Atomistry » Magnesium » PDB 3dtu-3e35 » 3dv0
Atomistry »
  Magnesium »
    PDB 3dtu-3e35 »
      3dv0 »

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

Go back to Magnesium Binding Sites List in 3dv0
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

Go back to Magnesium Binding Sites List in 3dv0
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

Go back to Magnesium Binding Sites List in 3dv0
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

Go back to Magnesium Binding Sites List in 3dv0
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

Go back to Magnesium Binding Sites List in 3dv0
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

Go back to Magnesium Binding Sites List in 3dv0
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy