 3dva). 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: 3dva:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3dva

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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:3.8
occ:1.00
 O A:PHE204 2.0 23.7 1.0
OD1 A:ASN202 2.1 23.4 1.0
OD1 A:ASP173 2.2 16.7 1.0
O12 A:TPW1370 2.2 14.7 1.0
O21 A:TPW1370 2.4 15.1 1.0
O A:HOH1410 2.4 16.1 1.0
CG A:ASP173 2.9 16.7 1.0
OD2 A:ASP173 3.1 16.6 1.0
C A:PHE204 3.1 23.8 1.0
CG A:ASN202 3.3 23.5 1.0
P1 A:TPW1370 3.4 14.8 1.0
P2 A:TPW1370 3.4 15.2 1.0
O11 A:TPW1370 3.8 15.0 1.0
ND2 A:ASN202 3.9 23.6 1.0
N A:ALA205 3.9 23.6 1.0
NH2 A:ARG267 4.0 34.2 1.0
N A:ASP173 4.0 17.0 1.0
O A:HOH1412 4.1 13.4 1.0
N A:PHE204 4.1 24.1 1.0
CA A:ALA205 4.1 23.5 1.0
O23 A:TPW1370 4.1 15.3 1.0
O5G A:TPW1370 4.1 14.4 1.0
CA A:PHE204 4.1 24.0 1.0
NH1 A:ARG267 4.1 34.1 1.0
N A:ASN202 4.2 22.7 1.0
O A:GLN200 4.3 20.8 1.0
CB A:ASP173 4.3 16.7 1.0
CB A:ASN202 4.4 23.4 1.0
CZ A:ARG267 4.6 34.2 1.0
O13 A:TPW1370 4.7 14.7 1.0
CA A:ASN202 4.7 23.3 1.0
CA A:GLY172 4.7 17.5 1.0
CA A:ASP173 4.7 16.7 1.0
N A:GLY174 4.7 16.1 1.0
CB A:ALA205 4.7 23.3 1.0
N A:ARG203 4.8 24.0 1.0
C A:GLY172 4.8 17.2 1.0
C A:ASN202 4.8 23.6 1.0
O22 A:TPW1370 4.8 15.2 1.0

Magnesium binding site 2 out of 6 in 3dva

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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
A:Mg1326

b:30.1
occ:1.00
 O A:HOH1421 2.2 30.6 1.0
O C:HOH1420 2.2 26.0 1.0
O C:HOH1483 2.3 17.7 1.0
O B:HOH1335 2.4 34.2 1.0
O C:HOH1408 4.3 13.3 1.0
OE2 A:GLU183 4.3 17.5 1.0
OE2 C:GLU183 4.3 16.0 1.0
OD1 A:ASP180 4.4 16.2 1.0
OD1 C:ASP180 4.4 15.0 1.0
O A:HOH1442 4.4 18.0 1.0
O C:HOH1474 4.5 22.2 1.0
CA A:GLY179 4.6 15.6 1.0
O B:GLU88 4.6 18.1 1.0
O D:GLU88 4.6 17.7 1.0
O C:HOH1421 4.6 11.7 1.0
CA C:GLY179 4.7 14.6 1.0
O A:HOH1437 4.7 9.9 1.0
CB D:SER60 4.7 15.7 1.0
CB B:SER60 4.8 18.2 1.0
OG D:SER60 4.8 15.7 1.0
OG B:SER60 4.9 18.2 1.0
N A:ASP180 5.0 16.0 1.0
N C:ASP180 5.0 14.7 1.0

Magnesium binding site 3 out of 6 in 3dva

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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:7.4
occ:1.00
 O C:PHE204 1.8 24.9 1.0
OD1 C:ASN202 2.0 23.6 1.0
O C:HOH1432 2.2 21.5 1.0
OD1 C:ASP173 2.2 15.5 1.0
O12 C:TPW1370 2.2 13.2 1.0
O21 C:TPW1370 2.2 13.3 1.0
C C:PHE204 2.9 25.0 1.0
CG C:ASN202 2.9 23.8 1.0
CG C:ASP173 3.0 15.5 1.0
OD2 C:ASP173 3.1 15.6 1.0
ND2 C:ASN202 3.3 23.9 1.0
P2 C:TPW1370 3.4 13.2 1.0
P1 C:TPW1370 3.4 13.2 1.0
O11 C:TPW1370 3.7 13.3 1.0
N C:PHE204 3.7 25.0 1.0
N C:ALA205 3.8 24.9 1.0
CA C:PHE204 3.9 25.1 1.0
O5G C:TPW1370 4.0 13.1 1.0
N C:ASP173 4.0 15.6 1.0
CA C:ALA205 4.1 24.9 1.0
N C:ASN202 4.1 22.8 1.0
O23 C:TPW1370 4.2 13.3 1.0
O C:HOH1394 4.2 15.7 1.0
CB C:ASN202 4.2 23.8 1.0
CB C:ASP173 4.4 15.4 1.0
O C:GLN200 4.4 20.6 1.0
CA C:ASN202 4.5 23.6 1.0
C C:ASN202 4.6 24.0 1.0
N C:ARG203 4.6 24.5 1.0
CA C:GLY172 4.7 16.0 1.0
O22 C:TPW1370 4.7 13.4 1.0
O13 C:TPW1370 4.7 13.2 1.0
N C:GLY174 4.7 15.0 1.0
CA C:ASP173 4.7 15.3 1.0
CB C:PHE204 4.8 25.3 1.0
CB C:ALA205 4.8 24.6 1.0
C C:GLY172 4.8 15.7 1.0
C C:ARG203 4.8 24.9 1.0

