Sodium in PDB 6rgr: Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose
Protein crystallography data
The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose, PDB code: 6rgr
was solved by
J.Houser,
E.Fujdiarova,
G.Jancarikova,
M.Wimmerova,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.99 /
1.89
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.499,
80.499,
113.413,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20 /
22.9
|
Other elements in 6rgr:
The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose
(pdb code 6rgr). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose, PDB code: 6rgr:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6rgr
Go back to
Sodium Binding Sites List in 6rgr
Sodium binding site 1 out
of 4 in the Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na405
b:29.1
occ:1.00
|
O
|
A:GLY185
|
2.6
|
22.8
|
1.0
|
OD1
|
A:ASN134
|
2.9
|
21.8
|
1.0
|
N
|
A:ASP207
|
3.0
|
24.1
|
1.0
|
N
|
A:THR135
|
3.2
|
21.6
|
1.0
|
OD1
|
A:ASP207
|
3.4
|
24.6
|
1.0
|
CA
|
A:ASN134
|
3.4
|
20.9
|
1.0
|
OE1
|
A:GLN203
|
3.4
|
24.1
|
1.0
|
CB
|
A:ASN134
|
3.5
|
20.9
|
1.0
|
CG
|
A:ASN134
|
3.6
|
20.8
|
1.0
|
CA
|
A:PRO206
|
3.7
|
24.4
|
1.0
|
CG2
|
A:THR135
|
3.7
|
24.6
|
1.0
|
C
|
A:GLY185
|
3.8
|
22.9
|
1.0
|
C
|
A:ASN134
|
3.8
|
22.1
|
1.0
|
C
|
A:PRO206
|
3.8
|
24.3
|
1.0
|
CA
|
A:ASP207
|
3.8
|
25.6
|
1.0
|
CB
|
A:PRO206
|
3.9
|
24.8
|
1.0
|
OG1
|
A:THR135
|
4.2
|
23.6
|
1.0
|
CG
|
A:ASP207
|
4.2
|
26.5
|
1.0
|
CG
|
A:LEU187
|
4.2
|
23.4
|
1.0
|
CD1
|
A:ILE181
|
4.2
|
24.0
|
1.0
|
CB
|
A:THR135
|
4.3
|
22.6
|
1.0
|
CD
|
A:GLN203
|
4.3
|
25.5
|
1.0
|
CA
|
A:THR135
|
4.3
|
21.6
|
1.0
|
NE2
|
A:GLN203
|
4.4
|
25.3
|
1.0
|
N
|
A:LEU187
|
4.5
|
23.0
|
1.0
|
CD2
|
A:LEU187
|
4.6
|
23.1
|
1.0
|
CB
|
A:ASP207
|
4.6
|
26.2
|
1.0
|
CA
|
A:GLY185
|
4.6
|
23.5
|
1.0
|
N
|
A:ASN134
|
4.7
|
20.2
|
1.0
|
N
|
A:ARG186
|
4.7
|
23.2
|
1.0
|
CA
|
A:ARG186
|
4.7
|
21.9
|
1.0
|
ND2
|
A:ASN134
|
4.9
|
19.1
|
1.0
|
CD1
|
A:LEU187
|
4.9
|
24.0
|
1.0
|
CG1
|
A:ILE181
|
4.9
|
24.4
|
1.0
|
O
|
A:PRO206
|
5.0
|
23.8
|
1.0
|
|
Sodium binding site 2 out
of 4 in 6rgr
Go back to
Sodium Binding Sites List in 6rgr
Sodium binding site 2 out
of 4 in the Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na406
b:35.5
occ:1.00
|
O
|
A:GLY233
|
2.7
|
36.2
|
1.0
|
OD1
|
A:ASN182
|
2.9
|
25.6
|
1.0
|
O
|
A:HOH628
|
2.9
|
43.0
|
1.0
|
OE1
|
A:GLN251
|
3.0
|
26.4
|
1.0
|
N
|
A:SER183
|
3.2
|
24.6
|
1.0
|
CA
|
A:ASN182
|
3.5
|
23.4
|
1.0
|
CB
|
A:ASN182
|
3.6
|
23.9
|
1.0
|
CG
|
A:ASN182
|
3.6
|
25.1
|
1.0
|
OG
|
A:SER183
|
3.6
|
26.0
|
1.0
|
C
|
A:GLY233
|
3.7
|
31.3
|
1.0
|
C
|
A:ASN182
|
3.8
|
24.6
|
1.0
|
CB
|
A:SER183
|
3.9
|
24.7
|
1.0
|
CD
|
A:GLN251
|
4.0
|
29.7
|
1.0
|
CA
|
A:ARG234
|
4.1
|
29.8
|
1.0
|
N
|
A:LEU235
|
4.1
|
26.6
|
1.0
|
CA
|
A:SER183
|
4.2
|
25.3
|
1.0
|
CG
|
A:LEU235
|
4.3
|
24.3
|
1.0
|
NE2
|
A:GLN251
|
4.3
|
26.9
|
1.0
|
N
|
A:ARG234
|
4.3
|
29.7
|
1.0
|
C
|
A:ARG234
|
4.3
|
28.1
|
1.0
|
CD2
|
A:LEU235
|
4.7
|
24.7
|
1.0
|
N
|
A:ASN182
|
4.8
|
22.8
|
1.0
|
CA
|
A:GLY233
|
4.8
|
32.1
|
1.0
|
ND2
|
A:ASN182
|
4.9
|
24.1
|
1.0
|
O
|
A:ILE181
|
5.0
|
22.9
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6rgr
Go back to
Sodium Binding Sites List in 6rgr
Sodium binding site 3 out
of 4 in the Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na407
b:55.5
occ:1.00
|
OG
|
A:SER357
|
2.7
|
39.4
|
1.0
|
OD2
|
A:ASP339
|
2.7
|
46.1
|
1.0
|
CB
|
A:SER357
|
3.4
|
40.8
|
1.0
|
CB
|
A:ALA341
|
3.6
|
34.1
|
1.0
|
CZ2
|
A:TRP343
|
3.7
|
45.2
|
1.0
|
CG
|
A:ASP339
|
3.8
|
49.1
|
1.0
|
CE2
|
A:TRP343
|
4.1
|
42.5
|
1.0
|
NE1
|
A:TRP343
|
4.2
|
42.7
|
1.0
|
OD1
|
A:ASP339
|
4.4
|
46.4
|
1.0
|
CH2
|
A:TRP343
|
4.5
|
41.6
|
1.0
|
CA
|
A:GLY359
|
4.7
|
33.9
|
1.0
|
CA
|
A:SER357
|
4.8
|
39.6
|
1.0
|
CB
|
A:ASP339
|
4.9
|
45.7
|
1.0
|
O
|
A:HOH507
|
4.9
|
44.6
|
1.0
|
N
|
A:GLY359
|
4.9
|
36.3
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6rgr
Go back to
Sodium Binding Sites List in 6rgr
Sodium binding site 4 out
of 4 in the Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na408
b:49.6
occ:1.00
|
O
|
A:VAL179
|
2.4
|
24.0
|
1.0
|
O
|
A:HOH607
|
2.6
|
27.5
|
1.0
|
O
|
A:HOH550
|
2.7
|
30.7
|
1.0
|
OG1
|
A:THR178
|
3.4
|
32.7
|
1.0
|
C
|
A:VAL179
|
3.6
|
27.0
|
1.0
|
N
|
A:VAL179
|
4.0
|
26.6
|
1.0
|
O
|
A:HOH606
|
4.0
|
22.5
|
1.0
|
ND1
|
A:HIS180
|
4.2
|
30.1
|
1.0
|
O
|
A:HOH631
|
4.2
|
24.9
|
1.0
|
CA
|
A:VAL179
|
4.4
|
25.8
|
1.0
|
CD1
|
A:TYR132
|
4.4
|
24.2
|
1.0
|
CG1
|
A:VAL227
|
4.5
|
29.2
|
1.0
|
CG1
|
A:VAL179
|
4.6
|
26.5
|
1.0
|
CE1
|
A:TYR132
|
4.6
|
26.0
|
1.0
|
N
|
A:HIS180
|
4.6
|
25.2
|
1.0
|
O
|
A:ILE131
|
4.7
|
22.0
|
1.0
|
CB
|
A:THR178
|
4.7
|
31.3
|
1.0
|
CA
|
A:HIS180
|
4.8
|
25.5
|
1.0
|
C
|
A:THR178
|
4.8
|
28.9
|
1.0
|
CB
|
A:HIS180
|
4.9
|
25.9
|
1.0
|
CG
|
A:HIS180
|
5.0
|
26.9
|
1.0
|
CA
|
A:THR178
|
5.0
|
28.8
|
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 13:11:58 2024
|