Sodium in PDB 6rgg: Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide
Protein crystallography data
The structure of Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide, PDB code: 6rgg
was solved by
J.Houser,
E.Fujdiarova,
M.Wimmerova,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
67.03 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.304,
89.347,
68.401,
90.00,
101.35,
90.00
|
R / Rfree (%)
|
19.9 /
22.4
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide
(pdb code 6rgg). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide, PDB code: 6rgg:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 6rgg
Go back to
Sodium Binding Sites List in 6rgg
Sodium binding site 1 out
of 5 in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na405
b:70.3
occ:1.00
|
O
|
A:GLY139
|
2.6
|
53.2
|
1.0
|
OD1
|
A:ASN89
|
3.1
|
62.9
|
1.0
|
N
|
A:THR90
|
3.2
|
63.8
|
1.0
|
CB
|
A:HIS161
|
3.4
|
73.8
|
1.0
|
OG1
|
A:THR90
|
3.4
|
75.8
|
1.0
|
CA
|
A:ASN89
|
3.5
|
57.9
|
1.0
|
CA
|
A:HIS161
|
3.6
|
75.1
|
1.0
|
C
|
A:GLY139
|
3.6
|
55.8
|
1.0
|
CG2
|
A:VAL135
|
3.6
|
71.8
|
1.0
|
CB
|
A:ASN89
|
3.6
|
58.5
|
1.0
|
N
|
A:HIS161
|
3.7
|
75.5
|
1.0
|
CG
|
A:ASN89
|
3.8
|
62.9
|
1.0
|
C
|
A:ASN89
|
3.8
|
59.6
|
1.0
|
CG2
|
A:THR90
|
3.9
|
71.5
|
1.0
|
CA
|
A:GLY139
|
4.0
|
56.4
|
1.0
|
CB
|
A:THR90
|
4.0
|
72.8
|
1.0
|
OE1
|
A:GLN157
|
4.0
|
67.3
|
1.0
|
CG1
|
A:ILE141
|
4.1
|
60.2
|
1.0
|
CA
|
A:THR90
|
4.2
|
68.6
|
1.0
|
CG
|
A:HIS161
|
4.5
|
74.0
|
1.0
|
CD1
|
A:ILE141
|
4.5
|
65.8
|
1.0
|
N
|
A:ARG140
|
4.6
|
55.4
|
1.0
|
N
|
A:ILE141
|
4.7
|
57.1
|
1.0
|
CB
|
A:VAL135
|
4.7
|
66.8
|
1.0
|
CD2
|
A:HIS161
|
4.7
|
76.9
|
1.0
|
N
|
A:ASN89
|
4.8
|
54.1
|
1.0
|
C
|
A:ALA160
|
4.9
|
74.6
|
1.0
|
CA
|
A:ARG140
|
5.0
|
55.5
|
1.0
|
CD
|
A:GLN157
|
5.0
|
66.7
|
1.0
|
|
Sodium binding site 2 out
of 5 in 6rgg
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Sodium Binding Sites List in 6rgg
Sodium binding site 2 out
of 5 in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na406
b:89.3
occ:1.00
|
O
|
A:ALA30
|
2.6
|
78.8
|
1.0
|
OG
|
A:SER32
|
2.9
|
97.8
|
1.0
|
N
|
A:ASP226
|
3.4
|
68.9
|
1.0
|
CG2
|
A:ILE29
|
3.4
|
92.7
|
1.0
|
CB
|
A:ALA274
|
3.4
|
59.8
|
1.0
|
OD2
|
A:ASP226
|
3.6
|
99.4
|
1.0
|
C
|
A:ALA30
|
3.6
|
81.0
|
1.0
|
CG
|
A:ASP226
|
3.7
|
95.4
|
1.0
|
CB
|
A:ASP226
|
3.9
|
80.7
|
1.0
|
N
|
A:ALA30
|
4.0
|
93.5
|
1.0
|
CB
|
A:SER32
|
4.0
|
90.3
|
1.0
|
CA
|
A:SER225
|
4.1
|
74.1
|
1.0
|
CA
|
A:SER32
|
4.1
|
86.5
|
1.0
|
O
|
A:LEU31
|
4.1
|
73.5
|
1.0
|
CB
|
A:SER225
|
4.1
|
74.2
|
1.0
|
CA
|
A:ALA30
|
4.2
|
84.5
