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Sodium in PDB 5mxe: Photorhabdus Asymbiotica Lectin (Phl) in Free Form

Protein crystallography data

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Free Form, PDB code: 5mxe 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) 44.16 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.235, 81.235, 113.441, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 19.1

Other elements in 5mxe:

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Free Form also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form (pdb code 5mxe). 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 Free Form, PDB code: 5mxe:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5mxe

Go back to Sodium Binding Sites List in 5mxe
Sodium binding site 1 out of 4 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:14.3
occ:1.00
O A:HOH610 2.3 13.0 1.0
O A:HOH747 2.4 8.0 1.0
O A:HOH818 2.4 16.2 1.0
O A:VAL179 2.4 7.6 1.0
O A:HOH578 2.4 7.9 1.0
OG1 A:THR178 3.1 8.4 1.0
C A:VAL179 3.6 7.8 1.0
N A:VAL179 3.8 7.7 1.0
O A:HOH855 3.9 22.4 1.0
CL A:CL405 4.1 14.4 1.0
O A:HOH691 4.1 10.2 1.0
O A:HOH841 4.1 16.9 1.0
CA A:VAL179 4.2 7.7 1.0
ND1 A:HIS180 4.4 8.7 1.0
CB A:THR178 4.4 8.1 1.0
CG1 A:VAL179 4.4 7.8 1.0
CD2 A:TYR132 4.5 10.2 1.0
O A:ILE131 4.6 7.6 1.0
C A:THR178 4.6 7.7 1.0
N A:HIS180 4.6 7.9 1.0
CG1 A:VAL227 4.6 9.6 1.0
CE2 A:TYR132 4.7 10.5 1.0
CA A:THR178 4.7 7.9 1.0
O A:HOH577 4.8 12.1 1.0
CA A:HIS180 4.9 8.1 1.0
O A:HOH814 5.0 12.9 1.0
CB A:VAL179 5.0 7.8 1.0

Sodium binding site 2 out of 4 in 5mxe

Go back to Sodium Binding Sites List in 5mxe
Sodium binding site 2 out of 4 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:14.0
occ:1.00
O A:HOH793 2.3 15.5 1.0
O A:HOH800 2.4 18.6 1.0
O A:THR38 2.4 10.0 1.0
OD1 A:ASN37 2.5 12.1 1.0
O A:ASN37 3.3 11.0 1.0
CG A:ASN37 3.4 11.7 1.0
C A:THR38 3.4 10.7 1.0
O A:HOH863 3.6 22.0 1.0
C A:ASN37 3.7 11.0 1.0
N A:THR38 4.0 10.9 1.0
CB A:ASN37 4.1 11.1 1.0
CA A:GLY41 4.1 10.6 1.0
N A:GLY41 4.1 10.3 1.0
ND2 A:ASN37 4.2 12.2 1.0
CA A:THR38 4.3 10.8 1.0
N A:SER39 4.3 10.8 1.0
CA A:SER39 4.4 11.2 1.0
CA A:ASN37 4.5 10.9 1.0
C A:SER39 4.6 11.1 1.0
O A:HOH516 4.7 15.2 1.0
O A:HOH821 4.8 7.1 1.0
O A:SER39 4.9 11.4 1.0

Sodium binding site 3 out of 4 in 5mxe

Go back to Sodium Binding Sites List in 5mxe
Sodium binding site 3 out of 4 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:20.6
occ:1.00
O A:HOH649 2.4 11.6 1.0
OD1 A:ASP40 2.4 13.1 1.0
O A:HOH686 2.5 20.0 1.0
O A:HOH781 2.5 15.5 1.0
O A:HOH626 2.6 14.8 1.0
OG1 A:THR38 2.6 11.0 1.0
CG A:ASP40 3.2 12.9 1.0
CB A:THR38 3.4 11.2 1.0
OD2 A:ASP40 3.4 13.5 1.0
O A:HOH760 3.5 16.8 1.0
CG2 A:THR38 3.8 11.6 1.0
O A:HOH621 4.1 18.3 1.0
CB A:ARG42 4.1 11.8 1.0
OE1 A:GLU44 4.1 10.8 1.0
CD A:ARG42 4.4 13.9 1.0
O A:ARG42 4.5 11.1 1.0
NE A:ARG58 4.6 17.4 1.0
CB A:ASP40 4.6 12.4 1.0
N A:ASP40 4.7 11.3 1.0
CD A:ARG58 4.8 16.0 1.0
CA A:THR38 4.8 10.8 1.0
N A:ARG42 4.8 10.8 1.0
O A:HOH725 4.8 25.9 1.0
CG A:ARG42 4.9 12.6 1.0
CA A:ARG42 4.9 11.1 1.0

Sodium binding site 4 out of 4 in 5mxe

Go back to Sodium Binding Sites List in 5mxe
Sodium binding site 4 out of 4 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:19.1
occ:1.00
O A:HOH777 2.2 15.8 1.0
O A:HOH634 2.3 17.9 1.0
O A:HOH598 2.3 8.9 1.0
O A:HOH814 2.4 12.9 1.0
O A:HOH719 2.6 11.6 1.0
O A:HOH583 2.9 18.0 1.0
O A:HOH715 3.7 12.5 1.0
NZ A:LYS81 3.8 10.7 1.0
O A:HOH688 3.8 7.0 1.0
O A:HOH548 4.0 11.3 1.0
O A:HOH577 4.2 12.1 1.0
O A:HOH708 4.2 12.7 1.0
O A:HOH828 4.4 12.6 1.0
OE2 A:GLU31 4.4 10.8 1.0
OD2 A:ASP224 4.5 9.3 1.0
CB A:ASP224 4.9 9.3 1.0
O A:PRO225 4.9 9.8 1.0
O A:HOH511 5.0 9.6 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: Tue Dec 15 11:19:31 2020

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