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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

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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

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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: Tue Aug 13 10:41:21 2024

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