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Sodium in PDB 5mb4: Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac

Protein crystallography data

The structure of Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac, PDB code: 5mb4 was solved by J.Ribeiro, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.91 / 2.00
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 120.550, 120.550, 198.950, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 21.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac (pdb code 5mb4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac, PDB code: 5mb4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5mb4

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Sodium binding site 1 out of 6 in the Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:24.8
occ:1.00
 OD2 A:ASP185 2.2 19.6 1.0
O A:LEU183 2.3 23.5 1.0
OD1 A:ASN181 2.4 28.8 1.0
OD1 A:ASP177 2.4 22.8 1.0
OG1 A:THR179 2.6 28.0 1.0
O A:HOH652 2.8 29.2 1.0
CG A:ASP185 3.0 21.2 1.0
CG A:ASP177 3.3 24.1 1.0
OD1 A:ASP185 3.3 20.3 1.0
CG A:ASN181 3.4 30.1 1.0
C A:LEU183 3.4 24.9 1.0
ND2 A:ASN181 3.8 27.7 1.0
N A:LEU183 3.8 24.7 1.0
N A:THR179 3.8 26.8 1.0
CA A:ASP177 3.8 21.1 1.0
CB A:THR179 3.8 26.6 1.0
CB A:ASP177 4.0 21.2 1.0
CA A:LEU183 4.0 25.8 1.0
N A:ILE178 4.0 22.1 1.0
CB A:LEU183 4.0 26.7 1.0
OD2 A:ASP177 4.1 24.8 1.0
CG2 A:THR179 4.2 26.6 1.0
C A:ASP177 4.3 20.2 1.0
N A:ASN181 4.3 30.1 1.0
CA A:THR179 4.3 27.8 1.0
CB A:ASP185 4.4 19.6 1.0
N A:ASP185 4.4 17.8 1.0
N A:GLY180 4.5 28.4 1.0
N A:LEU184 4.5 22.3 1.0
CB A:ASN181 4.6 30.5 1.0
N A:GLY182 4.7 28.9 1.0
C A:THR179 4.7 27.7 1.0
C A:LEU184 4.8 22.0 1.0
C A:ILE178 4.8 26.1 1.0
CA A:ASN181 4.8 29.0 1.0
C A:GLY182 4.9 25.9 1.0
CA A:LEU184 4.9 22.2 1.0
C A:ASN181 5.0 30.1 1.0
CA A:ILE178 5.0 24.6 1.0

Sodium binding site 2 out of 6 in 5mb4

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Sodium binding site 2 out of 6 in the Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:32.0
occ:1.00
 O A:GLY78 2.7 22.9 1.0
O A:LYS58 2.7 24.8 1.0
NH1 A:ARG118 3.0 19.1 1.0
N A:TYR106 3.2 25.0 1.0
O A:PHE77 3.2 22.5 1.0
O A:HOH664 3.4 22.7 1.0
CA A:SER105 3.7 25.3 1.0
CD2 A:HIS59 3.7 22.7 1.0
C A:GLY78 3.7 25.3 1.0
C A:SER105 3.8 24.4 1.0
C A:PHE77 3.8 21.1 1.0
C A:LYS58 3.8 25.6 1.0
CB A:TYR106 3.9 27.7 1.0
CA A:HIS59 3.9 22.3 1.0
CA A:TYR106 3.9 25.3 1.0
CZ A:ARG118 4.0 20.0 1.0
NH2 A:ARG118 4.0 20.1 1.0
N A:GLY78 4.2 21.6 1.0
CA A:GLY78 4.3 22.2 1.0
CB A:SER105 4.3 27.1 1.0
N A:HIS59 4.3 22.5 1.0
O A:PHE104 4.4 23.0 1.0
CG A:HIS59 4.4 22.0 1.0
CB A:PHE77 4.5 20.9 1.0
CB A:HIS59 4.5 22.3 1.0
N A:GLU79 4.8 24.7 1.0
NE2 A:HIS59 4.8 23.0 1.0
N A:SER105 4.8 23.4 1.0
CA A:PHE77 4.8 20.5 1.0
O A:TRP111 4.8 20.8 1.0
O A:SER105 4.8 26.8 1.0
C A:HIS59 4.9 22.9 1.0

Sodium binding site 3 out of 6 in 5mb4

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Sodium binding site 3 out of 6 in the Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:25.0
occ:1.00
 OD1 A:ASP233 2.2 23.1 1.0
OD1 A:ASP237 2.4 24.6 1.0
O A:ARG239 2.4 23.5 1.0
O A:HOH622 2.5 30.1 1.0
OD2 A:ASP241 2.5 24.4 1.0
OG1 A:THR235 2.5 28.6 1.0
CG A:ASP241 3.3 24.1 1.0
CG A:ASP233 3.3 22.1 1.0
CG A:ASP237 3.3 27.4 1.0
OD1 A:ASP241 3.4 24.0 1.0
C A:ARG239 3.5 26.5 1.0
OD2 A:ASP237 3.7 28.6 1.0
CB A:THR235 3.8 28.3 1.0
N A:ARG239 3.8 25.1 1.0
CA A:ASP233 3.9 22.0 1.0
N A:THR235 3.9 24.8 1.0
N A:LEU234 4.0 20.6 1.0
CB A:ASP233 4.0 21.7 1.0
CA A:ARG239 4.1 26.6 1.0
OD2 A:ASP233 4.2 20.4 1.0
CG2 A:THR235 4.2 29.3 1.0
CB A:ARG239 4.2 29.2 1.0
N A:ASP237 4.3 27.1 1.0
CA A:THR235 4.3 26.8 1.0
N A:GLY236 4.3 27.8 1.0
C A:ASP233 4.4 20.2 1.0
N A:ASP241 4.4 22.6 1.0
CB A:ASP237 4.6 28.1 1.0
N A:ALA240 4.6 23.5 1.0
N A:SER238 4.6 28.5 1.0
CB A:ASP241 4.6 24.4 1.0
C A:ALA240 4.6 21.5 1.0
C A:THR235 4.7 28.5 1.0
CA A:ASP237 4.8 27.2 1.0
C A:ASP237 4.8 27.9 1.0
CA A:ALA240 4.9 23.2 1.0
C A:SER238 4.9 26.9 1.0
C A:LEU234 4.9 24.8 1.0
CA A:LEU234 5.0 22.9 1.0

Sodium binding site 4 out of 6 in 5mb4

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Sodium binding site 4 out of 6 in the Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:26.9
occ:1.00
 O A:ALA349 2.2 23.3 1.0
O A:HOH667 2.3 24.1 1.0
OD1 A:ASP343 2.4 23.6 1.0
OD2 A:ASP351 2.5 25.1 1.0
OD1 A:ASP347 2.5 28.5 1.0
OG1 A:THR345 2.5 28.7 1.0
CG A:ASP351 3.2 27.6 1.0
OD1 A:ASP351 3.3 26.4 1.0
C A:ALA349 3.4 24.7 1.0
CG A:ASP347 3.5 31.0 1.0
CG A:ASP343 3.5 23.9 1.0
CB A:THR345 3.7 27.5 1.0
N A:THR345 3.9 24.2 1.0
OD2 A:ASP347 3.9 38.0 1.0
N A:ALA349 4.0 27.6 1.0
CG2 A:THR345 4.0 26.4 1.0
CA A:ALA349 4.1 26.8 1.0
OD2 A:ASP343 4.2 24.1 1.0
N A:ASP351 4.3 23.2 1.0
CA A:THR345 4.3 27.2 1.0
N A:LEU344 4.3 22.4 1.0
CB A:ALA349 4.3 26.5 1.0
N A:ASP347 4.3 25.8 1.0
CA A:ASP343 4.3 21.2 1.0
N A:ALA350 4.4 24.4 1.0
CB A:ASP343 4.4 24.0 1.0
N A:GLY346 4.5 26.6 1.0
C A:ALA350 4.5 23.1 1.0
CA A:ALA350 4.6 23.9 1.0
CB A:ASP351 4.6 23.8 1.0
CB A:ASP347 4.6 28.8 1.0
CB A:ASN365 4.7 23.6 1.0
N A:GLY348 4.7 24.9 1.0
C A:THR345 4.7 26.4 1.0
C A:ASP343 4.8 22.6 1.0
CA A:ASP347 4.8 27.7 1.0
CA A:ASP351 5.0 24.9 1.0
O A:ASN365 5.0 24.5 1.0
C A:LEU344 5.0 23.9 1.0

Sodium binding site 5 out of 6 in 5mb4

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Sodium binding site 5 out of 6 in the Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:31.8
occ:1.00
 OG1 A:THR67 2.4 30.4 1.0
O A:GLN71 2.4 24.4 1.0
OD1 A:ASP65 2.4 25.3 1.0
O A:HOH621 2.4 21.9 1.0
OD1 A:ASP69 2.5 31.2 1.0
OD2 A:ASP73 2.8 24.7 1.0
CG A:ASP69 3.4 30.9 1.0
CG A:ASP65 3.4 24.7 1.0
OD1 A:ASP73 3.5 19.1 1.0
C A:GLN71 3.5 27.5 1.0
CG A:ASP73 3.5 23.4 1.0
CB A:THR67 3.5 28.7 1.0
N A:THR67 3.6 26.2 1.0
OD2 A:ASP69 3.8 28.7 1.0
CG2 A:THR67 3.8 26.5 1.0
N A:GLN71 3.9 30.6 1.0
CA A:THR67 4.0 26.9 1.0
N A:THR66 4.0 23.5 1.0
CA A:GLN71 4.0 29.8 1.0
CB A:GLN71 4.0 30.2 1.0
CA A:ASP65 4.1 23.0 1.0
OD2 A:ASP65 4.2 28.4 1.0
N A:ASP69 4.2 30.1 1.0
N A:GLY68 4.3 26.8 1.0
CB A:ASP65 4.3 23.0 1.0
C A:ASP65 4.4 23.9 1.0
C A:THR67 4.5 27.3 1.0
NA A:NA506 4.5 37.2 1.0
N A:SER72 4.6 27.6 1.0
CB A:ASP69 4.6 30.4 1.0
C A:THR66 4.7 26.7 1.0
N A:ASN70 4.8 32.4 1.0
N A:ASP73 4.8 23.5 1.0
CA A:ASP69 4.8 32.0 1.0
C A:SER72 4.8 25.7 1.0
CA A:SER72 4.9 27.0 1.0
CB A:ASP73 4.9 23.1 1.0
CA A:THR66 4.9 24.5 1.0
C A:ASP69 5.0 30.4 1.0

Sodium binding site 6 out of 6 in 5mb4

Go back to Sodium Binding Sites List in 5mb4
Sodium binding site 6 out of 6 in the Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Psathyrella Asperospora Lectin Pal in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:37.2
occ:1.00
 O A:ASN87 2.2 22.0 1.0
OE1 A:GLN71 2.3 38.1 1.0
OD2 A:ASP69 2.4 28.7 1.0
O A:HOH883 2.5 40.0 1.0
O A:HOH621 2.6 21.9 1.0
C A:ASN87 3.4 23.6 1.0
CD A:GLN71 3.4 34.9 1.0
CG A:ASP69 3.5 30.9 1.0
OD1 A:ASP69 4.0 31.2 1.0
CB A:ASN87 4.0 23.1 1.0
CB A:GLN71 4.1 30.2 1.0
NE2 A:GLN71 4.1 35.2 1.0
CA A:ASN87 4.2 23.3 1.0
N A:GLY89 4.3 24.7 1.0
N A:ASN88 4.3 23.1 1.0
C A:ASN88 4.3 26.3 1.0
CG A:GLN71 4.3 32.5 1.0
CA A:ASN88 4.4 25.6 1.0
NA A:NA505 4.5 31.8 1.0
N A:ASN87 4.6 24.8 1.0
OG1 A:THR67 4.7 30.4 1.0
CG A:ASN87 4.7 21.4 1.0
OD1 A:ASN87 4.7 23.0 1.0
CA A:GLY89 4.7 24.3 1.0
CB A:ASP69 4.7 30.4 1.0
OD1 A:ASP73 4.8 19.1 1.0
O A:HOH684 4.8 35.9 1.0
O A:ASN88 4.8 26.3 1.0

Reference:

J.P.Ribeiro, M.Ali Abol Hassan, R.Rouf, E.Tiralongo, T.W.May, C.J.Day, A.Imberty, J.Tiralongo, A.Varrot. Biophysical Characterization and Structural Determination of the Potent Cytotoxic Psathyrella Asperospora Lectin. Proteins V. 85 969 2017.
ISSN: ESSN 1097-0134
PubMed: 28168856
DOI: 10.1002/PROT.25265
Page generated: Mon Oct 7 22:32:16 2024

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