Sodium in PDB 5o6y: Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide

The structure of Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide, PDB code: 5o6y was solved by V.E.Fadouloglou, D.Kotsifaki, M.Kokkinidis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.52 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.042, 93.042, 243.868, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25.4

The structure of Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Zinc	(Zn)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide (pdb code 5o6y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 21 binding sites of Sodium where determined in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide, PDB code: 5o6y:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 21 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:5.4 occ:1.00 OG A:SER220 2.6 10.3 1.0 OG A:SER194 2.8 7.5 1.0 O A:HOH486 2.9 5.2 1.0 O A:HOH464 3.0 6.7 1.0 CB A:SER220 3.4 3.9 1.0 CB A:SER194 3.5 5.9 1.0 CA A:SER220 3.6 7.5 1.0 O A:ASN215 4.2 3.6 1.0 N A:SER220 4.2 4.0 1.0 CG2 A:VAL195 4.2 9.8 1.0 N A:PHE217 4.3 3.7 1.0 CD2 A:PHE217 4.4 3.5 1.0 CB A:PHE217 4.4 3.7 1.0 O A:SER194 4.5 5.9 1.0 CB A:SER67 4.6 3.9 1.0 C A:SER194 4.6 5.3 1.0 CA A:SER194 4.7 5.7 1.0 O A:PHE217 4.8 5.7 1.0 C A:SER220 4.8 9.4 1.0 C A:GLY219 4.8 4.0 1.0 CA A:PHE217 4.9 3.7 1.0 N A:VAL221 4.9 8.5 1.0 CG A:PHE217 4.9 12.1 1.0 O B:HOH464 4.9 6.9 1.0 O A:GLY219 5.0 12.1 1.0

Sodium binding site 2 out of 21 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:10.5 occ:1.00 OG A:SER67 2.6 3.9 1.0 O A:HOH420 2.7 4.0 1.0 O B:PRO218 3.1 10.3 1.0 CD B:PRO218 3.6 3.7 1.0 CB A:PHE66 3.6 3.9 1.0 N A:SER67 3.6 4.0 1.0 N B:PRO218 3.7 9.6 1.0 CB B:PRO218 3.8 3.8 1.0 CB B:PHE217 3.8 3.6 1.0 CB A:SER67 3.8 3.9 1.0 CB B:TYR70 3.9 5.3 1.0 C B:PRO218 4.0 12.0 1.0 CG B:PRO218 4.0 3.8 1.0 CA B:PRO218 4.1 11.6 1.0 C A:PHE66 4.1 4.0 1.0 CA B:TYR70 4.1 4.2 1.0 CA A:PHE66 4.2 4.0 1.0 N A:PHE66 4.2 4.0 1.0 O B:TYR70 4.2 4.0 1.0 CA A:SER67 4.2 4.0 1.0 C B:PHE217 4.4 4.7 1.0 O B:HOH499 4.4 6.4 1.0 CG A:PHE66 4.5 3.9 1.0 CD1 A:PHE66 4.5 3.9 1.0 NA A:NA312 4.6 9.2 1.0 CA B:PHE217 4.7 3.6 1.0 CG B:PHE217 4.7 3.6 1.0 O A:SER67 4.7 4.1 1.0 C B:TYR70 4.7 10.2 1.0 C A:SER67 4.8 4.1 1.0 CD2 B:PHE217 4.8 3.7 1.0 O A:PHE66 5.0 4.0 1.0

Sodium binding site 3 out of 21 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:9.2 occ:1.00 O A:GLY68 2.6 4.0 1.0 OG A:SER67 2.6 3.9 1.0 O B:HOH403 2.7 3.8 1.0 O A:HOH464 2.9 6.7 1.0 CB A:SER67 3.2 3.9 1.0 O A:HOH416 3.5 19.2 1.0 N A:GLY68 3.7 4.1 1.0 C A:GLY68 3.7 4.1 1.0 C A:SER67 3.9 4.1 1.0 O B:HOH499 3.9 6.4 1.0 O A:PRO218 4.1 6.3 1.0 CB B:TYR70 4.1 5.3 1.0 CA A:SER67 4.1 4.0 1.0 O A:GLY219 4.3 12.1 1.0 CA A:GLY68 4.3 4.2 1.0 OG B:SER67 4.4 3.7 1.0 CA A:GLY219 4.4 4.0 1.0 O A:SER67 4.5 4.1 1.0 O B:GLY68 4.5 3.9 1.0 C A:GLY219 4.5 4.0 1.0 NA A:NA311 4.6 10.5 1.0 N A:TYR70 4.8 4.0 1.0 C A:PRO69 4.8 4.1 1.0 CA B:TYR70 4.8 4.2 1.0 N A:PRO69 4.8 9.0 1.0 N B:TYR70 4.9 4.0 1.0

Sodium binding site 4 out of 21 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na313 b:10.0 occ:1.00 OG B:SER67 2.6 3.7 1.0 O B:HOH442 2.8 3.8 1.0 O A:PRO218 2.9 6.3 1.0 CB A:PHE217 3.6 3.7 1.0 CD A:PRO218 3.6 3.8 1.0 N A:PRO218 3.7 12.9 1.0 CB A:PRO218 3.8 3.9 1.0 C A:PRO218 3.8 9.7 1.0 CB B:SER67 3.8 6.8 1.0 CB B:PHE66 3.8 3.6 1.0 N B:SER67 3.8 3.6 1.0 O A:HOH464 3.9 6.7 1.0 CA A:PRO218 4.0 4.7 1.0 CG A:PRO218 4.1 3.8 1.0 CB A:TYR70 4.1 3.9 1.0 CA A:TYR70 4.2 8.3 1.0 C A:PHE217 4.2 15.6 1.0 C B:PHE66 4.4 3.6 1.0 CA B:SER67 4.4 3.6 1.0 O A:TYR70 4.4 4.0 1.0 CA B:PHE66 4.5 3.6 1.0 CA A:PHE217 4.5 3.7 1.0 N B:PHE66 4.5 3.6 1.0 CG A:PHE217 4.6 12.1 1.0 OG B:SER194 4.7 10.7 0.5 CG B:PHE66 4.8 3.6 1.0 CD1 A:PHE217 4.8 3.5 1.0 CD2 B:PHE66 4.8 8.6 1.0 O B:HOH403 4.8 3.8 1.0 C A:TYR70 4.9 9.3 1.0 C B:SER67 4.9 3.7 1.0 O B:SER67 5.0 3.8 1.0

Sodium binding site 5 out of 21 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na314 b:37.4 occ:1.00 CD1 A:LEU85 4.7 27.6 1.0 CD2 A:LEU85 4.8 10.6 1.0 CB A:LEU85 4.9 18.5 1.0

Sodium binding site 6 out of 21 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na315 b:32.1 occ:1.00 O A:HOH553 3.4 40.1 1.0 O A:HOH555 3.4 27.0 1.0 NE1 A:TRP182 3.5 6.8 1.0 NE2 A:GLN186 4.3 17.0 1.0 CE2 A:TRP182 4.3 12.0 1.0 CZ2 A:TRP182 4.3 18.1 1.0 CD1 A:TRP182 4.6 13.7 1.0 CD A:GLN186 4.9 15.8 1.0 NH1 A:ARG147 5.0 46.8 1.0

Sodium binding site 7 out of 21 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na316 b:38.2 occ:1.00 NE1 A:TRP53 2.7 31.3 1.0 OH A:TYR64 3.0 12.9 1.0 CB A:PRO55 3.1 26.0 1.0 CD1 A:TRP53 3.6 37.7 1.0 CE2 A:TRP53 3.7 35.3 1.0 CG A:PRO55 3.8 15.1 1.0 CA A:PRO55 3.9 22.3 1.0 C2 B:DMS305 4.0 28.8 0.7 CD A:PRO55 4.1 12.5 1.0 CZ2 A:TRP53 4.1 41.0 1.0 CZ A:PHE66 4.2 3.9 1.0 CZ A:TYR64 4.2 10.1 1.0 C3 A:PEG308 4.3 49.8 0.7 N A:PRO55 4.4 15.3 1.0 CZ3 A:TRP58 4.5 16.9 1.0 O A:GLY173 4.6 13.8 1.0 CE2 A:TYR64 4.7 4.0 1.0 NE2 A:GLN192 4.7 4.5 1.0 CE2 A:PHE66 4.7 7.7 1.0 O2 A:PEG308 4.7 53.0 0.7 CG A:TRP53 4.8 42.5 1.0 CE3 A:TRP58 4.8 9.5 1.0 CD2 A:TRP53 4.8 43.0 1.0

Sodium binding site 8 out of 21 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na309 b:10.4 occ:1.00 O B:HOH499 2.6 6.4 1.0 O B:HOH464 2.8 6.9 1.0 OG B:SER220 3.1 3.5 1.0 OG B:SER194 3.2 8.7 0.5 CB B:SER194 3.2 3.5 0.5 CB B:SER194 3.3 3.5 0.5 OG B:SER194 3.5 10.7 0.5 CA B:SER220 3.9 8.3 1.0 CB B:SER220 3.9 8.3 1.0 CB B:SER67 4.3 6.8 1.0 N B:SER220 4.4 3.5 1.0 O A:HOH486 4.4 5.2 1.0 CB B:PHE217 4.5 3.6 1.0 CD1 B:PHE217 4.5 3.6 1.0 O B:ASN215 4.6 3.4 1.0 CA B:SER194 4.6 3.4 0.5 CA B:SER194 4.6 3.4 0.5 O B:SER194 4.7 4.0 1.0 OG B:SER67 4.7 3.7 1.0 N B:PHE217 4.8 3.5 1.0 C B:SER194 4.8 5.3 1.0 C B:GLY219 4.8 3.6 1.0 CG2 B:VAL195 4.9 3.3 1.0 O B:GLY219 4.9 4.7 1.0 O A:HOH464 4.9 6.7 1.0 CG B:PHE217 5.0 3.6 1.0

Sodium binding site 9 out of 21 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na310 b:28.6 occ:1.00 ND2 B:ASN187 2.7 27.0 1.0 C B:ARG266 2.8 13.7 1.0 O B:ARG266 3.1 18.8 1.0 CG B:ASN187 3.7 27.6 1.0 CB B:ASN187 3.8 20.2 1.0 O B:HOH536 3.8 37.3 1.0 CA B:ARG266 4.2 9.7 1.0 CG B:ARG266 4.4 10.1 1.0 OD1 B:ASN187 4.8 36.6 1.0 O B:HOH577 4.8 37.9 1.0 CB B:ARG266 4.9 9.7 1.0

Sodium binding site 10 out of 21 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na311 b:44.0 occ:1.00 OG B:SER134 3.0 22.0 1.0 O B:HOH562 3.2 41.6 1.0 O B:HOH459 3.3 15.3 1.0 CB B:SER134 3.8 15.7 1.0 CB B:PRO136 4.1 10.1 1.0 O B:SER134 4.2 24.4 1.0 NE2 B:GLN149 4.5 25.3 1.0 C B:SER134 4.7 18.3 1.0 CG B:PRO136 4.7 11.3 1.0 CA B:PRO136 4.8 6.4 1.0 CA B:SER134 4.9 15.0 1.0 N B:PRO136 5.0 14.5 1.0

V.E.Fadouloglou, D.Kotsifaki, M.Kokkinidis. Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide To Be Published.