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Sodium in PDB 6f5w: Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside

Protein crystallography data

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside, PDB code: 6f5w was solved by J.Houser, G.Jancarikova, M.Wimmerova, M.Csavas, A.Borbas, M.Herczeg, E.Fujdiarova, E.K.Kover, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.96 / 1.91
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.571, 80.571, 224.799, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 21.3

Other elements in 6f5w:

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

Chlorine (Cl) 11 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside (pdb code 6f5w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside, PDB code: 6f5w:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 6f5w

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Sodium binding site 1 out of 9 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


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 Propargyl- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:24.6
occ:1.00
 O A:HOH568 2.3 24.1 1.0
O A:VAL179 2.3 17.8 1.0
O A:HOH676 2.4 21.1 1.0
O A:HOH726 2.4 27.2 1.0
O A:HOH556 2.4 20.9 1.0
OG1 A:THR178 3.3 25.8 1.0
C A:VAL179 3.5 17.6 1.0
N A:VAL179 3.7 18.3 1.0
O A:HOH669 4.2 12.5 1.0
CA A:VAL179 4.2 17.3 1.0
CL A:CL407 4.3 27.5 1.0
ND1 A:HIS180 4.3 20.7 1.0
CG1 A:VAL179 4.3 16.3 1.0
CG1 A:VAL227 4.4 22.7 1.0
CD2 A:TYR132 4.5 19.8 1.0
N A:HIS180 4.5 17.2 1.0
CB A:THR178 4.6 24.2 1.0
C A:THR178 4.6 19.5 1.0
O A:ILE131 4.6 16.4 1.0
CE2 A:TYR132 4.7 19.8 1.0
CA A:HIS180 4.8 17.7 1.0
CA A:THR178 4.8 20.8 1.0
CB A:VAL179 4.9 16.7 1.0

Sodium binding site 2 out of 9 in 6f5w

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Sodium binding site 2 out of 9 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


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 Propargyl- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:30.8
occ:1.00
 OD1 A:ASN37 2.4 27.8 1.0
O A:THR38 2.4 19.9 1.0
O A:HOH593 2.5 38.1 1.0
O B:HOH574 2.7 27.1 1.0
O A:ASN37 3.3 27.1 1.0
CG A:ASN37 3.3 27.4 1.0
C A:THR38 3.5 20.5 1.0
C A:ASN37 3.7 24.2 1.0
CA A:GLY41 4.1 18.5 1.0
CB A:ASN37 4.1 26.8 1.0
N A:GLY41 4.1 18.4 1.0
N A:THR38 4.1 21.2 1.0
ND2 A:ASN37 4.2 30.0 1.0
O A:HOH521 4.3 33.6 1.0
CL A:CL408 4.3 30.6 1.0
N A:SER39 4.3 21.5 1.0
CA A:THR38 4.4 21.4 1.0
CA A:SER39 4.5 23.1 1.0
CA A:ASN37 4.5 24.9 1.0
C A:SER39 4.6 22.8 1.0
O A:SER39 4.7 24.2 1.0
O A:HOH734 4.7 23.8 1.0
O B:HOH702 4.8 38.0 1.0

Sodium binding site 3 out of 9 in 6f5w

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Sodium binding site 3 out of 9 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


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 Propargyl- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:29.8
occ:1.00
 O B:HOH526 2.3 33.1 1.0
O A:HOH711 2.4 27.8 1.0
OD2 A:ASP229 2.5 22.0 1.0
O A:THR230 2.5 19.5 1.0
O A:HOH705 2.7 34.6 1.0
CG A:ASP229 3.5 21.7 1.0
C A:THR230 3.6 20.9 1.0
O B:HOH605 3.7 32.2 1.0
CB A:ASP229 3.9 20.5 1.0
N A:GLY233 4.1 21.5 1.0
CA A:GLY233 4.2 21.8 1.0
O B:HOH698 4.2 42.4 1.0
O A:ALA231 4.2 22.6 1.0
C A:ASP229 4.2 19.9 1.0
C A:ALA231 4.3 22.6 1.0
CA A:ALA231 4.3 22.4 1.0
NZ A:LYS277 4.3 26.7 1.0
O A:ASP229 4.3 21.1 1.0
O A:HOH543 4.3 37.2 1.0
N A:ALA231 4.4 20.4 1.0
N A:THR230 4.4 20.1 1.0
O B:SER39 4.5 23.9 1.0
O A:HOH541 4.5 30.4 1.0
OD1 A:ASP229 4.6 22.4 1.0
CA A:THR230 4.7 21.2 1.0
CA A:ASP229 4.7 20.7 1.0
N A:ASP232 4.9 22.0 1.0

Sodium binding site 4 out of 9 in 6f5w

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Sodium binding site 4 out of 9 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


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 Propargyl- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:31.8
occ:1.00
 O A:TRP166 2.2 19.7 1.0
O A:HOH572 2.3 37.8 1.0
C A:TRP166 3.4 21.2 1.0
OG A:SER165 3.8 33.4 1.0
CA A:ALA167 3.8 21.0 1.0
CB A:ALA167 4.0 22.6 1.0
N A:ALA167 4.1 20.4 1.0
CB A:SER165 4.5 27.8 1.0
CA A:TRP166 4.7 20.8 1.0
N A:TRP166 4.7 21.6 1.0
C A:SER165 4.8 23.6 1.0

Sodium binding site 5 out of 9 in 6f5w

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Sodium binding site 5 out of 9 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:43.9
occ:1.00
 OG A:SER39 2.8 26.1 1.0
OG B:SER254 3.2 61.7 1.0
OG B:SER183 3.2 23.2 1.0
ND1 B:HIS255 3.4 47.7 1.0
O A:HOH635 3.5 47.0 1.0
CE1 B:HIS255 3.7 44.2 1.0
CB B:SER254 3.8 58.0 1.0
CG2 A:THR111 3.8 33.2 1.0
CB B:SER183 3.8 21.3 1.0
CB A:SER39 3.8 23.9 1.0
CB A:ASP40 3.8 20.9 1.0
N A:ASP40 3.9 20.2 1.0
C A:SER39 4.1 22.8 1.0
CB A:ASN112 4.3 40.9 1.0
CA A:ASP40 4.4 20.3 1.0
CG A:ASP40 4.4 23.5 1.0
O A:SER39 4.4 24.2 1.0
ND2 A:ASN112 4.5 44.3 1.0
OD1 A:ASP40 4.6 25.2 1.0
O B:SER183 4.6 21.9 1.0
CA A:SER39 4.6 23.1 1.0
CG A:ASN112 4.7 43.0 1.0
O A:HOH613 4.7 35.0 1.0
CG B:HIS255 4.7 46.0 1.0
C B:SER183 4.8 20.4 1.0
CB A:THR111 4.8 34.2 1.0
C B:SER254 4.9 53.4 1.0
CA B:SER254 4.9 55.7 1.0
CA B:SER183 4.9 21.4 1.0

Sodium binding site 6 out of 9 in 6f5w

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Sodium binding site 6 out of 9 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:28.9
occ:1.00
 O B:HOH582 2.1 26.8 1.0
O B:VAL179 2.3 17.0 1.0
O B:HOH519 2.4 17.3 1.0
O B:HOH706 2.5 27.0 1.0
O B:HOH647 2.6 17.5 1.0
OG1 B:THR178 3.5 25.2 1.0
C B:VAL179 3.5 18.4 1.0
O B:HOH709 3.7 36.9 1.0
N B:VAL179 3.8 19.1 1.0
O B:HOH718 4.2 44.6 1.0
O B:HOH672 4.2 14.2 1.0
CL B:CL409 4.2 27.5 1.0
CA B:VAL179 4.2 18.6 1.0
ND1 B:HIS180 4.3 18.4 1.0
CG1 B:VAL179 4.4 17.6 1.0
CD2 B:TYR132 4.4 18.9 1.0
CG1 B:VAL227 4.5 26.8 1.0
N B:HIS180 4.5 18.0 1.0
CE2 B:TYR132 4.6 20.9 1.0
O B:ILE131 4.6 14.7 1.0
C B:THR178 4.7 20.3 1.0
CB B:THR178 4.8 24.7 1.0
CA B:HIS180 4.8 18.6 1.0
CB B:VAL179 5.0 18.6 1.0
CA B:THR178 5.0 22.0 1.0
CB B:HIS180 5.0 19.2 1.0

