Atomistry » Sodium » PDB 6r7k-6rjc » 6rg2
Atomistry »
  Sodium »
    PDB 6r7k-6rjc »
      6rg2 »

Sodium in PDB 6rg2: Photorhabdus Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose

Protein crystallography data

The structure of Photorhabdus Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose, PDB code: 6rg2 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) 44.84 / 1.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.646, 56.708, 108.477, 90.00, 95.33, 90.00
R / Rfree (%) 13.6 / 16.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Photorhabdus Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose (pdb code 6rg2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Photorhabdus Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose, PDB code: 6rg2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6rg2

Go back to Sodium Binding Sites List in 6rg2
Sodium binding site 1 out of 2 in the Photorhabdus Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose


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 3-O-Methyl-D- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na413

b:39.1
occ:1.00
O A:HOH738 2.1 30.5 1.0
O A:HOH904 2.5 30.7 1.0
O A:HOH916 2.6 22.7 1.0
OD2 A:ASP186 2.7 12.8 1.0
O A:HOH853 3.1 36.2 1.0
NE A:ARG188 3.7 9.7 1.0
CG A:ASP186 3.7 10.7 1.0
O B:HOH866 4.1 26.6 1.0
CD A:ARG188 4.1 10.0 1.0
O A:HOH600 4.2 16.4 1.0
CB A:ASP186 4.2 11.7 1.0
ND1 A:HIS257 4.6 15.2 1.0
CZ A:ARG188 4.7 9.7 1.0
OD1 A:ASP186 4.7 10.8 1.0
O A:HOH773 4.8 25.4 1.0
CE1 A:HIS257 4.8 17.4 1.0
NH2 A:ARG188 4.9 11.1 1.0
CG A:ARG188 4.9 10.1 1.0

Sodium binding site 2 out of 2 in 6rg2

Go back to Sodium Binding Sites List in 6rg2
Sodium binding site 2 out of 2 in the Photorhabdus Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose


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 3-O-Methyl-D- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na414

b:36.1
occ:1.00
O A:HOH736 2.1 31.5 1.0
O A:GLY269 2.8 11.6 1.0
O A:ASN245 2.8 14.8 1.0
N A:ALA247 3.6 10.6 1.0
CG2 A:VAL270 3.7 14.9 1.0
CB A:ALA247 3.7 12.2 1.0
C A:ASN245 3.8 13.2 1.0
CA A:ALA247 3.9 11.1 1.0
C A:GLY269 3.9 11.2 1.0
CG A:ASN245 4.0 15.4 1.0
C A:ASN246 4.1 12.0 1.0
ND2 A:ASN245 4.1 18.5 1.0
O A:HOH717 4.2 25.1 1.0
CB A:ASN245 4.2 15.7 1.0
OD1 A:ASN245 4.2 15.7 1.0
CA A:VAL270 4.4 10.9 1.0
O A:ASN246 4.5 12.1 1.0
N A:VAL270 4.6 10.8 1.0
CB A:VAL270 4.6 12.7 1.0
N A:ASN246 4.6 12.9 1.0
CA A:ASN245 4.7 14.7 1.0
CA A:ASN246 4.8 12.6 1.0
CB A:ASN246 5.0 14.5 1.0
N A:GLY269 5.0 11.9 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 Dec 15 12:52:58 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy