Magnesium in PDB 5no9: Nlppya in Complex with Mannosamine
Protein crystallography data
The structure of Nlppya in Complex with Mannosamine, PDB code: 5no9
was solved by
M.Podobnik,
G.Anderluh,
T.Lenarcic,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.59 /
1.75
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
115.026,
122.284,
121.138,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.5 /
20.3
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Nlppya in Complex with Mannosamine
(pdb code 5no9). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Nlppya in Complex with Mannosamine, PDB code: 5no9:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5no9
Go back to
Magnesium Binding Sites List in 5no9
Magnesium binding site 1 out
of 4 in the Nlppya in Complex with Mannosamine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Nlppya in Complex with Mannosamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg301
b:35.8
occ:1.00
|
O
|
A:HOH450
|
2.1
|
48.2
|
1.0
|
O
|
A:HIS159
|
2.1
|
35.2
|
1.0
|
OE2
|
A:GLU106
|
2.2
|
36.0
|
1.0
|
OD2
|
A:ASP93
|
2.2
|
35.7
|
1.0
|
OD1
|
A:ASP104
|
2.5
|
22.1
|
1.0
|
OD2
|
A:ASP104
|
2.5
|
21.1
|
1.0
|
CG
|
A:ASP104
|
2.9
|
21.5
|
1.0
|
CG
|
A:ASP93
|
3.3
|
30.9
|
1.0
|
C
|
A:HIS159
|
3.3
|
32.2
|
1.0
|
CD
|
A:GLU106
|
3.4
|
34.6
|
1.0
|
CA
|
A:HIS159
|
4.0
|
32.4
|
1.0
|
N
|
A:HIS159
|
4.1
|
33.4
|
1.0
|
CG
|
A:GLU106
|
4.1
|
30.1
|
1.0
|
OD1
|
A:ASP93
|
4.1
|
32.4
|
1.0
|
CB
|
A:ASP93
|
4.1
|
26.7
|
1.0
|
CB
|
A:HIS159
|
4.1
|
28.3
|
1.0
|
OE1
|
A:GLU106
|
4.3
|
32.6
|
1.0
|
N
|
A:GLU160
|
4.3
|
29.1
|
1.0
|
CB
|
A:ASP104
|
4.4
|
18.4
|
1.0
|
OH
|
A:TYR151
|
4.5
|
23.2
|
1.0
|
CE1
|
A:TYR151
|
4.6
|
20.3
|
1.0
|
CB
|
A:ASP158
|
4.6
|
49.3
|
1.0
|
CA
|
A:GLU160
|
4.6
|
30.8
|
1.0
|
C
|
A:ASP158
|
4.7
|
44.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5no9
Go back to
Magnesium Binding Sites List in 5no9
Magnesium binding site 2 out
of 4 in the Nlppya in Complex with Mannosamine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Nlppya in Complex with Mannosamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg301
b:25.4
occ:1.00
|
O
|
B:HOH441
|
2.0
|
33.5
|
1.0
|
O
|
B:HIS159
|
2.1
|
29.5
|
1.0
|
OE2
|
B:GLU106
|
2.1
|
31.8
|
1.0
|
OD2
|
B:ASP93
|
2.2
|
27.9
|
1.0
|
OD2
|
B:ASP104
|
2.3
|
19.0
|
1.0
|
OD1
|
B:ASP104
|
2.4
|
19.2
|
1.0
|
CG
|
B:ASP104
|
2.7
|
18.6
|
1.0
|
C
|
B:HIS159
|
3.3
|
28.1
|
1.0
|
CD
|
B:GLU106
|
3.3
|
26.4
|
1.0
|
CG
|
B:ASP93
|
3.3
|
28.0
|
1.0
|
CG
|
B:GLU106
|
4.0
|
22.8
|
1.0
|
CA
|
B:HIS159
|
4.1
|
26.2
|
1.0
|
OD1
|
B:ASP93
|
4.1
|
26.4
|
1.0
|
N
|
B:HIS159
|
4.1
|
26.0
|
1.0
|
CB
|
B:ASP93
|
4.1
|
21.3
|
1.0
|
CB
|
B:ASP104
|
4.2
|
16.4
|
1.0
|
CB
|
B:HIS159
|
4.2
|
24.3
|
1.0
|
OE1
|
B:GLU106
|
4.2
|
26.6
|
1.0
|
N
|
B:GLU160
|
4.3
|
25.6
|
1.0
|
O
|
B:HOH485
|
4.3
|
34.4
|
1.0
|
CB
|
B:ASP158
|
4.4
|
35.6
|
1.0
|
CA
|
B:GLU160
|
4.5
|
26.1
|
1.0
|
OH
|
B:TYR151
|
4.5
|
20.2
|
1.0
|
CE1
|
B:TYR151
|
4.6
|
20.4
|
1.0
|
C
|
B:ASP158
|
4.6
|
31.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5no9
Go back to
Magnesium Binding Sites List in 5no9
Magnesium binding site 3 out
of 4 in the Nlppya in Complex with Mannosamine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Nlppya in Complex with Mannosamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg301
b:38.6
occ:1.00
|
OE2
|
C:GLU106
|
2.2
|
30.8
|
1.0
|
O
|
C:HOH404
|
2.4
|
42.5
|
1.0
|
OD2
|
C:ASP93
|
2.4
|
33.2
|
1.0
|
O
|
C:HIS159
|
2.5
|
35.0
|
1.0
|
OD2
|
C:ASP104
|
2.7
|
24.9
|
1.0
|
OD1
|
C:ASP104
|
2.9
|
25.8
|
1.0
|
CG
|
C:ASP104
|
3.2
|
24.8
|
1.0
|
C
|
C:HIS159
|
3.3
|
34.0
|
1.0
|
CG
|
C:ASP93
|
3.3
|
28.4
|
1.0
|
CD
|
C:GLU106
|
3.4
|
27.2
|
1.0
|
O
|
C:HOH425
|
3.8
|
37.0
|
1.0
|
CA
|
C:HIS159
|
3.9
|
30.1
|
1.0
|
OD1
|
C:ASP93
|
4.0
|
30.1
|
1.0
|
CB
|
C:HIS159
|
4.0
|
27.0
|
1.0
|
N
|
C:HIS159
|
4.0
|
31.7
|
1.0
|
OE1
|
C:GLU106
|
4.2
|
27.5
|
1.0
|
N
|
C:GLU160
|
4.2
|
26.8
|
1.0
|
CB
|
C:ASP93
|
4.3
|
24.8
|
1.0
|
O
|
C:HOH434
|
4.4
|
39.7
|
1.0
|
CG
|
C:GLU106
|
4.4
|
24.7
|
1.0
|
CA
|
C:GLU160
|
4.5
|
26.6
|
1.0
|
OH
|
C:TYR151
|
4.6
|
21.9
|
1.0
|
CE1
|
C:TYR151
|
4.6
|
20.9
|
1.0
|
CB
|
C:ASP104
|
4.7
|
21.7
|
1.0
|
CG
|
C:ASP158
|
4.7
|
42.3
|
1.0
|
OD1
|
C:ASP158
|
4.8
|
44.6
|
1.0
|
C
|
C:ASP158
|
4.9
|
32.8
|
1.0
|
OD2
|
C:ASP158
|
5.0
|
46.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5no9
Go back to
Magnesium Binding Sites List in 5no9
Magnesium binding site 4 out
of 4 in the Nlppya in Complex with Mannosamine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Nlppya in Complex with Mannosamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg301
b:29.6
occ:1.00
|
O
|
D:HOH404
|
1.9
|
24.4
|
1.0
|
O
|
D:HOH401
|
2.0
|
24.7
|
1.0
|
OE2
|
D:GLU106
|
2.0
|
24.5
|
1.0
|
O
|
D:HOH407
|
2.0
|
32.0
|
1.0
|
O
|
D:HOH405
|
2.1
|
23.8
|
1.0
|
O
|
D:HIS159
|
2.2
|
29.0
|
1.0
|
CD
|
D:GLU106
|
3.0
|
23.6
|
1.0
|
C
|
D:HIS159
|
3.3
|
28.7
|
1.0
|
O1
|
D:95Z302
|
3.3
|
70.3
|
0.9
|
OE1
|
D:GLU106
|
3.4
|
22.8
|
1.0
|
CA
|
D:GLU160
|
3.7
|
25.8
|
1.0
|
OD2
|
D:ASP158
|
3.8
|
35.5
|
0.6
|
N
|
D:GLU160
|
3.9
|
23.7
|
1.0
|
OD1
|
D:ASP104
|
3.9
|
25.0
|
1.0
|
OD2
|
D:ASP93
|
4.0
|
38.5
|
1.0
|
OD2
|
D:ASP104
|
4.1
|
18.6
|
1.0
|
CB
|
D:GLU160
|
4.1
|
27.2
|
1.0
|
CG
|
D:GLU106
|
4.3
|
20.7
|
1.0
|
CA
|
D:HIS159
|
4.3
|
27.6
|
1.0
|
CG
|
D:ASP104
|
4.5
|
22.5
|
1.0
|
O
|
D:ALA127
|
4.5
|
30.1
|
1.0
|
OD1
|
D:ASP158
|
4.5
|
35.5
|
0.4
|
CG
|
D:ASP158
|
4.5
|
32.5
|
0.6
|
N
|
D:HIS159
|
4.6
|
27.5
|
1.0
|
C1
|
D:95Z302
|
4.6
|
70.4
|
0.9
|
CB
|
D:HIS159
|
4.7
|
27.4
|
1.0
|
N2
|
D:95Z302
|
4.9
|
70.6
|
0.9
|
C
|
D:ALA127
|
4.9
|
28.2
|
1.0
|
CG
|
D:ASP93
|
4.9
|
28.6
|
1.0
|
C
|
D:GLU160
|
5.0
|
22.1
|
1.0
|
OD1
|
D:ASP158
|
5.0
|
39.4
|
0.6
|
|
Reference:
T.Lenarcic,
I.Albert,
H.Bohm,
V.Hodnik,
K.Pirc,
A.B.Zavec,
M.Podobnik,
D.Pahovnik,
E.Zagar,
R.Pruitt,
P.Greimel,
A.Yamaji-Hasegawa,
T.Kobayashi,
A.Zienkiewicz,
J.Gomann,
J.C.Mortimer,
L.Fang,
A.Mamode-Cassim,
M.Deleu,
L.Lins,
C.Oecking,
I.Feussner,
S.Mongrand,
G.Anderluh,
T.Nurnberger.
Eudicot Plant-Specific Sphingolipids Determine Host Selectivity of Microbial Nlp Cytolysins. Science V. 358 1431 2017.
ISSN: ESSN 1095-9203
PubMed: 29242345
DOI: 10.1126/SCIENCE.AAN6874
Page generated: Sun Sep 29 23:22:55 2024
|