Sodium binding site 7 out of 9 in 6f5w

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Sodium binding site 7 out of 9 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:31.6
occ:1.00
 O B:HOH698 2.3 42.4 1.0
OD1 B:ASN37 2.3 22.6 1.0
O B:THR38 2.4 19.9 1.0
O B:HOH652 2.4 37.6 1.0
O B:HOH679 2.5 28.5 1.0
O B:ASN37 2.9 22.1 1.0
CG B:ASN37 3.3 24.3 1.0
O A:HOH543 3.3 37.2 1.0
C B:THR38 3.4 22.2 1.0
C B:ASN37 3.4 23.0 1.0
N B:THR38 3.9 21.9 1.0
CB B:ASN37 4.0 22.1 1.0
N B:GLY41 4.1 20.2 1.0
CA B:THR38 4.2 21.3 1.0
CA B:GLY41 4.2 19.5 1.0
CA B:ASN37 4.2 22.4 1.0
ND2 B:ASN37 4.3 26.1 1.0
N B:SER39 4.3 23.1 1.0
CA B:SER39 4.4 25.0 1.0
C B:SER39 4.6 23.1 1.0
CL A:CL419 4.6 26.3 1.0
O B:SER39 4.7 23.9 1.0
O A:HOH724 4.7 25.7 1.0
O B:HOH526 4.7 33.1 1.0

Sodium binding site 8 out of 9 in 6f5w

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Sodium binding site 8 out of 9 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:30.7
occ:1.00
 O A:HOH521 2.3 33.6 1.0
OD2 B:ASP229 2.4 23.4 1.0
O B:HOH702 2.5 38.0 1.0
O B:THR230 2.5 20.7 1.0
O B:HOH692 2.6 28.8 1.0
CG B:ASP229 3.5 22.3 1.0
C B:THR230 3.6 21.5 1.0
CB B:ASP229 3.9 21.1 1.0
O A:HOH643 4.1 34.0 1.0
N B:GLY233 4.1 21.0 1.0
O B:ALA231 4.2 22.4 1.0
CA B:GLY233 4.2 21.5 1.0
O B:HOH537 4.2 36.6 1.0
CA B:ALA231 4.3 21.7 1.0
C B:ALA231 4.3 22.4 1.0
C B:ASP229 4.3 21.0 1.0
N B:ALA231 4.3 21.9 1.0
O B:ASP229 4.4 21.4 1.0
N B:THR230 4.4 22.1 1.0
O B:HOH574 4.4 27.1 1.0
NZ B:LYS277 4.4 30.0 1.0
OD1 B:ASP229 4.6 21.5 1.0
O A:SER39 4.6 24.2 1.0
CA B:THR230 4.6 21.9 1.0
O B:HOH561 4.6 43.0 1.0
CA B:ASP229 4.7 20.4 1.0
N B:ASP232 4.9 21.5 1.0

Sodium binding site 9 out of 9 in 6f5w

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Sodium binding site 9 out of 9 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:34.3
occ:1.00
 O B:HOH531 2.1 34.6 1.0
O B:HOH523 2.2 28.7 1.0
O B:ASN112 2.5 26.4 1.0
OD1 B:ASN112 2.7 37.3 1.0
C B:ASN112 3.3 27.4 1.0
CG B:ASN112 3.5 33.5 1.0
CA B:ASN112 3.8 28.6 1.0
O B:HOH556 4.0 24.0 1.0
NE2 B:GLN108 4.1 21.4 1.0
N B:ALA113 4.2 26.4 1.0
CB B:ASN112 4.3 32.2 1.0
O B:HOH509 4.3 33.7 1.0
O B:ALA113 4.3 26.1 1.0
ND2 B:ASN112 4.4 35.6 1.0
CA B:ALA113 4.6 24.4 1.0
OE2 B:GLU44 4.6 25.0 1.0
NH2 B:ARG42 4.6 20.1 1.0
C B:ALA113 4.9 24.8 1.0

Reference:

G.Jancarikova, M.Herczeg, E.Fujdiarova, J.Houser, K.E.Kover, A.Borbas, M.Wimmerova, M.Csavas. Synthesis of Alpha-L-Fucopyranoside-Presenting Glycoclusters and Investigation of Their Interaction with Photorhabdus Asymbiotica Lectin (Phl). Chemistry V. 24 4055 2018.
ISSN: ISSN 1521-3765
PubMed: 29341313
DOI: 10.1002/CHEM.201705853
Page generated: Tue Oct 8 08:42:05 2024

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