Atomistry » Chlorine » PDB 5mt8-5my9 » 5mxf
Atomistry »
  Chlorine »
    PDB 5mt8-5my9 »
      5mxf »

Chlorine in PDB 5mxf: Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside

Protein crystallography data

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside, PDB code: 5mxf was solved by G.Jancarikova, J.Houser, G.Demo, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.11 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.249, 81.249, 113.231, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 19.6

Other elements in 5mxf:

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside (pdb code 5mxf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside, PDB code: 5mxf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5mxf

Go back to Chlorine Binding Sites List in 5mxf
Chlorine binding site 1 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:25.1
occ:1.00
OG1 A:THR178 3.0 19.1 1.0
N A:VAL227 3.2 19.6 1.0
O A:HOH768 3.2 26.8 1.0
O A:HOH765 3.2 23.9 1.0
O A:HOH632 3.4 22.4 1.0
CA A:VAL226 3.7 22.1 1.0
O A:VAL227 3.7 19.0 1.0
C A:VAL226 3.9 20.5 1.0
CB A:THR178 4.0 19.0 1.0
CG1 A:VAL226 4.0 25.2 1.0
NA A:NA403 4.1 24.6 1.0
CG1 A:VAL227 4.2 21.7 1.0
CB A:VAL226 4.3 23.4 1.0
CA A:VAL227 4.3 19.9 1.0
CG2 A:THR178 4.4 19.4 1.0
O A:PRO225 4.4 22.7 1.0
C A:VAL227 4.4 20.2 1.0
CG2 A:VAL226 4.5 25.4 1.0
O A:HOH740 4.8 27.1 1.0
CB A:VAL227 4.8 19.9 1.0
N A:VAL226 4.8 20.8 1.0
O A:HOH784 4.9 25.9 1.0
O A:HOH605 5.0 23.5 1.0

Chlorine binding site 2 out of 8 in 5mxf

Go back to Chlorine Binding Sites List in 5mxf
Chlorine binding site 2 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:33.4
occ:1.00
CB A:PRO67 3.7 21.9 1.0
CG A:PRO67 3.8 21.9 1.0
CD A:PRO67 4.3 21.6 1.0
CA A:PRO67 4.9 21.5 1.0

Chlorine binding site 3 out of 8 in 5mxf

Go back to Chlorine Binding Sites List in 5mxf
Chlorine binding site 3 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:25.6
occ:0.90
O A:HOH787 3.0 28.4 1.0
N A:ASP51 3.2 28.7 1.0
NE1 A:TRP55 3.2 24.7 1.0
C A:GLY49 3.5 25.7 1.0
N A:ALA53 3.5 24.6 1.0
CA A:GLY49 3.5 23.9 1.0
N A:LYS52 3.5 27.4 1.0
CA A:ASP51 3.6 30.9 1.0
C A:ASP51 3.6 28.4 1.0
CB A:ASP51 3.6 33.5 1.0
N A:THR50 3.8 28.0 1.0
CB A:ALA53 3.8 25.3 1.0
O A:GLY49 3.8 24.5 1.0
N A:GLY49 4.0 23.4 1.0
CA A:ALA53 4.1 23.6 1.0
O A:ALA53 4.1 20.9 1.0
CE2 A:TRP55 4.2 24.7 1.0
CD1 A:TRP55 4.2 24.2 1.0
O A:ASP51 4.3 25.1 1.0
C A:THR50 4.3 29.5 1.0
CZ2 A:TRP55 4.4 24.6 1.0
C A:LYS52 4.4 25.4 1.0
CA A:LYS52 4.5 29.0 1.0
C A:ALA53 4.5 22.2 1.0
O A:HOH600 4.6 30.2 1.0
CA A:THR50 4.6 28.8 0.5
CA A:THR50 4.6 28.1 0.5
CG A:ASP51 4.7 37.2 1.0

Chlorine binding site 4 out of 8 in 5mxf

Go back to Chlorine Binding Sites List in 5mxf
Chlorine binding site 4 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:39.2
occ:1.00
N A:TRP118 3.3 24.2 1.0
O A:HOH591 3.3 30.3 1.0
O A:HOH620 3.6 40.4 1.0
CD1 A:TRP118 3.7 22.8 1.0
CA A:ASN117 3.8 25.7 1.0
CB A:ASN117 3.8 28.9 1.0
CB A:TRP118 3.9 23.8 1.0
OD1 A:ASN117 4.0 34.2 1.0
C A:ASN117 4.0 24.5 1.0
CA A:TRP118 4.2 23.8 1.0
CG A:TRP118 4.2 22.6 1.0
CG A:ASN117 4.2 32.4 1.0
O A:HOH553 4.6 31.2 1.0
O A:HOH572 4.7 48.1 1.0
O A:TRP118 4.8 24.2 1.0
NE1 A:TRP118 4.8 23.4 1.0
CB A:LYS75 5.0 30.6 1.0

Chlorine binding site 5 out of 8 in 5mxf

Go back to Chlorine Binding Sites List in 5mxf
Chlorine binding site 5 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:38.8
occ:1.00
O A:HOH699 3.1 35.1 1.0
O A:HOH737 3.2 33.0 1.0
N A:TRP310 3.2 26.8 1.0
CB A:SER309 3.7 32.0 1.0
CA A:SER309 3.7 29.4 1.0
CD1 A:TRP310 3.8 25.6 1.0
C A:SER309 4.0 29.1 1.0
CB A:TRP310 4.0 26.7 1.0
CA A:TRP310 4.2 27.3 1.0
CG A:TRP310 4.3 25.9 1.0
O A:TRP310 4.6 27.3 1.0
OG A:SER309 4.8 35.7 1.0
CB A:ASN266 4.9 27.3 1.0
NE1 A:TRP310 4.9 26.1 1.0
C A:TRP310 5.0 28.7 1.0

Chlorine binding site 6 out of 8 in 5mxf

Go back to Chlorine Binding Sites List in 5mxf
Chlorine binding site 6 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:30.6
occ:1.00
N A:ASP364 3.2 23.7 1.0
NH1 A:ARG336 3.4 30.6 1.0
CA A:ILE363 3.7 25.3 1.0
CB A:ILE363 3.8 27.0 1.0
C A:ILE363 4.0 26.0 1.0
CB A:ASP364 4.0 23.7 1.0
NH2 A:ARG336 4.1 31.2 1.0
CA A:ASP364 4.1 24.0 1.0
CZ A:ARG336 4.2 29.1 1.0
O A:ASP364 4.4 22.0 1.0
CG2 A:ILE363 4.4 28.7 1.0
C A:ASP364 4.7 23.5 1.0
O A:LEU362 5.0 25.0 1.0
O A:HOH517 5.0 25.0 1.0

Chlorine binding site 7 out of 8 in 5mxf

Go back to Chlorine Binding Sites List in 5mxf
Chlorine binding site 7 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:37.5
occ:1.00
N A:SER216 3.2 22.6 1.0
CA A:GLU215 3.7 23.6 1.0
C A:GLU215 3.9 23.6 1.0
CB A:SER216 4.0 22.6 1.0
CB A:GLU215 4.1 26.6 1.0
CA A:SER216 4.1 22.3 1.0
O A:SER216 4.4 22.2 1.0
CZ3 A:TRP199 4.4 24.4 1.0
CG A:GLU215 4.5 29.0 1.0
CH2 A:TRP199 4.7 24.6 1.0
O A:TRP214 4.7 24.2 1.0
C A:SER216 4.8 21.8 1.0
N A:GLU215 5.0 22.4 1.0

Chlorine binding site 8 out of 8 in 5mxf

Go back to Chlorine Binding Sites List in 5mxf
Chlorine binding site 8 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl414

b:25.9
occ:1.00
O A:HOH614 3.1 29.4 1.0
ND2 A:ASN281 3.2 20.8 1.0
O A:HOH780 4.1 23.7 1.0
CG A:ASN281 4.3 20.7 1.0
O A:HOH590 4.4 26.7 1.0
OD1 A:ASN281 4.5 22.9 1.0
CB A:ALA231 5.0 19.7 1.0

Reference:

G.Jancarikova, J.Houser, P.Dobes, G.Demo, P.Hyrsl, M.Wimmerova. Characterization of Novel Bangle Lectin From Photorhabdus Asymbiotica with Dual Sugar-Binding Specificity and Its Effect on Host Immunity. Plos Pathog. V. 13 06564 2017.
ISSN: ESSN 1553-7374
PubMed: 28806750
DOI: 10.1371/JOURNAL.PPAT.1006564
Page generated: Sat Dec 12 12:07:51 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy