Atomistry » Magnesium » PDB 1l3r-1lny » 1l8p
Atomistry »
  Magnesium »
    PDB 1l3r-1lny »
      1l8p »

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

Go back to Magnesium Binding Sites List in 1l8p
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

Go back to Magnesium Binding Sites List in 1l8p
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

Go back to Magnesium Binding Sites List in 1l8p
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

Go back to Magnesium Binding Sites List in 1l8p
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

Go back to Magnesium Binding Sites List in 1l8p
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

Go back to Magnesium Binding Sites List in 1l8p
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

Go back to Magnesium Binding Sites List in 1l8p
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

Go back to Magnesium Binding Sites List in 1l8p
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: Tue Aug 13 08:27:18 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy