Atomistry » Magnesium » PDB 1ofh-1oyj » 1one
Atomistry »
  Magnesium »
    PDB 1ofh-1oyj »
      1one »

Magnesium in PDB 1one: Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate

Enzymatic activity of Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate

All present enzymatic activity of Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate:
4.2.1.11;

Protein crystallography data

The structure of Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate, PDB code: 1one was solved by T.M.Larsen, J.E.Wedekind, I.Rayment, G.H.Reed, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.900, 73.200, 93.900, 90.00, 93.30, 90.00
R / Rfree (%) 17.7 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate (pdb code 1one). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate, PDB code: 1one:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1one

Go back to Magnesium Binding Sites List in 1one
Magnesium binding site 1 out of 4 in the Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg438

b:8.0
occ:1.00
OE2 A:GLU295 1.9 3.1 1.0
O A:HOH948 2.0 5.2 1.0
OD2 A:ASP246 2.0 4.9 1.0
OD2 A:ASP320 2.1 12.0 1.0
O2 A:2PG441 2.3 14.1 0.5
O1 A:PEP440 2.4 16.1 0.5
O2' A:PEP440 2.4 4.6 0.5
O1 A:2PG441 2.4 4.4 0.5
C1 A:2PG441 2.7 6.2 0.5
C1 A:PEP440 2.7 5.2 0.5
CG A:ASP246 2.9 5.1 1.0
CD A:GLU295 3.1 3.2 1.0
CG A:ASP320 3.1 11.0 1.0
OD1 A:ASP246 3.1 7.7 1.0
CB A:ASP320 3.5 7.9 1.0
NZ A:LYS396 3.7 2.9 1.0
O A:HOH949 3.8 7.0 1.0
OE1 A:GLU295 3.8 5.5 1.0
CG A:GLU295 3.9 5.1 1.0
OD2 A:ASP296 4.0 6.6 1.0
NZ A:LYS345 4.0 7.2 1.0
O A:HOH1091 4.1 7.3 1.0
OD1 A:ASP320 4.1 7.1 1.0
CD2 A:LEU343 4.2 8.4 1.0
MG A:MG439 4.2 9.5 1.0
C2 A:PEP440 4.2 5.0 0.5
NE2 A:GLN167 4.2 7.2 1.0
CB A:ASP246 4.2 5.1 1.0
C2 A:2PG441 4.3 9.3 0.5
OE2 A:GLU168 4.6 6.2 1.0
CE A:LYS396 4.8 4.0 1.0
CG A:ASP296 4.8 30.1 1.0
O2 A:PEP440 5.0 5.6 0.5

Magnesium binding site 2 out of 4 in 1one

Go back to Magnesium Binding Sites List in 1one
Magnesium binding site 2 out of 4 in the Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg439

b:9.5
occ:1.00
O1P A:PEP440 2.1 2.6 0.5
O A:HOH1091 2.1 7.3 1.0
O A:SER39 2.1 10.3 1.0
O A:HOH949 2.1 7.0 1.0
O3P A:2PG441 2.2 10.2 0.5
O2' A:PEP440 2.2 4.6 0.5
OG A:SER39 2.2 6.3 1.0
O1 A:2PG441 2.2 4.4 0.5
CB A:SER39 3.1 7.0 1.0
C A:SER39 3.1 7.4 1.0
C1 A:PEP440 3.1 5.2 0.5
P A:PEP440 3.2 3.5 0.5
O2 A:PEP440 3.2 5.6 0.5
C1 A:2PG441 3.2 6.2 0.5
P A:2PG441 3.2 9.0 0.5
O1P A:2PG441 3.2 3.5 0.5
C2 A:2PG441 3.5 9.3 0.5
CA A:SER39 3.6 7.8 1.0
C2 A:PEP440 3.7 5.0 0.5
O2P A:PEP440 3.8 8.8 0.5
OD2 A:ASP320 3.8 12.0 1.0
NZ A:LYS345 3.9 7.2 1.0
O4P A:2PG441 3.9 12.3 0.5
N A:SER39 4.0 8.3 1.0
NH2 A:ARG374 4.1 7.2 1.0
OD1 A:ASP321 4.1 12.9 1.0
MG A:MG438 4.2 8.0 1.0
O1 A:PEP440 4.2 16.1 0.5
OD2 A:ASP321 4.2 8.4 1.0
O A:HOH948 4.2 5.2 1.0
NE2 A:GLN167 4.2 7.2 1.0
N A:THR40 4.3 12.9 1.0
O2 A:2PG441 4.3 14.1 0.5
OE1 A:GLN167 4.3 9.5 1.0
O3P A:PEP440 4.3 1.8 0.5
O2P A:2PG441 4.4 2.2 0.5
CG A:ASP321 4.5 21.3 1.0
CA A:THR40 4.7 12.5 1.0
CD A:GLN167 4.7 8.5 1.0
CG A:ASP320 4.9 11.0 1.0
C3 A:PEP440 4.9 9.8 0.5

