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Magnesium in PDB 3exf: Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex

Enzymatic activity of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex

All present enzymatic activity of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex:
1.2.4.1;

Protein crystallography data

The structure of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex, PDB code: 3exf was solved by M.Kato, R.M.Wynn, J.L.Chuang, S.-C.Tso, M.Machius, J.Li, D.T.Chuang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.389, 129.668, 144.946, 90.00, 109.15, 90.00
R / Rfree (%) 18.5 / 26.3

Other elements in 3exf:

The structure of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex (pdb code 3exf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex, PDB code: 3exf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3exf

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:6.8
occ:1.00
 O2A A:TPP1003 1.8 16.5 1.0
OD1 A:ASN196 2.0 16.4 1.0
OD2 A:ASP167 2.0 14.9 1.0
O A:TYR198 2.1 24.1 1.0
O1B A:TPP1003 2.1 19.9 1.0
CG A:ASN196 3.0 14.4 1.0
PA A:TPP1003 3.0 18.9 1.0
CG A:ASP167 3.0 14.5 1.0
PB A:TPP1003 3.3 18.7 1.0
C A:TYR198 3.3 24.6 1.0
O3A A:TPP1003 3.4 20.0 1.0
OD1 A:ASP167 3.4 15.9 1.0
ND2 A:ASN196 3.4 15.6 1.0
O1A A:TPP1003 4.0 17.5 1.0
N A:ASP167 4.0 14.4 1.0
O7 A:TPP1003 4.1 21.6 1.0
O A:GLU194 4.1 14.9 1.0
N A:TYR198 4.1 21.0 1.0
N A:GLY199 4.2 27.0 1.0
CA A:GLY199 4.2 30.1 1.0
O2B A:TPP1003 4.3 18.9 1.0
CA A:TYR198 4.3 23.0 1.0
N A:ASN196 4.3 13.8 1.0
CB A:ASP167 4.3 14.3 1.0
O3B A:TPP1003 4.3 22.9 1.0
CB A:ASN196 4.4 13.4 1.0
N A:GLY168 4.5 14.0 1.0
CA A:ASP167 4.7 14.5 1.0
CA A:GLY166 4.7 14.6 1.0
CA A:ASN196 4.7 13.6 1.0
C A:ASN196 4.8 14.7 1.0
C A:GLY166 4.8 14.3 1.0
N A:ARG197 4.8 15.8 1.0

Magnesium binding site 2 out of 4 in 3exf

Go back to Magnesium Binding Sites List in 3exf
Magnesium binding site 2 out of 4 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1004

b:22.7
occ:1.00
 OD1 C:ASN196 1.9 15.5 1.0
OD2 C:ASP167 2.1 19.6 1.0
O1B C:TPP1006 2.1 25.2 1.0
O C:TYR198 2.3 30.0 1.0
O C:HOH2002 2.3 8.4 1.0
O2A C:TPP1006 2.3 21.4 1.0
O2B C:TPP1006 2.7 22.2 1.0
PB C:TPP1006 2.8 23.5 1.0
CG C:ASP167 3.0 16.6 1.0
CG C:ASN196 3.1 17.1 1.0
OD1 C:ASP167 3.2 18.8 1.0
PA C:TPP1006 3.5 20.9 1.0
C C:TYR198 3.5 30.2 1.0
O3A C:TPP1006 3.6 22.2 1.0
ND2 C:ASN196 3.7 17.6 1.0
N C:ASN196 4.1 18.8 1.0
N C:TYR198 4.1 27.4 1.0
O3B C:TPP1006 4.2 22.6 1.0
O C:GLU194 4.2 19.6 1.0
N C:ASP167 4.2 14.6 1.0
CB C:ASN196 4.3 18.0 1.0
CA C:TYR198 4.3 28.9 1.0
CB C:ASP167 4.4 14.5 1.0
O1A C:TPP1006 4.4 22.0 1.0
N C:GLY199 4.5 31.6 1.0
CA C:ASN196 4.5 18.8 1.0
O7 C:TPP1006 4.5 23.1 1.0
C C:ASN196 4.6 20.4 1.0
CA C:GLY199 4.7 33.3 1.0
CA C:GLY166 4.7 14.6 1.0
N C:GLY168 4.7 13.4 1.0
N C:ARG197 4.8 22.6 1.0
CA C:ASP167 4.9 14.2 1.0
C C:GLY166 4.9 14.3 1.0
O C:ASN196 4.9 20.4 1.0

Magnesium binding site 3 out of 4 in 3exf

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1007

b:30.3
occ:1.00
 OD1 E:ASN196 1.7 23.4 1.0
O1B E:TPP1009 1.8 18.9 1.0
OD2 E:ASP167 2.2 18.1 1.0
O2A E:TPP1009 2.2 27.0 1.0
O E:TYR198 2.2 30.3 1.0
CG E:ASN196 2.7 22.1 1.0
PB E:TPP1009 2.8 18.7 1.0
O2B E:TPP1009 3.1 19.2 1.0
ND2 E:ASN196 3.2 21.1 1.0
O3A E:TPP1009 3.3 23.4 1.0
PA E:TPP1009 3.3 22.6 1.0
CG E:ASP167 3.4 16.3 1.0
C E:TYR198 3.4 31.0 1.0
O E:GLU194 3.9 18.4 1.0
OD1 E:ASP167 4.0 20.2 1.0
CB E:ASN196 4.1 21.7 1.0
N E:ASN196 4.1 20.8 1.0
O3B E:TPP1009 4.1 18.6 1.0
O7 E:TPP1009 4.2 24.6 1.0
N E:ASP167 4.3 14.0 1.0
N E:GLY199 4.3 32.2 1.0
CA E:GLY199 4.4 34.4 1.0
N E:TYR198 4.4 29.5 1.0
CA E:TYR198 4.4 30.5 1.0
CA E:ASN196 4.5 22.1 1.0
O1A E:TPP1009 4.5 21.6 1.0
CB E:ASP167 4.5 13.9 1.0
N E:GLY168 4.7 14.2 1.0
CA E:GLY166 4.7 14.7 1.0
C E:ASN196 4.7 23.3 1.0
CA E:ASP167 5.0 13.9 1.0
C E:GLY166 5.0 13.9 1.0

Magnesium binding site 4 out of 4 in 3exf

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1010

b:11.7
occ:1.00
 OD2 G:ASP167 1.9 24.4 1.0
OD1 G:ASN196 2.0 13.6 1.0
O2A G:TPP1012 2.2 18.4 1.0
O1B G:TPP1012 2.3 24.1 1.0
O G:TYR198 2.4 28.0 1.0
CG G:ASP167 2.7 20.9 1.0
CG G:ASN196 2.9 15.2 1.0
OD1 G:ASP167 3.0 24.1 1.0
PB G:TPP1012 3.1 18.7 1.0
O3A G:TPP1012 3.2 19.1 1.0
PA G:TPP1012 3.2 17.6 1.0
ND2 G:ASN196 3.4 12.8 1.0
O2B G:TPP1012 3.6 17.6 1.0
C G:TYR198 3.7 28.9 1.0
N G:ASP167 3.8 16.8 1.0
O G:GLU194 3.8 16.1 1.0
N G:ASN196 4.0 17.3 1.0
CB G:ASP167 4.1 18.3 1.0
CB G:ASN196 4.2 17.4 1.0
O1A G:TPP1012 4.2 18.1 1.0
CA G:GLY166 4.4 16.1 1.0
O7 G:TPP1012 4.4 20.1 1.0
CA G:ASN196 4.4 18.0 1.0
CA G:GLY199 4.5 32.8 1.0
N G:TYR198 4.5 26.2 1.0
CA G:ASP167 4.5 17.8 1.0
O3B G:TPP1012 4.5 18.7 1.0
N G:GLY199 4.5 30.8 1.0
C G:ASN196 4.5 19.6 1.0
C G:GLY166 4.6 16.4 1.0
N G:GLY168 4.6 17.6 1.0
N G:ARG197 4.6 21.0 1.0
CA G:TYR198 4.6 27.8 1.0
C G:GLU194 4.9 17.3 1.0

Reference:

M.Kato, R.M.Wynn, J.L.Chuang, S.C.Tso, M.Machius, J.Li, D.T.Chuang. Structural Basis For Inactivation of the Human Pyruvate Dehydrogenase Complex By Phosphorylation: Role of Disordered Phosphorylation Loops. Structure V. 16 1849 2008.
ISSN: ISSN 0969-2126
PubMed: 19081061
DOI: 10.1016/J.STR.2008.10.010
Page generated: Wed Aug 14 13:23:03 2024

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