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Magnesium in PDB 3duf: 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: 3duf 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) 59.44 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.247, 231.995, 92.614, 90.00, 90.74, 90.00
R / Rfree (%) 18.8 / 26.3

Other elements in 3duf:

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

Magnesium binding site 1 out of 5 in 3duf

Go back to Magnesium Binding Sites List in 3duf
Magnesium binding site 1 out of 5 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:17.5
occ:1.00
 O1A A:R1T1370 2.2 28.7 1.0
O A:PHE204 2.2 27.0 1.0
O3B A:R1T1370 2.2 31.9 1.0
OD1 A:ASP173 2.3 22.1 1.0
OD1 A:ASN202 2.3 32.4 1.0
O A:HOH1374 2.5 20.6 1.0
CG A:ASP173 3.1 27.4 1.0
CG A:ASN202 3.2 34.4 1.0
C A:PHE204 3.2 32.9 1.0
OD2 A:ASP173 3.2 38.6 1.0
PB A:R1T1370 3.3 25.2 1.0
PA A:R1T1370 3.4 22.6 1.0
ND2 A:ASN202 3.5 34.5 1.0
O3A A:R1T1370 3.6 22.1 1.0
N A:PHE204 3.9 30.0 1.0
N A:ALA205 4.1 28.9 1.0
CA A:PHE204 4.1 32.7 1.0
O7 A:R1T1370 4.1 28.9 1.0
O2B A:R1T1370 4.2 27.4 1.0
N A:ASP173 4.2 23.8 1.0
CA A:ALA205 4.2 25.4 1.0
N A:ASN202 4.3 21.0 1.0
O A:HOH1375 4.4 29.6 1.0
O A:GLN200 4.5 26.5 1.0
CB A:ASP173 4.5 23.7 1.0
CB A:ASN202 4.5 32.7 1.0
O2A A:R1T1370 4.6 21.5 1.0
O1B A:R1T1370 4.6 30.9 1.0
C A:ASN202 4.7 31.8 1.0
CA A:ASN202 4.7 31.0 1.0
N A:ARG203 4.8 23.0 1.0
N A:GLY174 4.8 34.7 1.0
NH1 A:ARG267 4.8 68.9 1.0
CA A:ASP173 4.9 27.0 1.0
CA A:GLY172 4.9 26.0 1.0
C A:GLY172 5.0 29.8 1.0
CB A:ALA205 5.0 16.8 1.0
C A:ARG203 5.0 27.8 1.0

Magnesium binding site 2 out of 5 in 3duf

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Magnesium binding site 2 out of 5 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
D:Mg1326

b:64.8
occ:1.00
 O B:HOH1344 2.4 45.0 1.0
O A:HOH1391 3.4 34.3 1.0
O D:GLU88 3.9 43.5 1.0
OG D:SER60 4.3 36.2 1.0
CB D:SER60 4.4 35.2 1.0
OE2 C:GLU183 4.4 57.4 1.0
O C:HOH1374 4.4 13.9 1.0
O B:GLU88 4.7 40.5 1.0
OD1 A:ASP180 4.9 43.4 1.0
OD1 C:ASP180 4.9 68.4 1.0
C D:GLU88 4.9 43.1 1.0
OG B:SER60 5.0 45.4 1.0

Magnesium binding site 3 out of 5 in 3duf

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Magnesium binding site 3 out of 5 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:33.9
occ:1.00
 OD1 C:ASP173 2.2 35.5 1.0
O3B C:R1T1370 2.2 28.7 1.0
O1A C:R1T1370 2.3 35.4 1.0
OD1 C:ASN202 2.3 36.7 1.0
O C:PHE204 2.5 33.1 1.0
CG C:ASN202 2.8 31.9 1.0
ND2 C:ASN202 3.0 18.5 1.0
CG C:ASP173 3.1 27.9 1.0
PB C:R1T1370 3.3 27.6 1.0
OD2 C:ASP173 3.4 34.8 1.0
PA C:R1T1370 3.4 23.0 1.0
O3A C:R1T1370 3.6 19.2 1.0
C C:PHE204 3.6 36.5 1.0
N C:ASN202 3.8 31.1 1.0
O C:GLN200 3.9 34.1 1.0
N C:ASP173 3.9 22.2 1.0
O2B C:R1T1370 3.9 32.3 1.0
CB C:ASN202 4.0 23.3 1.0
N C:PHE204 4.1 32.5 1.0
CA C:ASN202 4.3 29.4 1.0
CB C:ASP173 4.4 35.3 1.0
CA C:GLY172 4.4 27.3 1.0
O7 C:R1T1370 4.4 25.6 1.0
CA C:PHE204 4.4 28.3 1.0
C C:ASN202 4.4 33.1 1.0
O2A C:R1T1370 4.5 31.9 1.0
N C:ARG203 4.6 29.7 1.0
N C:ALA205 4.6 35.6 1.0
C C:GLY172 4.7 28.3 1.0
O1B C:R1T1370 4.7 33.8 1.0
CA C:ASP173 4.7 27.8 1.0
C C:ASN201 4.8 28.7 1.0
CA C:ALA205 4.9 31.9 1.0
N C:GLY174 4.9 24.0 1.0
O C:ASN202 5.0 30.4 1.0
CA C:ASN201 5.0 27.8 1.0

Magnesium binding site 4 out of 5 in 3duf

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Magnesium binding site 4 out of 5 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:Mg1371

b:37.5
occ:1.00
 O1A E:R1T1370 2.1 29.6 1.0
O E:PHE204 2.2 27.8 1.0
OD1 E:ASN202 2.3 37.9 1.0
OD1 E:ASP173 2.5 45.0 1.0
O3B E:R1T1370 2.5 31.0 1.0
O E:HOH1382 2.5 31.4 1.0
CG E:ASN202 3.0 43.2 1.0
CG E:ASP173 3.2 38.5 1.0
C E:PHE204 3.2 35.3 1.0
ND2 E:ASN202 3.3 26.6 1.0
OD2 E:ASP173 3.4 42.8 1.0
PA E:R1T1370 3.5 32.7 1.0
PB E:R1T1370 3.7 40.5 1.0
N E:PHE204 3.7 39.4 1.0
O3A E:R1T1370 3.8 33.5 1.0
CA E:PHE204 4.0 36.7 1.0
N E:ASN202 4.1 33.9 1.0
O E:HOH1373 4.1 37.5 1.0
N E:ASP173 4.1 25.1 1.0
N E:ALA205 4.1 35.2 1.0
O7 E:R1T1370 4.2 34.9 1.0
CB E:ASN202 4.3 27.5 1.0
O2B E:R1T1370 4.4 30.2 1.0
CA E:ALA205 4.4 37.8 1.0
CB E:ASP173 4.4 33.4 1.0
C E:ASN202 4.4 36.3 1.0
N E:ARG203 4.4 37.1 1.0
CA E:ASN202 4.5 34.2 1.0
O2A E:R1T1370 4.5 49.2 1.0
O E:GLN200 4.6 43.6 1.0
O1B E:R1T1370 4.7 50.5 1.0
N E:GLY174 4.7 41.3 1.0
C E:ARG203 4.8 38.4 1.0
O E:HOH1380 4.8 30.9 1.0
CA E:ASP173 4.8 33.3 1.0
CA E:GLY172 4.9 23.1 1.0
O E:ASN202 4.9 31.1 1.0
CB E:PHE204 4.9 44.0 1.0
C E:GLY172 5.0 24.4 1.0

Magnesium binding site 5 out of 5 in 3duf

Go back to Magnesium Binding Sites List in 3duf
Magnesium binding site 5 out of 5 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:Mg1371

b:23.5
occ:1.00
 O1A G:R1T1370 2.2 44.9 1.0
O3B G:R1T1370 2.2 34.1 1.0
O G:PHE204 2.2 42.2 1.0
O G:HOH1383 2.2 30.0 1.0
OD1 G:ASN202 2.3 31.2 1.0
OD1 G:ASP173 2.5 47.8 1.0
OD2 G:ASP173 3.0 49.6 1.0
CG G:ASN202 3.0 41.4 1.0
CG G:ASP173 3.1 37.0 1.0
C G:PHE204 3.1 36.4 1.0
ND2 G:ASN202 3.3 37.0 1.0
PA G:R1T1370 3.4 30.7 1.0
N G:PHE204 3.5 28.9 1.0
PB G:R1T1370 3.6 40.5 1.0
O3A G:R1T1370 3.8 33.7 1.0
CA G:PHE204 3.9 34.5 1.0
N G:ASN202 4.0 34.9 1.0
N G:ALA205 4.1 33.8 1.0
O G:HOH1376 4.1 25.0 1.0
O2B G:R1T1370 4.2 20.2 1.0
N G:ASP173 4.3 30.5 1.0
CB G:ASN202 4.3 30.7 1.0
O2A G:R1T1370 4.3 45.3 1.0
N G:ARG203 4.3 33.9 1.0
C G:ASN202 4.3 32.1 1.0
O7 G:R1T1370 4.4 35.9 1.0
CA G:ALA205 4.4 30.4 1.0
CA G:ASN202 4.4 31.6 1.0
CB G:ASP173 4.5 26.7 1.0
O1B G:R1T1370 4.6 56.7 1.0
C G:ARG203 4.6 28.2 1.0
O G:GLN200 4.6 30.0 1.0
O G:ASN202 4.8 32.5 1.0
CB G:PHE204 4.8 36.0 1.0
O G:HOH1382 4.9 30.0 1.0
N G:GLY174 4.9 30.5 1.0
CA G:GLY172 4.9 23.5 1.0
CA G:ASP173 4.9 30.3 1.0
CA G:ARG203 5.0 31.7 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 12:41:58 2024

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