|
1.0
|
C
|
A:SER225
|
4.2
|
70.1
|
1.0
|
C
|
A:LEU31
|
4.2
|
76.4
|
1.0
|
CA
|
A:ASP226
|
4.2
|
75.1
|
1.0
|
CB
|
A:ALA30
|
4.2
|
76.2
|
1.0
|
N
|
A:SER32
|
4.2
|
79.0
|
1.0
|
CA
|
A:ALA274
|
4.2
|
61.0
|
1.0
|
OD1
|
A:ASP226
|
4.3
|
0.0
|
1.0
|
N
|
A:ALA274
|
4.4
|
62.2
|
1.0
|
N
|
A:LEU31
|
4.6
|
73.4
|
1.0
|
C
|
A:ILE29
|
4.6
|
96.1
|
1.0
|
CB
|
A:ILE29
|
4.7
|
98.1
|
1.0
|
CD1
|
A:ILE29
|
4.9
|
0.5
|
1.0
|
OG
|
A:SER225
|
4.9
|
69.8
|
1.0
|
CA
|
A:ILE29
|
5.0
|
0.5
|
1.0
|
O
|
A:ASP226
|
5.0
|
62.1
|
1.0
|
CA
|
A:LEU31
|
5.0
|
75.6
|
1.0
|
|
Sodium binding site 3 out
of 5 in 6rgg
Go back to
Sodium Binding Sites List in 6rgg
Sodium binding site 3 out
of 5 in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na407
b:86.7
occ:1.00
|
O
|
A:GLY187
|
2.5
|
53.1
|
1.0
|
OE1
|
A:GLN205
|
3.1
|
62.7
|
1.0
|
OD1
|
A:ASN136
|
3.1
|
59.1
|
1.0
|
N
|
A:ASP209
|
3.4
|
78.8
|
1.0
|
N
|
A:THR137
|
3.4
|
61.0
|
1.0
|
CA
|
A:ASN136
|
3.7
|
64.2
|
1.0
|
C
|
A:GLY187
|
3.7
|
50.5
|
1.0
|
CB
|
A:ASN136
|
3.8
|
64.4
|
1.0
|
CG2
|
A:THR137
|
3.8
|
63.5
|
1.0
|
CG
|
A:ASN136
|
3.8
|
67.4
|
1.0
|
CA
|
A:PRO208
|
3.9
|
73.2
|
1.0
|
CD
|
A:GLN205
|
3.9
|
65.4
|
1.0
|
OG1
|
A:THR137
|
3.9
|
67.7
|
1.0
|
OD1
|
A:ASP209
|
3.9
|
94.2
|
1.0
|
C
|
A:ASN136
|
4.0
|
62.1
|
1.0
|
NE2
|
A:GLN205
|
4.0
|
54.6
|
1.0
|
CD1
|
A:ILE183
|
4.1
|
58.2
|
1.0
|
C
|
A:PRO208
|
4.1
|
72.4
|
1.0
|
CG
|
A:LEU189
|
4.2
|
64.8
|
1.0
|
CA
|
A:ASP209
|
4.2
|
82.7
|
1.0
|
CB
|
A:THR137
|
4.3
|
66.7
|
1.0
|
CB
|
A:PRO208
|
4.3
|
75.1
|
1.0
|
N
|
A:LEU189
|
4.3
|
58.9
|
1.0
|
CA
|
A:THR137
|
4.4
|
67.2
|
1.0
|
CA
|
A:ARG188
|
4.5
|
54.9
|
1.0
|
N
|
A:ARG188
|
4.5
|
50.2
|
1.0
|
CA
|
A:GLY187
|
4.7
|
52.7
|
1.0
|
CD2
|
A:LEU189
|
4.7
|
70.7
|
1.0
|
CD1
|
A:LEU189
|
4.7
|
69.4
|
1.0
|
CG
|
A:ASP209
|
4.8
|
88.8
|
1.0
|
C
|
A:ARG188
|
4.8
|
57.1
|
1.0
|
CG1
|
A:ILE183
|
4.9
|
56.9
|
1.0
|
N
|
A:ASN136
|
5.0
|
64.2
|
1.0
|
|
Sodium binding site 4 out
of 5 in 6rgg
Go back to
Sodium Binding Sites List in 6rgg
Sodium binding site 4 out
of 5 in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na408
b:81.9
occ:1.00
|
O
|
A:ALA322
|
2.5
|
56.8
|
1.0
|
OG1
|
A:THR324
|
2.8
|
74.5
|
1.0
|
O
|
A:PHE336
|
3.5
|
53.5
|
1.0
|
N
|
A:ILE34
|
3.5
|
76.0
|
1.0
|
N
|
A:THR324
|
3.6
|
57.6
|
1.0
|
C
|
A:PRO323
|
3.6
|
59.1
|
1.0
|
CG2
|
A:VAL35
|
3.6
|
70.1
|
1.0
|
C
|
A:ALA322
|
3.7
|
59.8
|
1.0
|
CB
|
A:THR324
|
3.7
|
65.2
|
1.0
|
OG
|
A:SER321
|
3.7
|
64.1
|
1.0
|
CA
|
A:GLU33
|
3.9
|
86.8
|
1.0
|
CG2
|
A:ILE34
|
3.9
|
84.6
|
1.0
|
N
|
A:VAL35
|
3.9
|
62.0
|
1.0
|
O
|
A:PRO323
|
4.0
|
59.2
