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Magnesium in PDB 1l8p: Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1

Enzymatic activity of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1

All present enzymatic activity of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1:
4.2.1.11;

Protein crystallography data

The structure of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1, PDB code: 1l8p was solved by R.R.Poyner, T.M.Larsen, S.W.Wong, G.H.Reed, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.200, 164.100, 84.600, 90.00, 90.40, 90.00
R / Rfree (%) 18.1 / 22.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1 (pdb code 1l8p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1, PDB code: 1l8p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1l8p

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Magnesium binding site 1 out of 8 in the Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg438

b:13.3
occ:1.00
 OE2 A:GLU295 2.0 15.7 1.0
O A:HOH2011 2.1 11.3 1.0
OD2 A:ASP246 2.2 13.6 1.0
O3 A:PAH440 2.2 14.7 1.0
O2 A:PAH440 2.3 11.9 1.0
OD2 A:ASP320 2.3 13.0 1.0
CG A:ASP246 3.0 16.4 1.0
C2 A:PAH440 3.0 11.4 1.0
N3 A:PAH440 3.0 12.3 1.0
OD1 A:ASP246 3.2 16.0 1.0
CD A:GLU295 3.2 15.0 1.0
CG A:ASP320 3.4 12.8 1.0
O A:HOH2009 3.7 12.1 1.0
OE1 A:GLU295 3.9 14.2 1.0
CB A:ASP320 3.9 12.1 1.0
NZ A:LYS396 3.9 15.8 1.0
NZ A:LYS345 3.9 7.8 1.0
O A:HOH2007 4.0 9.4 1.0
CD2 A:LEU343 4.0 4.8 1.0
MG A:MG439 4.2 23.0 1.0
OD2 A:ASP296 4.2 13.2 1.0
CG A:GLU295 4.2 15.1 1.0
CB A:ASP246 4.4 14.4 1.0
OD1 A:ASP320 4.4 12.3 1.0
C1 A:PAH440 4.4 10.8 1.0
OE2 A:GLU168 4.5 19.6 1.0

Magnesium binding site 2 out of 8 in 1l8p

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Magnesium binding site 2 out of 8 in the Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg439

b:23.0
occ:1.00
 O A:HOH2010 2.1 19.4 1.0
O A:HOH2008 2.2 16.6 1.0
O2P A:PAH440 2.2 11.1 1.0
O A:HOH2009 2.2 12.1 1.0
O A:HOH2007 2.2 9.4 1.0
O2 A:PAH440 2.3 11.9 1.0
C2 A:PAH440 3.1 11.4 1.0
P A:PAH440 3.2 11.6 1.0
C1 A:PAH440 3.3 10.8 1.0
OD2 A:ASP320 3.9 13.0 1.0
OD2 A:ASP321 3.9 20.9 1.0
NZ A:LYS345 4.0 7.8 1.0
O3P A:PAH440 4.0 10.4 1.0
OD1 A:ASP321 4.1 18.8 1.0
O A:HOH2011 4.1 11.3 1.0
MG A:MG438 4.2 13.3 1.0
N3 A:PAH440 4.2 12.3 1.0
O A:ALA38 4.2 15.3 1.0
NH2 A:ARG374 4.4 9.7 1.0
CG A:ASP321 4.4 18.2 1.0
O A:ALA39 4.4 17.0 1.0
O1P A:PAH440 4.4 11.0 1.0
O3 A:PAH440 4.6 14.7 1.0
CG A:ASP320 4.8 12.8 1.0
NE2 A:GLN167 4.9 22.7 1.0
O A:HOH2853 4.9 24.1 1.0

Magnesium binding site 3 out of 8 in 1l8p

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Magnesium binding site 3 out of 8 in the Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg938

b:10.8
occ:1.00
 OE2 B:GLU795 2.0 10.2 1.0
O3 B:PAH940 2.2 7.9 1.0
O B:HOH2016 2.2 5.4 1.0
OD2 B:ASP820 2.2 10.1 1.0
OD2 B:ASP746 2.3 10.8 1.0
O2 B:PAH940 2.3 6.7 1.0
N3 B:PAH940 3.0 9.0 1.0
C2 B:PAH940 3.0 8.6 1.0
CG B:ASP746 3.1 9.6 1.0
CD B:GLU795 3.2 10.2 1.0
OD1 B:ASP746 3.2 9.2 1.0
CG B:ASP820 3.2 11.2 1.0
NZ B:LYS896 3.8 7.3 1.0
CB B:ASP820 3.8 8.3 1.0
O B:HOH2012 3.9 7.8 1.0
NZ B:LYS845 3.9 9.8 1.0
OE1 B:GLU795 3.9 11.8 1.0
CD2 B:LEU843 4.0 3.5 1.0
O B:HOH2013 4.0 8.4 1.0
MG B:MG939 4.0 16.1 1.0
CG B:GLU795 4.2 7.4 1.0
OD2 B:ASP796 4.2 10.5 1.0
OD1 B:ASP820 4.2 10.5 1.0
CB B:ASP746 4.4 7.9 1.0
C1 B:PAH940 4.5 6.6 1.0
OE2 B:GLU668 4.6 15.8 1.0
CE B:LYS845 5.0 11.4 1.0

Magnesium binding site 4 out of 8 in 1l8p

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Magnesium binding site 4 out of 8 in the Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg939

b:16.1
occ:1.00
 O B:HOH2013 2.1 8.4 1.0
O2P B:PAH940 2.2 8.7 1.0
O B:HOH2012 2.2 7.8 1.0
O2 B:PAH940 2.2 6.7 1.0
O B:HOH2015 2.2 14.4 1.0
O B:HOH2014 2.3 17.0 1.0
C2 B:PAH940 3.0 8.6 1.0
P B:PAH940 3.3 8.4 1.0
C1 B:PAH940 3.3 6.6 1.0
OD2 B:ASP820 3.7 10.1 1.0
OD2 B:ASP821 3.8 18.2 1.0
NZ B:LYS845 3.9 9.8 1.0
OD1 B:ASP821 4.0 14.3 1.0
MG B:MG938 4.0 10.8 1.0
O B:HOH2016 4.1 5.4 1.0
N3 B:PAH940 4.1 9.0 1.0
O3P B:PAH940 4.2 8.9 1.0
NH2 B:ARG874 4.3 2.3 1.0
CG B:ASP821 4.3 14.8 1.0
O B:ALA538 4.3 11.7 1.0
O B:HOH2017 4.3 23.7 1.0
O1P B:PAH940 4.4 8.4 1.0
O B:ALA539 4.5 12.3 1.0
O3 B:PAH940 4.5 7.9 1.0
CG B:ASP820 4.8 11.2 1.0
NE2 B:GLN667 4.9 19.4 1.0
O B:HOH2827 4.9 9.7 1.0

Magnesium binding site 5 out of 8 in 1l8p

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Magnesium binding site 5 out of 8 in the Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1438

b:22.9
occ:1.00
 O C:HOH2027 2.1 27.4 1.0
O C:HOH2026 2.1 11.6 1.0
O C:HOH2025 2.2 8.1 1.0
O2P C:PAH1440 2.2 11.0 1.0
O C:HOH2024 2.2 14.9 1.0
O2 C:PAH1440 2.3 14.1 1.0
C2 C:PAH1440 3.0 13.5 1.0
P C:PAH1440 3.2 12.2 1.0
C1 C:PAH1440 3.3 13.3 1.0
OD2 C:ASP1321 3.9 19.7 1.0
OD2 C:ASP1320 4.0 10.5 1.0
OD1 C:ASP1321 4.0 19.1 1.0
NZ C:LYS1345 4.0 6.7 1.0
O3P C:PAH1440 4.0 12.5 1.0
O C:HOH2028 4.1 9.3 1.0
MG C:MG1439 4.1 12.2 1.0
N3 C:PAH1440 4.1 14.0 1.0
O C:ALA1038 4.2 19.4 1.0
O C:HOH2687 4.2 29.4 1.0
NH2 C:ARG1374 4.3 10.4 1.0
CG C:ASP1321 4.4 17.9 1.0
O1P C:PAH1440 4.5 13.9 1.0
O C:ALA1039 4.5 17.7 1.0
O3 C:PAH1440 4.5 14.1 1.0
NE2 C:GLN1167 4.8 21.6 1.0
O C:HOH2603 4.8 21.7 1.0
CG C:ASP1320 5.0 11.2 1.0

Magnesium binding site 6 out of 8 in 1l8p

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Magnesium binding site 6 out of 8 in the Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1439

b:12.2
occ:1.00
 OE2 C:GLU1295 2.0 12.2 1.0
OD2 C:ASP1246 2.2 14.1 1.0
O C:HOH2028 2.2 9.3 1.0
O3 C:PAH1440 2.2 14.1 1.0
OD2 C:ASP1320 2.2 10.5 1.0
O2 C:PAH1440 2.3 14.1 1.0
CG C:ASP1246 3.0 13.9 1.0
C2 C:PAH1440 3.1 13.5 1.0
N3 C:PAH1440 3.1 14.0 1.0
CD C:GLU1295 3.2 12.1 1.0
OD1 C:ASP1246 3.2 15.3 1.0
CG C:ASP1320 3.4 11.2 1.0
NZ C:LYS1396 3.7 11.5 1.0
O C:HOH2025 3.7 8.1 1.0
OE1 C:GLU1295 3.8 12.4 1.0
CD2 C:LEU1343 3.9 10.4 1.0
CB C:ASP1320 3.9 11.2 1.0
NZ C:LYS1345 4.0 6.7 1.0
O C:HOH2026 4.0 11.6 1.0
MG C:MG1438 4.1 22.9 1.0
OD2 C:ASP1296 4.2 14.7 1.0
CG C:GLU1295 4.2 13.4 1.0
OD1 C:ASP1320 4.4 14.1 1.0
CB C:ASP1246 4.4 13.0 1.0
C1 C:PAH1440 4.5 13.3 1.0
OE2 C:GLU1168 4.5 18.1 1.0
NE2 C:GLN1167 4.7 21.6 1.0
CG C:ASP1296 5.0 13.2 1.0
CE C:LYS1345 5.0 8.1 1.0

Magnesium binding site 7 out of 8 in 1l8p

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Magnesium binding site 7 out of 8 in the Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1938

b:14.7
occ:1.00
 O D:HOH2019 2.1 12.2 1.0
O D:HOH2020 2.2 12.1 1.0
O2P D:PAH1940 2.2 9.5 1.0
O D:HOH2022 2.3 16.3 1.0
O D:HOH2021 2.3 11.9 1.0
O2 D:PAH1940 2.3 10.7 1.0
C2 D:PAH1940 3.1 11.2 1.0
P D:PAH1940 3.3 9.2 1.0
C1 D:PAH1940 3.4 9.5 1.0
OD2 D:ASP1821 3.8 23.6 1.0
OD2 D:ASP1820 3.8 9.7 1.0
OD1 D:ASP1821 4.0 19.9 1.0
NZ D:LYS1845 4.0 4.8 1.0
MG D:MG1939 4.1 11.9 1.0
N3 D:PAH1940 4.2 9.3 1.0
O D:HOH2023 4.2 7.0 1.0
O3P D:PAH1940 4.2 10.7 1.0
O D:ALA1538 4.3 13.5 1.0
NH2 D:ARG1874 4.3 8.3 1.0
CG D:ASP1821 4.3 19.5 1.0
O1P D:PAH1940 4.5 10.0 1.0
O D:HOH3092 4.5 26.7 1.0
O D:ALA1539 4.5 15.4 1.0
O3 D:PAH1940 4.6 9.4 1.0
NE2 D:GLN1667 4.8 18.1 1.0
CG D:ASP1820 4.9 11.1 1.0

Magnesium binding site 8 out of 8 in 1l8p

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Magnesium binding site 8 out of 8 in the Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mg-Phosphonoacetohydroxamate Complex of S39A Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1939

b:11.9
occ:1.00
 OE2 D:GLU1795 2.0 7.4 1.0
O3 D:PAH1940 2.2 9.4 1.0
OD2 D:ASP1746 2.2 9.3 1.0
OD2 D:ASP1820 2.2 9.7 1.0
O D:HOH2023 2.3 7.0 1.0
O2 D:PAH1940 2.3 10.7 1.0
CG D:ASP1746 3.0 11.1 1.0
N3 D:PAH1940 3.0 9.3 1.0
C2 D:PAH1940 3.0 11.2 1.0
OD1 D:ASP1746 3.2 9.9 1.0
CD D:GLU1795 3.2 9.6 1.0
CG D:ASP1820 3.3 11.1 1.0
O D:HOH2021 3.7 11.9 1.0
NZ D:LYS1896 3.8 11.5 1.0
CB D:ASP1820 3.8 9.3 1.0
NZ D:LYS1845 3.9 4.8 1.0
OE1 D:GLU1795 4.0 8.7 1.0
O D:HOH2020 4.1 12.1 1.0
MG D:MG1938 4.1 14.7 1.0
CD2 D:LEU1843 4.2 5.7 1.0
CG D:GLU1795 4.2 7.9 1.0
OD2 D:ASP1796 4.2 12.5 1.0
OD1 D:ASP1820 4.3 10.5 1.0
CB D:ASP1746 4.3 10.0 1.0
C1 D:PAH1940 4.5 9.5 1.0
NE2 D:GLN1667 4.6 18.1 1.0
OE2 D:GLU1668 4.7 13.8 1.0

Reference:

R.R.Poyner, T.M.Larsen, S.W.Wong, G.H.Reed. Functional and Structural Changes Due to A Serine to Alanine Mutation in the Active-Site Flap of Enolase. Arch.Biochem.Biophys. V. 401 155 2002.
ISSN: ISSN 0003-9861
PubMed: 12054465
DOI: 10.1016/S0003-9861(02)00024-3
Page generated: Mon Dec 14 06:23:07 2020

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