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
|