Sodium in PDB 3k1s: Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis

The structure of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis, PDB code: 3k1s was solved by S.M.Anderson, Z.Wawrzak, O.Onopriyenko, K.Kwon, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.75 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.887, 92.887, 260.639, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.6

The structure of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Chlorine	(Cl)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis (pdb code 3k1s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis, PDB code: 3k1s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia 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 Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:48.2 occ:1.00 OH A:TYR99 2.2 41.6 1.0 O C:GLU94 2.6 29.8 1.0 CZ A:TYR99 3.2 30.3 1.0 OE1 C:GLU94 3.3 34.8 1.0 C C:GLU94 3.4 28.3 1.0 CE2 A:TYR99 3.5 28.4 1.0 CA C:GLU94 3.6 27.4 1.0 CG C:LEU98 3.7 35.7 1.0 CB C:GLU94 3.7 26.9 1.0 CE A:LYS31 3.8 33.2 1.0 CB C:ASP97 3.8 37.9 1.0 N C:LEU98 3.9 33.8 1.0 CD1 C:LEU98 4.2 39.1 1.0 NZ A:LYS31 4.3 38.8 1.0 CB C:LEU98 4.3 34.8 1.0 CD C:GLU94 4.3 31.2 1.0 CE1 A:TYR99 4.4 37.6 1.0 CA C:LEU98 4.5 34.1 1.0 C C:ASP97 4.5 35.6 1.0 CD2 C:LEU98 4.6 33.0 1.0 CD1 A:PHE95 4.6 29.3 1.0 CG C:GLU94 4.6 25.5 1.0 N C:PHE95 4.6 27.1 1.0 CA C:ASP97 4.7 36.5 1.0 CD A:LYS31 4.7 42.6 1.0 CG A:LYS31 4.8 41.9 1.0 CE1 A:PHE95 4.8 31.7 1.0 CD2 A:LEU27 4.9 37.0 1.0 CD2 A:TYR99 4.9 31.6 1.0 OD2 C:ASP97 4.9 46.5 1.0 CG C:ASP97 5.0 43.4 1.0

Sodium binding site 2 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia 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 Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:55.3 occ:1.00 OE1 A:GLU47 1.9 32.2 0.5 NE2 E:GLN32 2.8 53.6 1.0 CD A:GLU47 3.0 29.9 0.5 ND2 A:ASN50 3.1 29.8 1.0 O A:HOH353 3.2 26.6 1.0 CB A:ASN50 3.4 22.7 1.0 CG E:GLN28 3.5 52.4 1.0 OE2 A:GLU47 3.6 38.7 0.5 NE2 E:GLN28 3.7 56.1 1.0 CG A:ASN50 3.8 26.7 1.0 CD E:GLN32 3.9 58.8 1.0 O A:GLU47 4.0 27.7 1.0 CA A:GLU47 4.0 24.9 0.5 CA A:GLU47 4.0 24.8 0.5 CD E:GLN28 4.1 59.4 1.0 CG A:GLU47 4.1 25.8 0.5 CB A:GLU47 4.2 26.6 0.5 CG A:GLU47 4.2 25.5 0.5 CB A:GLU47 4.3 26.4 0.5 O E:HOH407 4.4 57.5 1.0 C A:GLU47 4.5 25.6 1.0 OE1 E:GLN32 4.6 61.9 1.0 OE2 A:GLU51 4.7 28.2 1.0 CA A:ASN50 4.8 24.8 1.0 CB E:GLN28 4.9 40.8 1.0 CG E:GLN32 4.9 54.9 1.0 OD1 A:ASN50 5.0 26.1 1.0

Sodium binding site 3 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


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 Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:60.3 occ:1.00 OE2 A:GLU63 2.3 40.1 1.0 CD A:GLU63 3.0 44.2 1.0 N A:THR69 3.1 46.1 1.0 CG A:GLU63 3.2 37.8 1.0 CD A:LYS68 3.3 64.2 1.0 NZ A:LYS68 3.3 60.2 1.0 CA A:LYS68 3.7 49.8 1.0 CE A:LYS68 3.7 65.1 1.0 C A:LYS68 3.9 48.1 1.0 O A:HOH378 4.0 40.6 1.0 CB A:THR69 4.0 44.4 1.0 CA A:THR69 4.0 44.3 1.0 O A:THR69 4.1 41.8 1.0 OE1 A:GLU63 4.2 38.2 1.0 CB A:GLU63 4.2 32.3 1.0 CG A:LYS68 4.2 56.1 1.0 CB B:SER72 4.3 23.8 1.0 CA B:SER72 4.3 24.5 1.0 O A:GLU67 4.4 49.0 1.0 CB A:LYS68 4.4 50.6 1.0 N B:VAL73 4.5 23.4 1.0 C A:THR69 4.6 43.2 1.0 OG1 A:THR69 4.7 45.0 1.0 N A:LYS68 4.7 49.7 1.0 CA A:GLU63 4.8 33.4 1.0 O B:ILE71 4.8 29.1 1.0 O A:HOH134 4.9 42.0 1.0 C A:GLU67 5.0 47.9 1.0

Sodium binding site 4 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


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 Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na108 b:35.1 occ:1.00 OH B:TYR99 2.3 28.5 1.0 OE1 A:GLU94 2.7 34.2 1.0 O A:GLU94 2.7 27.5 1.0 CE B:LYS31 3.3 27.2 1.0 CZ B:TYR99 3.4 32.6 1.0 C A:GLU94 3.5 26.4 1.0 CA A:GLU94 3.6 25.9 1.0 CE2 B:TYR99 3.6 27.8 1.0 CB A:GLU94 3.7 25.9 1.0 CD A:GLU94 3.8 36.1 1.0 NZ B:LYS31 3.8 26.6 1.0 CB A:ASP97 3.8 33.9 1.0 N A:LEU98 3.9 32.7 1.0 CD2 B:LEU27 3.9 24.8 1.0 CD1 B:PHE95 4.2 32.5 1.0 CB A:LEU98 4.2 32.6 1.0 CG A:GLU94 4.3 27.1 1.0 CE1 B:PHE95 4.4 27.6 1.0 CA A:LEU98 4.4 32.6 1.0 C A:ASP97 4.5 33.8 1.0 O B:HOH478 4.5 79.9 1.0 CD B:LYS31 4.6 35.8 1.0 CE1 B:TYR99 4.6 35.6 1.0 CA A:ASP97 4.6 33.0 1.0 N A:PHE95 4.8 25.8 1.0 OE2 A:GLU94 4.8 35.3 1.0 CG B:LYS31 4.9 36.8 1.0 N A:GLU94 4.9 24.9 1.0 CG B:PHE95 4.9 26.0 1.0 N A:ASP97 5.0 30.0 1.0 CD2 B:TYR99 5.0 29.5 1.0 CG A:ASP97 5.0 44.3 1.0

Sodium binding site 5 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


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 Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ C:Na107 b:35.1 occ:1.00 OH C:TYR99 2.3 30.9 1.0 O B:GLU94 2.8 30.7 1.0 OE1 B:GLU94 2.9 30.6 1.0 CZ C:TYR99 3.3 32.2 1.0 CE C:LYS31 3.4 38.5 1.0 CE2 C:TYR99 3.4 30.1 1.0 CB B:GLU94 3.5 26.8 1.0 C B:GLU94 3.5 27.7 1.0 CA B:GLU94 3.6 27.4 1.0 NZ C:LYS31 3.7 33.2 1.0 CD2 C:LEU27 3.9 32.2 1.0 CD B:GLU94 3.9 35.1 1.0 CB B:ASP97 4.1 38.0 1.0 N B:LEU98 4.1 34.8 1.0 CD1 C:PHE95 4.2 29.1 1.0 CG B:GLU94 4.2 29.1 1.0 CB B:LEU98 4.3 33.2 1.0 CE1 C:PHE95 4.3 36.0 1.0 CA B:LEU98 4.6 35.3 1.0 CE1 C:TYR99 4.6 32.6 1.0 OD2 B:ASP97 4.6 48.0 1.0 CD C:LYS31 4.7 38.4 1.0 C B:ASP97 4.7 37.1 1.0 N B:PHE95 4.8 28.2 1.0 CD2 C:TYR99 4.8 34.2 1.0 CA B:ASP97 4.9 36.7 1.0 CG B:ASP97 4.9 45.2 1.0 CG C:PHE95 4.9 26.5 1.0 CD1 C:LEU27 4.9 31.3 1.0 CD1 B:LEU98 5.0 39.5 1.0 N B:GLU94 5.0 27.2 1.0

Sodium binding site 6 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


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 Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ D:Na107 b:55.0 occ:1.00 OE1 D:GLU94 2.5 49.2 1.0 OH E:TYR99 2.7 47.5 1.0 O D:GLU94 3.0 33.0 1.0 CB D:GLU94 3.2 33.1 1.0 CA D:GLU94 3.4 31.6 1.0 CE2 E:TYR99 3.4 40.1 1.0 CD D:GLU94 3.5 40.6 1.0 CZ E:TYR99 3.5 46.9 1.0 C D:GLU94 3.5 29.8 1.0 CE E:LYS31 3.7 42.1 1.0 CG D:GLU94 3.9 32.8 1.0 NZ E:LYS31 4.0 43.9 1.0 CB D:ASP97 4.2 37.6 1.0 CD1 E:PHE95 4.3 30.8 1.0 CG D:LEU98 4.4 33.3 1.0 OE2 D:GLU94 4.5 44.9 1.0 CD1 D:LEU98 4.6 36.9 1.0 CD2 E:TYR99 4.7 43.8 1.0 N D:PHE95 4.7 29.0 1.0 OD2 D:ASP97 4.7 45.1 1.0 CE1 E:PHE95 4.8 30.4 1.0 N D:GLU94 4.8 30.9 1.0 CG E:PHE95 4.8 29.4 1.0 CE1 E:TYR99 4.9 47.1 1.0 N D:LEU98 4.9 33.0 1.0

Sodium binding site 7 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


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 Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ D:Na108 b:53.9 occ:1.00 OE2 D:GLU51 2.1 43.3 1.0 O B:HOH521 2.9 37.3 1.0 CD D:GLU51 3.0 41.4 1.0 CZ B:PHE29 3.2 44.6 1.0 OE1 D:GLU51 3.3 45.7 1.0 CE2 B:PHE29 3.5 40.4 1.0 O B:HOH523 4.3 37.8 1.0 CG D:GLU51 4.4 32.8 1.0 CE1 B:PHE29 4.5 40.8 1.0 O B:HOH522 4.6 43.4 1.0 OE1 B:GLU25 4.8 43.6 1.0 CD B:GLU25 4.8 39.3 1.0 CD2 B:PHE29 4.8 38.5 1.0 OE2 B:GLU25 4.9 36.0 1.0

Sodium binding site 8 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


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 Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ F:Na107 b:48.2 occ:1.00 O F:GLU51 2.3 30.0 1.0 C F:GLU51 3.0 30.6 1.0 OE1 F:GLU51 3.0 33.6 1.0 CE2 F:PHE55 3.1 43.3 1.0 CA F:GLU51 3.2 32.0 1.0 CZ F:PHE55 3.2 46.2 1.0 CB F:GLU51 3.6 30.5 1.0 CD2 F:PHE55 3.8 41.3 1.0 CE1 F:PHE55 3.9 50.5 1.0 CD F:GLU51 4.1 37.9 1.0 CB F:HIS54 4.1 39.0 1.0 N F:ALA52 4.3 30.9 1.0 CG F:PHE55 4.4 41.4 1.0 CG F:GLU51 4.4 30.0 1.0 CD1 F:PHE55 4.5 45.4 1.0 N F:GLU51 4.5 33.3 1.0 CD2 F:HIS54 4.5 45.7 1.0 CG F:HIS54 4.7 42.9 1.0 O F:ASN50 4.7 32.7 1.0 N F:PHE55 4.9 36.4 1.0 CA F:ALA52 4.9 32.3 1.0

Sodium binding site 9 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


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 Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ F:Na108 b:46.8 occ:1.00 OH D:TYR99 2.5 36.9 1.0 OE1 F:GLU94 2.7 34.8 1.0 O F:GLU94 2.7 34.4 1.0 C F:GLU94 3.4 31.5 1.0 CZ D:TYR99 3.4 34.8 1.0 CA F:GLU94 3.5 29.8 1.0 CE D:LYS31 3.5 37.9 1.0 CE2 D:TYR99 3.5 31.4 1.0 CB F:GLU94 3.5 33.3 1.0 CD F:GLU94 3.8 36.8 1.0 CB F:ASP97 3.8 40.8 1.0 NZ D:LYS31 4.1 44.8 1.0 N F:LEU98 4.2 38.6 1.0 CG F:GLU94 4.2 32.2 1.0 CG F:LEU98 4.2 36.3 1.0 CD1 F:LEU98 4.5 44.0 1.0 CD D:LYS31 4.5 41.3 1.0 CD1 D:PHE95 4.6 34.9 1.0 N F:PHE95 4.6 29.9 1.0 CB F:LEU98 4.6 38.2 1.0 C F:ASP97 4.6 39.0 1.0 CE1 D:TYR99 4.7 39.2 1.0 CA F:ASP97 4.7 39.1 1.0 CG D:LYS31 4.7 35.9 1.0 CD1 D:LEU27 4.8 36.7 1.0 CA F:LEU98 4.8 38.3 1.0 CE1 D:PHE95 4.8 33.6 1.0 OE2 F:GLU94 4.9 40.4 1.0 CD2 D:TYR99 4.9 31.4 1.0 N F:GLU94 4.9 29.3 1.0 OD2 F:ASP97 4.9 52.6 1.0 CG F:ASP97 4.9 47.5 1.0

Sodium binding site 10 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


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 Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ F:Na109 b:52.9 occ:1.00 OH F:TYR99 2.4 41.1 1.0 O E:GLU94 2.9 34.3 1.0 OE1 E:GLU94 3.0 39.8 1.0 CE F:LYS31 3.3 46.8 1.0 CZ F:TYR99 3.4 36.6 1.0 CB E:ASP97 3.5 48.7 1.0 CE2 F:TYR99 3.5 36.6 1.0 CA E:GLU94 3.6 33.2 1.0 C E:GLU94 3.6 32.9 1.0 CB E:GLU94 3.6 32.0 1.0 CD2 F:LEU27 3.9 43.0 1.0 NZ F:LYS31 3.9 49.7 1.0 N E:LEU98 4.0 44.9 1.0 CD E:GLU94 4.1 43.1 1.0 CG E:GLU94 4.4 35.6 1.0 CD1 F:PHE95 4.4 31.0 1.0 CB E:LEU98 4.4 45.5 1.0 CD F:LYS31 4.5 51.8 1.0 CA E:LEU98 4.5 46.3 1.0 CG E:ASP97 4.5 56.0 1.0 C E:ASP97 4.5 47.7 1.0 CE1 F:PHE95 4.6 36.6 1.0 CA E:ASP97 4.6 47.6 1.0 OD2 E:ASP97 4.6 62.6 1.0 CE1 F:TYR99 4.6 37.3 1.0 CG F:LYS31 4.8 48.5 1.0 N E:PHE95 4.9 32.5 1.0 CD1 E:LEU98 4.9 51.2 1.0 CD2 F:TYR99 4.9 34.9 1.0 N E:GLU94 5.0 33.1 1.0

S.M.Anderson, Z.Wawrzak, O.Onopriyenko, K.Kwon, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectiousdiseases (Csgid). Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis To Be Published.