Magnesium in PDB 1e4e: D-Alanyl-D-Lacate Ligase
Enzymatic activity of D-Alanyl-D-Lacate Ligase
All present enzymatic activity of D-Alanyl-D-Lacate Ligase:
6.1.2.1;
Protein crystallography data
The structure of D-Alanyl-D-Lacate Ligase, PDB code: 1e4e
was solved by
D.I.Roper,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
2.50
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
123.204,
225.359,
72.439,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.3 /
25.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the D-Alanyl-D-Lacate Ligase
(pdb code 1e4e). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
D-Alanyl-D-Lacate Ligase, PDB code: 1e4e:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1e4e
Go back to
Magnesium Binding Sites List in 1e4e
Magnesium binding site 1 out
of 4 in the D-Alanyl-D-Lacate Ligase
![](/pictures/MG/pdb/e4/1e4e-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/e4/1e4e-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of D-Alanyl-D-Lacate Ligase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg360
b:46.0
occ:1.00
|
ND2
|
A:ASN307
|
2.0
|
36.5
|
1.0
|
O1B
|
A:ADP350
|
2.1
|
46.2
|
1.0
|
O
|
A:HOH2095
|
2.1
|
41.0
|
1.0
|
OE2
|
A:GLU305
|
2.3
|
48.9
|
1.0
|
OE1
|
A:GLU305
|
2.4
|
62.0
|
1.0
|
CD
|
A:GLU305
|
2.7
|
57.0
|
1.0
|
CG
|
A:ASN307
|
3.1
|
43.7
|
1.0
|
P2
|
A:PHY355
|
3.2
|
41.1
|
1.0
|
PB
|
A:ADP350
|
3.3
|
45.8
|
1.0
|
O4P
|
A:PHY355
|
3.3
|
44.1
|
1.0
|
O2B
|
A:ADP350
|
3.4
|
44.9
|
1.0
|
OD1
|
A:ASN307
|
3.5
|
47.7
|
1.0
|
MG
|
A:MG365
|
3.7
|
42.0
|
1.0
|
CA
|
A:GLY176
|
3.8
|
43.2
|
1.0
|
O
|
A:HOH2153
|
4.0
|
40.6
|
1.0
|
N1
|
A:PHY355
|
4.0
|
38.8
|
1.0
|
O2P
|
A:PHY355
|
4.0
|
40.2
|
1.0
|
NZ
|
A:LYS133
|
4.0
|
38.6
|
1.0
|
O
|
A:SER175
|
4.1
|
43.8
|
1.0
|
O3A
|
A:ADP350
|
4.2
|
48.5
|
1.0
|
O3B
|
A:ADP350
|
4.2
|
45.0
|
1.0
|
O
|
A:HOH2059
|
4.3
|
39.2
|
1.0
|
O3P
|
A:PHY355
|
4.3
|
41.3
|
1.0
|
CG
|
A:GLU305
|
4.3
|
50.9
|
1.0
|
CB
|
A:ASN307
|
4.4
|
46.6
|
1.0
|
N
|
A:SER177
|
4.4
|
43.0
|
1.0
|
CE
|
A:LYS133
|
4.6
|
36.6
|
1.0
|
C
|
A:GLY176
|
4.7
|
44.2
|
1.0
|
O
|
A:HOH2078
|
4.7
|
45.9
|
1.0
|
N
|
A:GLY176
|
4.8
|
43.7
|
1.0
|
O2A
|
A:ADP350
|
4.9
|
46.8
|
1.0
|
C
|
A:SER175
|
4.9
|
43.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1e4e
Go back to
Magnesium Binding Sites List in 1e4e
Magnesium binding site 2 out
of 4 in the D-Alanyl-D-Lacate Ligase
![](/pictures/MG/pdb/e4/1e4e-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/e4/1e4e-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of D-Alanyl-D-Lacate Ligase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg365
b:42.0
occ:1.00
|
O4P
|
A:PHY355
|
1.9
|
44.1
|
1.0
|
O2B
|
A:ADP350
|
2.0
|
44.9
|
1.0
|
O
|
A:HOH2151
|
2.2
|
38.1
|
1.0
|
O
|
A:HOH2167
|
2.2
|
44.1
|
1.0
|
O2A
|
A:ADP350
|
2.3
|
46.8
|
1.0
|
OE2
|
A:GLU305
|
2.3
|
48.9
|
1.0
|
P2
|
A:PHY355
|
3.1
|
41.1
|
1.0
|
CD
|
A:GLU305
|
3.2
|
57.0
|
1.0
|
PB
|
A:ADP350
|
3.3
|
45.8
|
1.0
|
PA
|
A:ADP350
|
3.4
|
47.5
|
1.0
|
O
|
A:HOH2168
|
3.4
|
40.1
|
1.0
|
O3A
|
A:ADP350
|
3.7
|
48.5
|
1.0
|
MG
|
A:MG360
|
3.7
|
46.0
|
1.0
|
OD2
|
A:ASP292
|
3.8
|
47.6
|
1.0
|
O1B
|
A:ADP350
|
3.8
|
46.2
|
1.0
|
O3P
|
A:PHY355
|
3.8
|
41.3
|
1.0
|
CG
|
A:GLU305
|
3.9
|
50.9
|
1.0
|
O
|
A:HOH2097
|
4.0
|
48.7
|
1.0
|
ND2
|
A:ASN304
|
4.1
|
43.3
|
1.0
|
OE1
|
A:GLU305
|
4.2
|
62.0
|
1.0
|
OD1
|
A:ASN307
|
4.2
|
47.7
|
1.0
|
C5'
|
A:ADP350
|
4.2
|
46.1
|
1.0
|
O3'
|
A:ADP350
|
4.3
|
46.2
|
1.0
|
O5'
|
A:ADP350
|
4.3
|
50.5
|
1.0
|
O2P
|
A:PHY355
|
4.4
|
40.2
|
1.0
|
NH2
|
A:ARG290
|
4.5
|
46.2
|
1.0
|
O3B
|
A:ADP350
|
4.5
|
45.0
|
1.0
|
O1A
|
A:ADP350
|
4.6
|
51.7
|
1.0
|
ND2
|
A:ASN307
|
4.8
|
36.5
|
1.0
|
C3'
|
A:ADP350
|
4.8
|
48.2
|
1.0
|
O
|
A:HOH2111
|
4.9
|
56.4
|
1.0
|
CG
|
A:ASN307
|
4.9
|
43.7
|
1.0
|
CG
|
A:ASP292
|
4.9
|
43.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1e4e
Go back to
Magnesium Binding Sites List in 1e4e
Magnesium binding site 3 out
of 4 in the D-Alanyl-D-Lacate Ligase
![](/pictures/MG/pdb/e4/1e4e-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/e4/1e4e-MG-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of D-Alanyl-D-Lacate Ligase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg360
b:42.2
occ:1.00
|
ND2
|
B:ASN307
|
2.1
|
39.3
|
1.0
|
O1B
|
B:ADP350
|
2.1
|
39.0
|
1.0
|
OE1
|
B:GLU305
|
2.2
|
47.4
|
1.0
|
O
|
B:HOH2094
|
2.3
|
38.4
|
1.0
|
OE2
|
B:GLU305
|
2.4
|
37.4
|
1.0
|
CD
|
B:GLU305
|
2.7
|
43.4
|
1.0
|
CG
|
B:ASN307
|
3.0
|
41.9
|
1.0
|
OD1
|
B:ASN307
|
3.2
|
40.5
|
1.0
|
P2
|
B:PHY355
|
3.2
|
38.8
|
1.0
|
PB
|
B:ADP350
|
3.4
|
40.9
|
1.0
|
CA
|
B:GLY176
|
3.6
|
41.4
|
1.0
|
O2B
|
B:ADP350
|
3.7
|
33.1
|
1.0
|
O4P
|
B:PHY355
|
3.8
|
35.9
|
1.0
|
O
|
B:HOH2153
|
3.9
|
48.4
|
1.0
|
N1
|
B:PHY355
|
3.9
|
36.1
|
1.0
|
MG
|
B:MG365
|
4.0
|
38.8
|
1.0
|
NZ
|
B:LYS133
|
4.0
|
32.5
|
1.0
|
O2P
|
B:PHY355
|
4.0
|
38.7
|
1.0
|
O
|
B:HOH2055
|
4.1
|
38.8
|
1.0
|
O
|
B:SER175
|
4.2
|
41.2
|
1.0
|
CG
|
B:GLU305
|
4.2
|
41.1
|
1.0
|
O3P
|
B:PHY355
|
4.3
|
39.5
|
1.0
|
O3B
|
B:ADP350
|
4.4
|
42.3
|
1.0
|
CB
|
B:ASN307
|
4.4
|
43.7
|
1.0
|
N
|
B:SER177
|
4.5
|
42.2
|
1.0
|
O3A
|
B:ADP350
|
4.5
|
44.9
|
1.0
|
O
|
B:HOH2072
|
4.6
|
39.7
|
1.0
|
C
|
B:GLY176
|
4.6
|
41.2
|
1.0
|
N
|
B:GLY176
|
4.7
|
43.0
|
1.0
|
CE
|
B:LYS133
|
4.8
|
38.6
|
1.0
|
C
|
B:SER175
|
4.9
|
42.2
|
1.0
|
O
|
B:HOH2054
|
4.9
|
38.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1e4e
Go back to
Magnesium Binding Sites List in 1e4e
Magnesium binding site 4 out
of 4 in the D-Alanyl-D-Lacate Ligase
![](/pictures/MG/pdb/e4/1e4e-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/e4/1e4e-MG-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of D-Alanyl-D-Lacate Ligase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg365
b:38.8
occ:1.00
|
O
|
B:HOH2150
|
1.9
|
47.4
|
1.0
|
O2A
|
B:ADP350
|
2.1
|
45.8
|
1.0
|
O2B
|
B:ADP350
|
2.1
|
33.1
|
1.0
|
O
|
B:HOH2171
|
2.2
|
32.2
|
1.0
|
OE2
|
B:GLU305
|
2.2
|
37.4
|
1.0
|
O4P
|
B:PHY355
|
2.4
|
35.9
|
1.0
|
CD
|
B:GLU305
|
3.1
|
43.4
|
1.0
|
PA
|
B:ADP350
|
3.3
|
44.9
|
1.0
|
PB
|
B:ADP350
|
3.3
|
40.9
|
1.0
|
P2
|
B:PHY355
|
3.4
|
38.8
|
1.0
|
O1B
|
B:ADP350
|
3.6
|
39.0
|
1.0
|
O3A
|
B:ADP350
|
3.7
|
44.9
|
1.0
|
CG
|
B:GLU305
|
3.7
|
41.1
|
1.0
|
O
|
B:HOH2160
|
3.9
|
37.8
|
1.0
|
C5'
|
B:ADP350
|
3.9
|
47.4
|
1.0
|
OD2
|
B:ASP292
|
3.9
|
46.3
|
1.0
|
OE1
|
B:GLU305
|
4.0
|
47.4
|
1.0
|
MG
|
B:MG360
|
4.0
|
42.2
|
1.0
|
O
|
B:HOH2096
|
4.0
|
46.5
|
1.0
|
O3P
|
B:PHY355
|
4.1
|
39.5
|
1.0
|
ND2
|
B:ASN304
|
4.1
|
38.2
|
1.0
|
O3'
|
B:ADP350
|
4.1
|
44.8
|
1.0
|
O5'
|
B:ADP350
|
4.1
|
50.2
|
1.0
|
OD1
|
B:ASN307
|
4.2
|
40.5
|
1.0
|
O1A
|
B:ADP350
|
4.4
|
50.6
|
1.0
|
C3'
|
B:ADP350
|
4.6
|
43.6
|
1.0
|
O3B
|
B:ADP350
|
4.7
|
42.3
|
1.0
|
O2P
|
B:PHY355
|
4.7
|
38.7
|
1.0
|
O
|
B:HOH2111
|
4.8
|
50.9
|
1.0
|
NH2
|
B:ARG290
|
4.8
|
38.1
|
1.0
|
OD1
|
B:ASN304
|
4.9
|
39.7
|
1.0
|
C4'
|
B:ADP350
|
4.9
|
45.2
|
1.0
|
CG
|
B:ASN304
|
5.0
|
39.5
|
1.0
|
|
Reference:
D.I.Roper,
T.Huyton,
A.Vagin,
G.Dodson.
The Molecular Basis of Vancomycin Resistance in Clinically Relevant Enterococci: Crystal Structure of D-Alanyl-D-Lactate Ligase (Vana). Proc. Natl. Acad. Sci. V. 97 8921 2000U.S.A..
ISSN: ISSN 0027-8424
PubMed: 10908650
DOI: 10.1073/PNAS.150116497
Page generated: Tue Aug 13 02:51:31 2024
|