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Magnesium in PDB 1ebg: Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution

Enzymatic activity of Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution

All present enzymatic activity of Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution:
4.2.1.11;

Protein crystallography data

The structure of Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution, PDB code: 1ebg was solved by J.E.Wedekind, G.H.Reed, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.500, 73.900, 94.800, 90.00, 93.30, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution (pdb code 1ebg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution, PDB code: 1ebg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ebg

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Magnesium binding site 1 out of 4 in the Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg438

b:12.9
occ:1.00
 OE2 A:GLU295 1.9 11.6 1.0
O3 A:PAH440 1.9 11.6 1.0
OD2 A:ASP320 2.1 16.2 1.0
OD2 A:ASP246 2.2 11.9 1.0
O A:HOH448 2.2 7.8 1.0
O2 A:PAH440 2.2 15.7 1.0
N3 A:PAH440 2.9 11.0 1.0
C2 A:PAH440 2.9 8.5 1.0
CG A:ASP246 3.2 14.6 1.0
CG A:ASP320 3.2 26.6 1.0
CD A:GLU295 3.2 21.1 1.0
OD1 A:ASP246 3.5 13.6 1.0
CB A:ASP320 3.6 7.7 1.0
NZ A:LYS345 3.7 8.7 1.0
NZ A:LYS396 3.7 8.1 1.0
O A:HOH442 3.8 15.7 1.0
O A:HOH441 3.9 18.4 1.0
OE1 A:GLU295 3.9 13.3 1.0
CG A:GLU295 4.1 2.4 1.0
OD1 A:ASP320 4.1 17.5 1.0
NE2 A:GLN167 4.2 11.8 1.0
MG A:MG439 4.2 19.1 1.0
CD2 A:LEU343 4.2 8.5 1.0
OD2 A:ASP296 4.3 15.6 1.0
C1 A:PAH440 4.4 10.8 1.0
CB A:ASP246 4.5 11.5 1.0
OE2 A:GLU168 4.7 15.3 1.0
CE A:LYS396 4.8 15.3 1.0
CE A:LYS345 4.8 17.6 1.0

Magnesium binding site 2 out of 4 in 1ebg

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Magnesium binding site 2 out of 4 in the Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg439

b:19.1
occ:1.00
 O2P A:PAH440 2.0 18.2 1.0
O A:HOH441 2.0 18.4 1.0
O A:SER39 2.1 16.5 1.0
O A:HOH442 2.1 15.7 1.0
O2 A:PAH440 2.4 15.7 1.0
OG A:SER39 2.5 26.3 1.0
C A:SER39 3.0 17.8 1.0
C2 A:PAH440 3.0 8.5 1.0
P A:PAH440 3.1 13.7 1.0
CB A:SER39 3.2 16.9 1.0
C1 A:PAH440 3.3 10.8 1.0
CA A:SER39 3.5 17.4 1.0
N A:SER39 3.9 17.1 1.0
OD2 A:ASP320 3.9 16.2 1.0
O3P A:PAH440 4.0 9.7 1.0
OD1 A:ASP321 4.0 16.0 1.0
NZ A:LYS345 4.0 8.7 1.0
N A:THR40 4.0 19.9 1.0
NH2 A:ARG374 4.1 17.7 1.0
N3 A:PAH440 4.1 11.0 1.0
MG A:MG438 4.2 12.9 1.0
O1P A:PAH440 4.3 17.2 1.0
O A:HOH448 4.3 7.8 1.0
OD2 A:ASP321 4.3 15.7 1.0
CA A:THR40 4.5 20.4 1.0
O3 A:PAH440 4.5 11.6 1.0
CG A:ASP321 4.5 18.8 1.0
OE1 A:GLN167 4.7 11.5 1.0
NE2 A:GLN167 4.7 11.8 1.0

