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Magnesium in PDB 1w88: The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2

Enzymatic activity of The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2

All present enzymatic activity of The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2:
1.2.4.1; 2.3.1.12;

Protein crystallography data

The structure of The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2, PDB code: 1w88 was solved by R.A.W.Frank, J.V.Pratap, X.Y.Pei, R.N.Perham, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.3
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.180, 133.690, 245.610, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 26.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2 (pdb code 1w88). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2, PDB code: 1w88:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1w88

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Magnesium binding site 1 out of 4 in the The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1368

b:28.9
occ:1.00
 OD1 A:ASN202 2.1 52.9 1.0
O21 A:TDP1370 2.2 31.1 1.0
O A:PHE204 2.2 52.8 1.0
OD1 A:ASP173 2.3 45.8 1.0
O12 A:TDP1370 2.4 29.9 1.0
CG A:ASP173 3.0 44.9 1.0
OD2 A:ASP173 3.1 38.3 1.0
CG A:ASN202 3.3 51.1 1.0
C A:PHE204 3.3 53.4 1.0
P2 A:TDP1370 3.4 37.9 1.0
P1 A:TDP1370 3.5 35.5 1.0
O11 A:TDP1370 3.7 36.4 1.0
N A:ALA205 4.1 54.1 1.0
N A:PHE204 4.1 52.7 1.0
O5G A:TDP1370 4.1 35.6 1.0
ND2 A:ASN202 4.1 54.9 1.0
O23 A:TDP1370 4.1 37.1 1.0
CA A:ALA205 4.2 50.5 1.0
N A:ASN202 4.2 41.4 1.0
N A:ASP173 4.3 34.6 1.0
CA A:PHE204 4.3 52.5 1.0
CB A:ASN202 4.3 47.8 1.0
CB A:ASP173 4.4 38.9 1.0
CA A:ASN202 4.5 46.7 1.0
C A:ASN202 4.6 47.0 1.0
O22 A:TDP1370 4.6 35.7 1.0
N A:ARG203 4.6 49.7 1.0
O A:GLN200 4.7 32.6 1.0
O13 A:TDP1370 4.8 33.6 1.0
N A:GLY174 4.8 42.9 1.0
CB A:ALA205 4.8 46.3 1.0
CA A:ASP173 4.9 39.5 1.0

Magnesium binding site 2 out of 4 in 1w88

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Magnesium binding site 2 out of 4 in the The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1368

b:28.0
occ:1.00
 OD1 C:ASP173 2.2 46.1 1.0
OD1 C:ASN202 2.2 53.9 1.0
O21 C:TDP1370 2.3 34.6 1.0
O C:PHE204 2.3 56.0 1.0
O12 C:TDP1370 2.4 39.4 1.0
O C:HOH2095 2.5 34.1 1.0
CG C:ASP173 3.0 47.6 1.0
OD2 C:ASP173 3.2 45.2 1.0
C C:PHE204 3.3 57.6 1.0
P2 C:TDP1370 3.3 41.6 1.0
CG C:ASN202 3.4 52.1 1.0
P1 C:TDP1370 3.5 41.4 1.0
O11 C:TDP1370 3.6 39.7 1.0
O23 C:TDP1370 3.9 38.2 1.0
NH2 C:ARG267 4.0 68.5 1.0
O5G C:TDP1370 4.1 43.4 1.0
N C:ASP173 4.1 44.2 1.0
N C:PHE204 4.1 58.5 1.0
N C:ALA205 4.1 57.2 1.0
ND2 C:ASN202 4.2 51.2 1.0
N C:ASN202 4.2 46.3 1.0
CA C:ALA205 4.3 56.4 1.0
NH1 C:ARG267 4.3 68.0 1.0
O C:GLN200 4.3 38.2 1.0
CA C:PHE204 4.3 59.0 1.0
CB C:ASP173 4.4 46.0 1.0
CB C:ASN202 4.5 50.4 1.0
O22 C:TDP1370 4.6 37.1 1.0
CZ C:ARG267 4.6 70.2 1.0
N C:ARG203 4.7 53.7 1.0
CA C:ASN202 4.7 50.5 1.0
O13 C:TDP1370 4.7 41.7 1.0
C C:ASN202 4.7 52.9 1.0
N C:GLY174 4.7 44.5 1.0
CA C:ASP173 4.7 45.7 1.0
CB C:ALA205 4.8 55.6 1.0
CA C:GLY172 4.8 38.7 1.0
C C:GLY172 4.9 43.1 1.0

Magnesium binding site 3 out of 4 in 1w88

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Magnesium binding site 3 out of 4 in the The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1368

b:78.1
occ:1.00
 O21 E:TDP1370 2.1 0.6 1.0
OD1 E:ASP173 2.3 62.5 1.0
O23 E:TDP1370 2.3 0.7 1.0
P2 E:TDP1370 2.6 0.8 1.0
OD1 E:ASN202 2.6 71.5 1.0
O E:GLN200 3.1 45.0 1.0
O11 E:TDP1370 3.1 0.9 1.0
CG E:ASP173 3.5 62.6 1.0
N E:ASP173 3.5 50.6 1.0
O12 E:TDP1370 3.7 0.2 1.0
CG E:ASN202 3.8 70.5 1.0
CA E:GLY172 3.8 44.5 1.0
N E:ASN202 3.9 61.5 1.0
O22 E:TDP1370 4.0 0.9 1.0
P1 E:TDP1370 4.0 0.7 1.0
C E:GLN200 4.2 43.5 1.0
C E:GLY172 4.2 48.4 1.0
OD2 E:ASP173 4.3 66.1 1.0
CA E:ASN201 4.4 51.0 1.0
CB E:ASP173 4.4 57.4 1.0
CA E:ASP173 4.5 53.9 1.0
ND2 E:ASN202 4.5 71.2 1.0
C E:ASN201 4.7 54.1 1.0
N E:ASN201 4.7 47.2 1.0
CA E:ASN202 4.8 68.2 1.0
CB E:ASN202 4.8 68.9 1.0
O5G E:TDP1370 4.9 1.0 1.0

Magnesium binding site 4 out of 4 in 1w88

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Magnesium binding site 4 out of 4 in the The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Pyruvate Dehydrogenase E1(D180N, E183Q) Bound to the Peripheral Subunit Binding Domain of E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1368

b:66.1
occ:1.00
 OD1 G:ASP173 2.6 57.2 1.0
O12 G:TDP1370 3.1 0.9 1.0
OD2 G:ASP173 3.3 59.2 1.0
CG G:ASP173 3.3 55.6 1.0
CB G:ASN202 3.4 62.2 1.0
O23 G:TDP1370 3.6 0.8 1.0
N G:ARG203 3.8 71.2 1.0
O21 G:TDP1370 4.0 0.9 1.0
CA G:ASN202 4.0 63.9 1.0
C G:ASN202 4.0 68.0 1.0
N G:ASN202 4.1 58.9 1.0
P2 G:TDP1370 4.2 0.3 1.0
P1 G:TDP1370 4.3 0.9 1.0
O11 G:TDP1370 4.6 0.7 1.0
O G:ARG203 4.6 77.8 1.0
O G:ASN202 4.7 70.2 1.0
CB G:ASP173 4.8 51.6 1.0
CA G:ARG203 4.8 76.6 1.0
O5G G:TDP1370 5.0 0.6 1.0
N G:ASP173 5.0 45.9 1.0

Reference:

R.A.W.Frank, C.M.Titman, J.V.Pratap, B.F.Luisi, R.N.Perham. A Molecular Switch and Proton-Wire Synchronize the Active Sites in Thiamine-Dependent Enzymes Science V. 306 872 2004.
ISSN: ISSN 0036-8075
PubMed: 15514159
DOI: 10.1126/SCIENCE.1101030
Page generated: Sun Aug 10 06:45:39 2025

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