Magnesium binding site 3 out of 4 in 1one

Go back to Magnesium Binding Sites List in 1one
Magnesium binding site 3 out of 4 in the Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg438

b:5.5
occ:1.00
OE2 B:GLU295 1.9 6.3 1.0
OD2 B:ASP320 1.9 6.6 1.0
OD2 B:ASP246 2.0 7.2 1.0
O B:HOH1114 2.2 7.2 1.0
O2 B:2PG441 2.3 3.6 0.5
O1 B:PEP440 2.4 4.8 0.5
O2' B:PEP440 2.5 10.7 0.5
O1 B:2PG441 2.5 10.3 0.5
C1 B:2PG441 2.7 11.2 0.5
C1 B:PEP440 2.8 11.8 0.5
CG B:ASP246 2.9 31.9 1.0
CD B:GLU295 3.0 12.9 1.0
CG B:ASP320 3.1 3.4 1.0
OD1 B:ASP246 3.2 8.0 1.0
CB B:ASP320 3.5 5.1 1.0
NZ B:LYS396 3.6 6.1 1.0
OE1 B:GLU295 3.7 9.8 1.0
O B:HOH1276 3.9 5.0 1.0
CG B:GLU295 3.9 6.7 1.0
O B:HOH945 4.0 6.3 1.0
OD2 B:ASP296 4.0 12.6 1.0
CD2 B:LEU343 4.1 8.9 1.0
NZ B:LYS345 4.1 8.0 1.0
OD1 B:ASP320 4.1 7.7 1.0
NE2 B:GLN167 4.2 3.8 1.0
C2 B:PEP440 4.2 6.5 0.5
CB B:ASP246 4.2 10.7 1.0
MG B:MG439 4.3 7.6 1.0
C2 B:2PG441 4.3 16.6 0.5
OE2 B:GLU168 4.6 6.4 1.0
CE B:LYS396 4.7 11.3 1.0
CG B:ASP296 4.9 5.4 1.0

Magnesium binding site 4 out of 4 in 1one

Go back to Magnesium Binding Sites List in 1one
Magnesium binding site 4 out of 4 in the Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast Enolase Complexed with An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg439

b:7.6
occ:1.00
O B:HOH945 2.0 6.3 1.0
O B:SER39 2.0 14.0 1.0
OG B:SER39 2.0 3.7 1.0
O1P B:PEP440 2.2 7.6 0.5
O B:HOH1276 2.2 5.0 1.0
O2' B:PEP440 2.2 10.7 0.5
O1 B:2PG441 2.2 10.3 0.5
O3P B:2PG441 2.3 22.3 0.5
C B:SER39 3.0 13.6 1.0
CB B:SER39 3.1 2.3 1.0
C1 B:PEP440 3.1 11.8 0.5
C1 B:2PG441 3.2 11.2 0.5
O2 B:PEP440 3.3 7.0 0.5
P B:PEP440 3.3 8.5 0.5
P B:2PG441 3.3 14.4 0.5
O1P B:2PG441 3.3 5.0 0.5
CA B:SER39 3.5 5.5 1.0
C2 B:2PG441 3.6 16.6 0.5
C2 B:PEP440 3.7 6.5 0.5
NZ B:LYS345 3.9 8.0 1.0
O2P B:PEP440 3.9 2.1 0.5
OD2 B:ASP320 4.0 6.6 1.0
N B:SER39 4.0 5.0 1.0
O4P B:2PG441 4.0 7.5 0.5
N B:THR40 4.1 7.3 1.0
OD2 B:ASP321 4.1 9.1 1.0
OD1 B:ASP321 4.2 8.9 1.0
NH2 B:ARG374 4.2 12.6 1.0
NE2 B:GLN167 4.2 3.8 1.0
O1 B:PEP440 4.2 4.8 0.5
MG B:MG438 4.3 5.5 1.0
O2 B:2PG441 4.3 3.6 0.5
O B:HOH1114 4.4 7.2 1.0
OE1 B:GLN167 4.4 10.8 1.0
O3P B:PEP440 4.5 5.6 0.5
CG B:ASP321 4.6 15.9 1.0
CA B:THR40 4.6 6.2 1.0
O2P B:2PG441 4.6 12.3 0.5
CD B:GLN167 4.8 3.7 1.0

Reference:

T.M.Larsen, J.E.Wedekind, I.Rayment, G.H.Reed. A Carboxylate Oxygen of the Substrate Bridges the Magnesium Ions at the Active Site of Enolase: Structure of the Yeast Enzyme Complexed with the Equilibrium Mixture of 2-Phosphoglycerate and Phosphoenolpyruvate at 1.8 A Resolution. Biochemistry V. 35 4349 1996.
ISSN: ISSN 0006-2960
PubMed: 8605183
DOI: 10.1021/BI952859C
Page generated: Sun Aug 10 02:11:34 2025

Last articles

Mg in 4JI1
Mg in 4JI0
Mg in 4JI2
Mg in 4JI3
Mg in 4JHD
Mg in 4JH6
Mg in 4JH8
Mg in 4JH7
Mg in 4JH3
Mg in 4JH5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy