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Manganese in PDB 3exe: 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: 3exe 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 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.572, 129.617, 124.303, 90.00, 92.48, 90.00
R / Rfree (%) 15.8 / 20.6

Other elements in 3exe:

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

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 3exe

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Manganese 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 Manganese with other atoms in the Mn 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:Mn1004

b:10.2
occ:1.00
 O A:TYR198 2.1 17.3 1.0
OD2 A:ASP167 2.2 12.4 1.0
O1B A:TPP1005 2.2 5.9 1.0
O2A A:TPP1005 2.2 10.0 1.0
OD1 A:ASN196 2.2 16.6 1.0
O A:HOH2039 2.3 8.0 1.0
CG A:ASP167 3.0 13.1 1.0
CG A:ASN196 3.1 16.9 1.0
C A:TYR198 3.3 16.5 1.0
PB A:TPP1005 3.3 9.7 1.0
OD1 A:ASP167 3.4 13.7 1.0
PA A:TPP1005 3.4 10.7 1.0
ND2 A:ASN196 3.5 13.8 1.0
O3A A:TPP1005 3.6 10.3 1.0
O2B A:TPP1005 3.9 13.4 1.0
N A:ASP167 4.0 13.9 1.0
N A:TYR198 4.0 14.6 1.0
O A:HOH2043 4.0 8.0 1.0
N A:GLY199 4.1 17.1 1.0
CA A:GLY199 4.1 17.4 1.0
O7 A:TPP1005 4.2 9.4 1.0
N A:ASN196 4.2 16.0 1.0
CA A:TYR198 4.2 16.2 1.0
CB A:ASP167 4.3 14.2 1.0
N A:GLY168 4.4 13.8 1.0
O A:GLU194 4.4 16.5 1.0
CB A:ASN196 4.5 17.4 1.0
O1A A:TPP1005 4.5 10.2 1.0
O3B A:TPP1005 4.6 13.2 1.0
CA A:ASP167 4.6 14.0 1.0
CA A:ASN196 4.7 16.4 1.0
C A:ASN196 4.7 16.1 1.0
N A:ARG197 4.7 16.7 1.0
CA A:GLY166 4.7 13.7 1.0
C A:GLY166 4.8 13.6 1.0

Manganese binding site 2 out of 4 in 3exe

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Manganese 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 Manganese with other atoms in the Mn 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:Mn1001

b:10.3
occ:1.00
 OD2 C:ASP167 2.1 14.1 1.0
O C:TYR198 2.2 15.1 1.0
OD1 C:ASN196 2.2 14.2 1.0
O1B C:TPP1002 2.2 8.8 1.0
O C:HOH2234 2.2 12.2 1.0
O2A C:TPP1002 2.2 6.9 1.0
CG C:ASP167 3.0 14.4 1.0
CG C:ASN196 3.1 14.7 1.0
C C:TYR198 3.2 14.3 1.0
PA C:TPP1002 3.3 9.6 1.0
PB C:TPP1002 3.3 11.0 1.0
OD1 C:ASP167 3.4 12.5 1.0
O3A C:TPP1002 3.5 9.5 1.0
ND2 C:ASN196 3.5 12.8 1.0
O2B C:TPP1002 3.9 11.9 1.0
N C:ASP167 4.0 12.9 1.0
N C:GLY199 4.0 14.7 1.0
CA C:GLY199 4.0 15.7 1.0
O C:HOH2222 4.0 12.1 1.0
N C:TYR198 4.0 14.1 1.0
O7 C:TPP1002 4.2 11.8 1.0
CA C:TYR198 4.2 14.6 1.0
N C:ASN196 4.2 14.3 1.0
CB C:ASP167 4.3 11.9 1.0
CB C:ASN196 4.4 13.3 1.0
N C:GLY168 4.4 13.0 1.0
O1A C:TPP1002 4.5 8.8 1.0
O C:GLU194 4.5 15.6 1.0
O3B C:TPP1002 4.6 13.4 1.0
CA C:ASP167 4.6 13.6 1.0
CA C:GLY166 4.7 13.3 1.0
CA C:ASN196 4.7 13.4 1.0
C C:ASN196 4.7 14.0 1.0
C C:GLY166 4.7 13.6 1.0
N C:ARG197 4.8 13.0 1.0

Manganese binding site 3 out of 4 in 3exe

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Manganese 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 Manganese with other atoms in the Mn 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:Mn1010

b:12.1
occ:1.00
 O2A E:TPP1011 2.2 9.7 1.0
OD2 E:ASP167 2.2 14.4 1.0
O1B E:TPP1011 2.2 11.7 1.0
OD1 E:ASN196 2.2 13.5 1.0
O E:TYR198 2.2 12.4 1.0
O E:HOH2223 2.4 12.1 1.0
CG E:ASP167 3.0 13.8 1.0
CG E:ASN196 3.2 15.6 1.0
C E:TYR198 3.3 14.2 1.0
OD1 E:ASP167 3.3 13.7 1.0
PA E:TPP1011 3.3 11.5 1.0
PB E:TPP1011 3.3 11.4 1.0
O3A E:TPP1011 3.5 13.0 1.0
ND2 E:ASN196 3.6 11.2 1.0
N E:ASP167 4.0 13.2 1.0
O2B E:TPP1011 4.0 16.0 1.0
N E:TYR198 4.0 14.9 1.0
N E:GLY199 4.0 14.2 1.0
CA E:GLY199 4.1 16.4 1.0
O E:HOH2179 4.1 11.4 1.0
N E:ASN196 4.2 15.3 1.0
CA E:TYR198 4.3 13.8 1.0
O7 E:TPP1011 4.3 12.4 1.0
CB E:ASP167 4.3 13.6 1.0
O1A E:TPP1011 4.4 11.4 1.0
N E:GLY168 4.4 13.9 1.0
O E:GLU194 4.5 15.8 1.0
CB E:ASN196 4.5 14.9 1.0
O3B E:TPP1011 4.6 15.4 1.0
CA E:GLY166 4.6 13.0 1.0
CA E:ASP167 4.7 14.3 1.0
CA E:ASN196 4.7 15.6 1.0
C E:ASN196 4.7 16.5 1.0
C E:GLY166 4.7 13.3 1.0
N E:ARG197 4.7 16.0 1.0

Manganese binding site 4 out of 4 in 3exe

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Manganese 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 Manganese with other atoms in the Mn 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:Mn1007

b:12.8
occ:1.00
 O G:TYR198 2.0 16.2 1.0
O1B G:TPP1008 2.1 15.1 1.0
O2A G:TPP1008 2.2 9.9 1.0
OD2 G:ASP167 2.2 13.4 1.0
O G:HOH2294 2.3 13.2 1.0
OD1 G:ASN196 2.3 15.2 1.0
CG G:ASP167 3.1 17.0 1.0
C G:TYR198 3.2 15.3 1.0
CG G:ASN196 3.2 15.2 1.0
PA G:TPP1008 3.3 11.3 1.0
PB G:TPP1008 3.3 13.1 1.0
OD1 G:ASP167 3.4 17.4 1.0
O3A G:TPP1008 3.6 11.5 1.0
ND2 G:ASN196 3.6 18.2 1.0
O2B G:TPP1008 3.9 13.7 1.0
N G:GLY199 4.0 15.5 1.0
N G:ASP167 4.0 14.7 1.0
N G:TYR198 4.0 14.7 1.0
CA G:GLY199 4.0 15.1 1.0
O G:HOH2447 4.1 16.0 1.0
O7 G:TPP1008 4.2 9.6 1.0
CA G:TYR198 4.2 15.6 1.0
N G:ASN196 4.2 14.8 1.0
CB G:ASP167 4.4 14.1 1.0
N G:GLY168 4.4 13.8 1.0
O G:GLU194 4.4 17.8 1.0
O1A G:TPP1008 4.5 10.1 1.0
CB G:ASN196 4.5 15.0 1.0
O3B G:TPP1008 4.6 15.1 1.0
CA G:ASP167 4.7 15.2 1.0
N G:ARG197 4.7 14.5 1.0
C G:ASN196 4.7 14.8 1.0
CA G:GLY166 4.7 13.2 1.0
CA G:ASN196 4.7 13.7 1.0
C G:GLY166 4.8 14.2 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: Sat Oct 5 16:12:59 2024

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