Magnesium binding site 4 out of 6 in 3dva

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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:Mg369

b:45.8
occ:1.00
 OD1 E:ASP173 2.3 23.5 1.0
O21 E:TPW1370 2.4 19.9 1.0
O12 E:TPW1370 2.5 20.0 1.0
OD1 E:ASN202 2.8 31.1 1.0
P2 E:TPW1370 3.0 20.0 1.0
O11 E:TPW1370 3.2 20.0 1.0
ND2 E:ASN202 3.2 31.4 1.0
CG E:ASN202 3.2 31.2 1.0
O E:GLN200 3.2 28.9 1.0
O23 E:TPW1370 3.3 19.9 1.0
P1 E:TPW1370 3.4 20.0 1.0
CG E:ASP173 3.5 23.4 1.0
N E:ASP173 3.5 23.7 1.0
CA E:GLY172 3.6 24.1 1.0
O E:PHE204 3.7 30.6 1.0
C E:GLY172 4.1 23.8 1.0
N E:ASN202 4.1 30.4 1.0
OD2 E:ASP173 4.1 23.4 1.0
C E:GLN200 4.4 28.9 1.0
O5G E:TPW1370 4.4 19.9 1.0
CB E:ASN202 4.5 31.1 1.0
O13 E:TPW1370 4.5 20.0 1.0
O22 E:TPW1370 4.5 20.1 1.0
CB E:ASP173 4.6 23.4 1.0
CA E:ASP173 4.6 23.3 1.0
O E:HOH1458 4.6 24.7 1.0
CA E:ASN202 4.8 30.9 1.0
C E:PHE204 4.8 30.6 1.0
N E:GLY172 4.9 24.4 1.0
CA E:ASN201 4.9 29.6 1.0
N E:GLY174 4.9 22.8 1.0
C E:ASN201 5.0 30.0 1.0

Magnesium binding site 5 out of 6 in 3dva

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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
E:Mg370

b:33.5
occ:1.00
 O H:HOH1481 1.9 27.6 1.0
O E:HOH1466 2.2 25.8 1.0
O H:HOH1480 2.3 31.9 1.0
O F:HOH1358 2.4 31.0 1.0
O G:HOH1410 2.4 20.2 1.0
O H:HOH1482 4.0 52.7 1.0
OD1 E:ASP180 4.1 21.4 1.0
O E:HOH1461 4.3 19.6 1.0
OE2 E:GLU183 4.3 21.8 1.0
CB F:SER60 4.4 24.5 1.0
O F:GLU88 4.4 24.6 1.0
O G:HOH1409 4.4 27.1 1.0
O G:HOH1431 4.4 21.1 1.0
OG F:SER60 4.5 24.6 1.0
OD1 G:ASP180 4.5 21.9 1.0
OE2 G:GLU183 4.6 22.9 1.0
CA G:GLY179 4.6 21.6 1.0
O H:GLU88 4.7 22.7 1.0
CA E:GLY179 4.9 20.8 1.0
CB H:SER60 5.0 23.0 1.0

Magnesium binding site 6 out of 6 in 3dva

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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:Mg369

b:17.0
occ:1.00
 O G:PHE204 1.8 29.6 1.0
OD1 G:ASN202 2.0 28.3 1.0
O21 G:TPW1370 2.1 24.0 1.0
O G:HOH1407 2.5 17.9 1.0
O12 G:TPW1370 2.6 24.1 1.0
OD1 G:ASP173 2.7 21.8 1.0
CG G:ASN202 2.9 28.3 1.0
C G:PHE204 3.0 29.6 1.0
P2 G:TPW1370 3.2 24.0 1.0
ND2 G:ASN202 3.2 28.2 1.0
CG G:ASP173 3.4 21.9 1.0
OD2 G:ASP173 3.5 21.8 1.0
O11 G:TPW1370 3.6 24.1 1.0
P1 G:TPW1370 3.6 24.0 1.0
O G:HOH1411 3.8 42.2 1.0
O23 G:TPW1370 3.8 24.1 1.0
N G:PHE204 3.9 29.7 1.0
N G:ALA205 3.9 29.6 1.0
CA G:PHE204 3.9 29.6 1.0
CA G:ALA205 4.1 29.6 1.0
O5G G:TPW1370 4.2 24.0 1.0
N G:ASN202 4.2 27.7 1.0
CB G:ASN202 4.2 28.3 1.0
N G:ASP173 4.4 21.9 1.0
O22 G:TPW1370 4.5 24.2 1.0
CA G:ASN202 4.5 28.3 1.0
O G:GLN200 4.6 25.5 1.0
C G:ASN202 4.6 28.7 1.0
CB G:PHE204 4.7 29.6 1.0
N G:ARG203 4.7 29.2 1.0
CB G:ASP173 4.8 21.9 1.0
CB G:ALA205 4.9 29.6 1.0
CA G:GLY172 4.9 21.8 1.0
O13 G:TPW1370 5.0 24.1 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 12:44:40 2024

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