|
1.0
|
CA
|
A:PRO323
|
4.0
|
59.1
|
1.0
|
CB
|
A:GLU33
|
4.0
|
87.7
|
1.0
|
C
|
A:GLU33
|
4.2
|
80.1
|
1.0
|
CA
|
A:THR324
|
4.2
|
60.0
|
1.0
|
CA
|
A:ALA337
|
4.3
|
51.9
|
1.0
|
C
|
A:PHE336
|
4.3
|
53.8
|
1.0
|
N
|
A:PRO323
|
4.3
|
61.2
|
1.0
|
O
|
A:VAL35
|
4.3
|
65.6
|
1.0
|
CG
|
A:GLU33
|
4.5
|
95.7
|
1.0
|
CA
|
A:ILE34
|
4.5
|
77.3
|
1.0
|
CB
|
A:SER321
|
4.6
|
57.6
|
1.0
|
N
|
A:ALA337
|
4.6
|
54.0
|
1.0
|
CB
|
A:ILE34
|
4.7
|
81.6
|
1.0
|
C
|
A:ILE34
|
4.7
|
66.2
|
1.0
|
CB
|
A:VAL35
|
4.8
|
66.8
|
1.0
|
CA
|
A:VAL35
|
4.8
|
65.0
|
1.0
|
CA
|
A:ALA322
|
4.8
|
65.1
|
1.0
|
N
|
A:ALA322
|
4.9
|
63.0
|
1.0
|
CG2
|
A:THR324
|
5.0
|
72.3
|
1.0
|
|
Sodium binding site 5 out
of 5 in 6rgg
Go back to
Sodium Binding Sites List in 6rgg
Sodium binding site 5 out
of 5 in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na406
b:74.5
occ:1.00
|
O
|
B:GLY187
|
2.7
|
48.9
|
1.0
|
OD1
|
B:ASN136
|
3.0
|
57.6
|
1.0
|
N
|
B:THR137
|
3.2
|
58.4
|
1.0
|
N
|
B:ASP209
|
3.3
|
73.6
|
1.0
|
OE1
|
B:GLN205
|
3.3
|
63.3
|
1.0
|
OD1
|
B:ASP209
|
3.3
|
90.0
|
1.0
|
CA
|
B:ASN136
|
3.4
|
53.4
|
1.0
|
CB
|
B:ASN136
|
3.5
|
56.8
|
1.0
|
CG2
|
B:THR137
|
3.5
|
64.0
|
1.0
|
CG
|
B:ASN136
|
3.7
|
55.7
|
1.0
|
C
|
B:ASN136
|
3.8
|
54.8
|
1.0
|
C
|
B:GLY187
|
3.9
|
50.7
|
1.0
|
CA
|
B:ASP209
|
3.9
|
78.1
|
1.0
|
CA
|
B:PRO208
|
4.0
|
67.7
|
1.0
|
C
|
B:PRO208
|
4.0
|
68.4
|
1.0
|
CD1
|
B:ILE183
|
4.1
|
55.8
|
1.0
|
OG1
|
B:THR137
|
4.1
|
65.1
|
1.0
|
CB
|
B:THR137
|
4.2
|
63.0
|
1.0
|
CG
|
B:LEU189
|
4.2
|
53.1
|
1.0
|
CD
|
B:GLN205
|
4.2
|
65.9
|
1.0
|
CG
|
B:ASP209
|
4.3
|
95.2
|
1.0
|
CA
|
B:THR137
|
4.3
|
58.2
|
1.0
|
CB
|
B:PRO208
|
4.4
|
66.7
|
1.0
|
NE2
|
B:GLN205
|
4.5
|
56.1
|
1.0
|
N
|
B:LEU189
|
4.5
|
55.5
|
1.0
|
CD2
|
B:LEU189
|
4.6
|
51.6
|
1.0
|
N
|
B:ASN136
|
4.7
|
53.7
|
1.0
|
CA
|
B:GLY187
|
4.7
|
49.9
|
1.0
|
CB
|
B:ASP209
|
4.7
|
83.8
|
1.0
|
CG1
|
B:ILE183
|
4.8
|
53.2
|
1.0
|
N
|
B:ARG188
|
4.8
|
53.8
|
1.0
|
CA
|
B:ARG188
|
4.8
|
52.1
|
1.0
|
CD1
|
B:LEU189
|
4.8
|
52.7
|
1.0
|
O
|
B:VAL135
|
4.9
|
54.3
|
1.0
|
ND2
|
B:ASN136
|
5.0
|
54.1
|
1.0
|
O
|
B:ASN136
|
5.0
|
55.0
|
1.0
|
C
|
B:ARG188
|
5.0
|
52.2
|
1.0
|
|
Reference:
E.Fujdiarova,
J.Houser,
P.Dobes,
G.Paulikova,
N.Kondakov,
L.Kononov,
P.Hyrsl,
M.Wimmerova.
Heptabladed Beta-Propeller Lectins PLL2 and Phl From Photorhabdus Spp. Recognize O-Methylated Sugars and Influence the Host Immune System. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32559333
DOI: 10.1111/FEBS.15457
Page generated: Tue Oct 8 13:11:30 2024
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