Sodium in PDB 4fet: Catalytic Domain of Germination-Specific Lytic Tansglycosylase Sleb From Bacillus Anthracis

The structure of Catalytic Domain of Germination-Specific Lytic Tansglycosylase Sleb From Bacillus Anthracis, PDB code: 4fet was solved by X.Jing, J.Heffron, D.L.Popham, F.D.Schubot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.22 / 1.91
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.850, 64.450, 84.020, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.9

The binding sites of Sodium atom in the Catalytic Domain of Germination-Specific Lytic Tansglycosylase Sleb From Bacillus Anthracis (pdb code 4fet). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Catalytic Domain of Germination-Specific Lytic Tansglycosylase Sleb From Bacillus Anthracis, PDB code: 4fet:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Catalytic Domain of Germination-Specific Lytic Tansglycosylase Sleb From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Catalytic Domain of Germination-Specific Lytic Tansglycosylase Sleb From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:10.3 occ:1.00 O B:SER173 2.2 11.5 1.0 O B:VAL171 2.3 10.8 1.0 O B:PRO177 2.4 11.2 1.0 O B:ARG170 2.4 8.6 1.0 O B:PHE176 2.4 10.5 1.0 OD1 B:ASN178 2.4 12.0 1.0 C B:VAL171 3.0 10.7 1.0 C B:PRO177 3.1 11.7 1.0 C B:PHE176 3.2 10.5 1.0 C B:SER173 3.4 12.2 1.0 CA B:VAL171 3.5 10.1 1.0 C B:ARG170 3.5 9.0 1.0 CG B:ASN178 3.6 13.4 1.0 CA B:ASN178 3.7 13.1 1.0 N B:ASN178 3.7 12.3 1.0 N B:SER173 3.8 11.5 1.0 C B:THR172 4.0 12.6 1.0 N B:PRO177 4.0 10.9 1.0 N B:THR172 4.0 11.4 1.0 CA B:PRO177 4.0 11.3 1.0 N B:VAL171 4.0 9.2 1.0 CB B:PHE176 4.0 10.0 1.0 CA B:PHE176 4.0 10.2 1.0 CA B:SER173 4.0 11.8 1.0 O B:HOH406 4.1 16.1 1.0 N B:PHE176 4.1 10.5 1.0 CB B:ASN178 4.2 13.7 1.0 O B:THR172 4.2 12.7 1.0 N B:ALA174 4.5 11.8 1.0 CA B:THR172 4.5 12.6 1.0 O B:HOH487 4.5 19.2 1.0 CB B:SER173 4.6 11.0 1.0 ND2 B:ASN178 4.7 13.3 1.0 CA B:ALA174 4.8 13.1 1.0 CA B:ARG170 4.8 8.8 1.0 C B:ALA174 4.8 13.0 1.0 CB B:VAL171 4.9 10.3 1.0 C B:ASN178 5.0 14.1 1.0 N B:SER175 5.0 12.4 1.0

Sodium binding site 2 out of 2 in the Catalytic Domain of Germination-Specific Lytic Tansglycosylase Sleb From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Catalytic Domain of Germination-Specific Lytic Tansglycosylase Sleb From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:9.7 occ:1.00 O A:SER173 2.2 11.7 1.0 O A:VAL171 2.3 12.0 1.0 O A:PRO177 2.3 11.8 1.0 OD1 A:ASN178 2.4 14.9 1.0 O A:ARG170 2.4 9.8 1.0 O A:PHE176 2.4 9.5 1.0 C A:VAL171 3.0 11.9 1.0 C A:PRO177 3.1 11.5 1.0 C A:PHE176 3.3 10.6 1.0 C A:SER173 3.4 11.6 1.0 CA A:VAL171 3.5 11.4 1.0 C A:ARG170 3.5 10.1 1.0 CG A:ASN178 3.6 15.0 1.0 CA A:ASN178 3.6 13.6 1.0 N A:ASN178 3.7 12.2 1.0 N A:SER173 3.7 11.4 1.0 N A:THR172 4.0 12.6 1.0 N A:VAL171 4.0 10.0 1.0 N A:PRO177 4.0 10.4 1.0 CA A:PRO177 4.0 11.3 1.0 C A:THR172 4.0 13.7 1.0 CA A:SER173 4.0 11.4 1.0 CA A:PHE176 4.1 9.9 1.0 CB A:PHE176 4.1 9.4 1.0 CB A:ASN178 4.1 14.0 1.0 N A:PHE176 4.1 9.9 1.0 O A:THR172 4.4 13.2 1.0 N A:ALA174 4.4 11.5 1.0 CA A:THR172 4.5 14.2 1.0 CB A:SER173 4.6 10.4 1.0 CA A:ALA174 4.7 12.5 1.0 ND2 A:ASN178 4.7 14.3 1.0 CA A:ARG170 4.8 9.7 1.0 C A:ALA174 4.8 12.2 1.0 C A:ASN178 4.9 14.3 1.0 CB A:VAL171 4.9 11.4 1.0

X.Jing, H.R.Robinson, J.D.Heffron, D.L.Popham, F.D.Schubot. The Catalytic Domain of the Germination-Specific Lytic Transglycosylase Sleb From Bacillus Anthracis Displays A Unique Active Site Topology. Proteins V. 80 2469 2012.
ISSN: ISSN 0887-3585
PubMed: 22777830
DOI: 10.1002/PROT.24140