Magnesium binding site 3 out of 4 in 1ebg

Go back to Magnesium Binding Sites List in 1ebg
Magnesium binding site 3 out of 4 in the Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg438

b:14.0
occ:1.00
 OD2 B:ASP246 2.1 13.8 1.0
O3 B:PAH440 2.2 24.4 1.0
OE2 B:GLU295 2.2 16.6 1.0
O B:HOH460 2.2 10.2 1.0
OD2 B:ASP320 2.2 10.0 1.0
O2 B:PAH440 2.3 22.4 1.0
CG B:ASP246 2.9 43.6 1.0
N3 B:PAH440 3.0 13.6 1.0
C2 B:PAH440 3.0 37.4 1.0
OD1 B:ASP246 3.1 19.2 1.0
CD B:GLU295 3.3 33.5 1.0
CG B:ASP320 3.4 10.6 1.0
O B:HOH453 3.7 9.2 1.0
NZ B:LYS396 3.9 10.3 1.0
CB B:ASP320 3.9 17.1 1.0
OE1 B:GLU295 3.9 17.0 1.0
NE2 B:GLN167 3.9 20.8 1.0
NZ B:LYS345 4.0 14.7 1.0
MG B:MG439 4.0 14.9 1.0
O B:HOH454 4.0 8.7 1.0
OD2 B:ASP296 4.2 15.1 1.0
CB B:ASP246 4.2 17.8 1.0
CG B:GLU295 4.2 11.4 1.0
C1 B:PAH440 4.4 7.2 1.0
OD1 B:ASP320 4.4 12.4 1.0
CD2 B:LEU343 4.4 9.7 1.0
OE2 B:GLU168 4.7 16.0 1.0
CE B:LYS396 5.0 18.7 1.0

Magnesium binding site 4 out of 4 in 1ebg

Go back to Magnesium Binding Sites List in 1ebg
Magnesium binding site 4 out of 4 in the Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Chelation of Ser 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg439

b:14.9
occ:1.00
 O B:HOH454 1.9 8.7 1.0
O2P B:PAH440 2.0 21.4 1.0
O2 B:PAH440 2.1 22.4 1.0
O B:SER39 2.2 14.7 1.0
O B:HOH453 2.2 9.2 1.0
OG B:SER39 2.2 17.9 1.0
C2 B:PAH440 3.0 37.4 1.0
C B:SER39 3.1 14.2 1.0
P B:PAH440 3.2 12.0 1.0
CB B:SER39 3.3 11.1 1.0
C1 B:PAH440 3.4 7.2 1.0
CA B:SER39 3.7 13.0 1.0
OD2 B:ASP321 3.9 14.6 1.0
OD2 B:ASP320 3.9 10.0 1.0
MG B:MG438 4.0 14.0 1.0
O3P B:PAH440 4.0 7.9 1.0
N3 B:PAH440 4.0 13.6 1.0
N B:SER39 4.1 13.0 1.0
OD1 B:ASP321 4.1 17.0 1.0
NH2 B:ARG374 4.2 16.7 1.0
N B:THR40 4.3 13.0 1.0
O B:HOH460 4.3 10.2 1.0
NZ B:LYS345 4.3 14.7 1.0
O1P B:PAH440 4.4 9.7 1.0
OE1 B:GLN167 4.4 19.7 1.0
CG B:ASP321 4.4 29.0 1.0
NE2 B:GLN167 4.4 20.8 1.0
O3 B:PAH440 4.6 24.4 1.0
CA B:THR40 4.7 12.8 1.0
O B:HOH486 4.8 27.8 1.0
CD B:GLN167 4.9 11.8 1.0
CG B:ASP320 5.0 10.6 1.0

Reference:

J.E.Wedekind, R.R.Poyner, G.H.Reed, I.Rayment. Chelation of Serine 39 to MG2+ Latches A Gate at the Active Site of Enolase: Structure of the Bis(MG2+) Complex of Yeast Enolase and the Intermediate Analog Phosphonoacetohydroxamate at 2.1-A Resolution. Biochemistry V. 33 9333 1994.
ISSN: ISSN 0006-2960
PubMed: 8049235
DOI: 10.1021/BI00197A038
Page generated: Tue Aug 13 02:54:08 2024

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