Atomistry » Magnesium » PDB 1ngj-1nn5 » 1ni4
Atomistry »
  Magnesium »
    PDB 1ngj-1nn5 »
      1ni4 »

Magnesium in PDB 1ni4: Human Pyruvate Dehydrogenase

Enzymatic activity of Human Pyruvate Dehydrogenase

All present enzymatic activity of Human Pyruvate Dehydrogenase:
1.2.4.1;

Protein crystallography data

The structure of Human Pyruvate Dehydrogenase, PDB code: 1ni4 was solved by E.Ciszak, L.G.Korotchkina, P.M.Dominiak, S.Sidhu, M.S.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.17 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.337, 126.889, 190.638, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.4

Other elements in 1ni4:

The structure of Human Pyruvate Dehydrogenase also contains other interesting chemical elements:

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Pyruvate Dehydrogenase (pdb code 1ni4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Pyruvate Dehydrogenase, PDB code: 1ni4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1ni4

Go back to Magnesium Binding Sites List in 1ni4
Magnesium binding site 1 out of 2 in the Human Pyruvate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Pyruvate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1331

b:5.9
occ:1.00
O C:HOH2332 2.3 11.3 1.0
OD1 C:ASN196 2.3 11.8 1.0
O1B C:TPP1330 2.4 15.6 1.0
O C:TYR198 2.4 22.8 1.0
O2A C:TPP1330 2.4 8.5 1.0
OD2 C:ASP167 2.5 16.2 1.0
OD1 C:ASP167 3.1 17.1 1.0
CG C:ASP167 3.1 14.3 1.0
CG C:ASN196 3.1 11.9 1.0
ND2 C:ASN196 3.3 10.9 1.0
C C:TYR198 3.3 22.9 1.0
PB C:TPP1330 3.5 15.3 1.0
PA C:TPP1330 3.5 10.2 1.0
O3A C:TPP1330 3.6 12.8 1.0
N C:TYR198 4.0 20.1 1.0
N C:ASP167 4.0 6.0 1.0
O2B C:TPP1330 4.1 16.3 1.0
O C:HOH2333 4.1 13.9 1.0
N C:GLY199 4.1 24.8 1.0
CA C:TYR198 4.2 21.5 1.0
CA C:GLY199 4.3 26.8 1.0
N C:ASN196 4.3 12.1 1.0
O7 C:TPP1330 4.3 16.0 1.0
CB C:ASN196 4.4 11.1 1.0
CB C:ASP167 4.4 11.3 1.0
O C:GLU194 4.4 14.2 1.0
N C:GLY168 4.4 9.5 1.0
C C:ASN196 4.7 13.1 1.0
O1A C:TPP1330 4.7 9.9 1.0
CA C:ASN196 4.7 12.8 1.0
CA C:GLY166 4.7 5.9 1.0
CA C:ASP167 4.7 8.7 1.0
O3B C:TPP1330 4.7 18.0 1.0
O C:HOH2334 4.8 28.9 1.0
C C:GLY166 4.8 5.8 1.0
N C:ARG197 4.9 15.9 1.0
O C:ASN196 4.9 12.4 1.0

Magnesium binding site 2 out of 2 in 1ni4

Go back to Magnesium Binding Sites List in 1ni4
Magnesium binding site 2 out of 2 in the Human Pyruvate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Pyruvate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2331

b:5.3
occ:1.00
OD1 A:ASN196 2.2 9.6 1.0
O A:TYR198 2.3 13.6 1.0
O2A A:TPP2330 2.4 6.9 1.0
O1B A:TPP2330 2.4 6.2 1.0
O A:HOH2331 2.4 10.6 1.0
OD2 A:ASP167 2.4 13.8 1.0
OD1 A:ASP167 2.9 11.2 1.0
CG A:ASP167 2.9 11.7 1.0
CG A:ASN196 3.1 6.9 1.0
C A:TYR198 3.3 12.9 1.0
ND2 A:ASN196 3.5 5.3 1.0
PA A:TPP2330 3.5 6.8 1.0
PB A:TPP2330 3.6 11.3 1.0
O3A A:TPP2330 3.6 9.7 1.0
N A:TYR198 3.9 10.7 1.0
N A:ASP167 4.0 6.9 1.0
N A:GLY199 4.1 15.0 1.0
N A:ASN196 4.2 6.5 1.0
CA A:TYR198 4.2 12.0 1.0
CA A:GLY199 4.2 17.9 1.0
O A:HOH2332 4.2 15.7 1.0
O2B A:TPP2330 4.3 12.6 1.0
CB A:ASP167 4.3 8.4 1.0
O7 A:TPP2330 4.3 8.6 1.0
N A:GLY168 4.3 7.0 1.0
CB A:ASN196 4.4 5.9 1.0
O A:GLU194 4.5 9.2 1.0
CA A:ASN196 4.6 7.2 1.0
CA A:ASP167 4.6 8.0 1.0
C A:ASN196 4.7 8.2 1.0
O1A A:TPP2330 4.7 9.4 1.0
N A:ARG197 4.7 7.8 1.0
O3B A:TPP2330 4.7 13.1 1.0
CA A:GLY166 4.8 6.9 1.0
C A:GLY166 4.8 8.2 1.0

Reference:

E.M.Ciszak, L.G.Korotchkina, P.M.Dominiak, S.Sidhu, M.S.Patel. Structural Basis For Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed By Human Pyruvate Dehydrogenase J.Biol.Chem. V. 278 21240 2003.
ISSN: ISSN 0021-9258
PubMed: 12651851
DOI: 10.1074/JBC.M300339200
Page generated: Mon Dec 14 06:32:46 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy