Sodium in PDB 6f92: Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)

The structure of Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani), PDB code: 6f92 was solved by A.J.Thompson, R.J.Spears, Y.Zhu, M.D.L.Suits, S.J.Williams, H.J.Gilbert, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.73 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.507, 186.904, 95.050, 90.00, 91.74, 90.00
R / Rfree (%)	17.7 / 20.8

The structure of Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) (pdb code 6f92). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani), PDB code: 6f92:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:19.9 occ:1.00 O A:PRO96 2.2 19.9 1.0 O A:HOH1449 2.3 23.6 1.0 O A:ARG101 2.3 17.2 1.0 O A:HOH1059 2.3 20.8 1.0 O A:GLY99 2.3 17.7 1.0 C A:PRO96 3.1 24.5 1.0 C A:GLY99 3.4 18.5 1.0 C A:ARG101 3.4 17.0 1.0 CA A:ASP97 3.7 27.3 1.0 N A:ARG101 3.8 15.5 1.0 N A:ASP97 3.8 25.4 1.0 C A:TYR100 3.9 15.6 1.0 CA A:ARG101 4.0 16.3 1.0 C A:ASP97 4.1 26.4 1.0 CA A:PRO96 4.1 24.1 1.0 O A:HOH977 4.2 44.6 1.0 N A:TYR100 4.2 17.0 1.0 CB A:PRO96 4.2 24.5 1.0 N A:GLY99 4.2 19.8 1.0 CA A:TYR100 4.2 16.0 1.0 O A:ASP97 4.3 25.9 1.0 CA A:GLY99 4.4 19.3 1.0 CB A:ARG101 4.4 15.9 1.0 O A:TYR100 4.4 15.4 1.0 OD1 A:ASP97 4.5 32.9 1.0 N A:SER102 4.5 16.7 1.0 OD2 A:ASP122 4.6 19.1 1.0 OH A:TYR123 4.8 19.4 1.0 CA A:SER102 4.9 17.2 1.0 N A:GLN98 4.9 23.9 1.0 CB A:ASP97 4.9 29.4 1.0

Sodium binding site 2 out of 4 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na801 b:23.3 occ:1.00 O B:GLY99 2.2 20.5 1.0 O B:HOH1351 2.2 27.3 1.0 O B:ARG101 2.2 23.0 1.0 O B:PRO96 2.3 24.9 1.0 O B:HOH1038 2.3 22.9 1.0 C B:PRO96 3.2 25.7 1.0 C B:GLY99 3.3 20.0 1.0 C B:ARG101 3.4 21.6 1.0 CA B:ASP97 3.7 25.2 1.0 N B:ARG101 3.8 19.7 1.0 N B:ASP97 3.8 25.6 1.0 C B:TYR100 3.9 18.8 1.0 CA B:ARG101 4.1 19.4 1.0 N B:TYR100 4.1 19.4 1.0 C B:ASP97 4.1 25.6 1.0 CA B:TYR100 4.2 19.6 1.0 N B:GLY99 4.2 21.3 1.0 CA B:PRO96 4.2 23.2 1.0 O B:ASP97 4.3 24.6 1.0 CB B:PRO96 4.3 22.4 1.0 O B:TYR100 4.3 20.5 1.0 CA B:GLY99 4.3 20.2 1.0 CB B:ARG101 4.5 19.7 1.0 N B:SER102 4.5 21.3 1.0 OH B:TYR123 4.6 23.2 1.0 OD2 B:ASP122 4.6 23.0 1.0 OD1 B:ASP97 4.6 31.7 1.0 CA B:SER102 4.8 21.8 1.0 N B:GLN98 4.9 24.4 1.0

Sodium binding site 3 out of 4 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na801 b:32.1 occ:1.00 O C:ARG101 2.2 27.9 1.0 O C:HOH991 2.2 31.4 1.0 O C:GLY99 2.2 28.7 1.0 O C:PRO96 2.3 36.6 1.0 O C:HOH1191 2.3 34.7 1.0 C C:PRO96 3.2 37.8 1.0 C C:GLY99 3.4 28.9 1.0 C C:ARG101 3.4 27.5 1.0 CA C:ASP97 3.7 39.1 1.0 N C:ARG101 3.8 25.4 1.0 N C:ASP97 3.8 36.7 1.0 C C:TYR100 3.9 27.0 1.0 CA C:ARG101 4.1 26.5 1.0 C C:ASP97 4.1 38.1 1.0 N C:TYR100 4.2 27.7 1.0 CA C:TYR100 4.2 26.7 1.0 N C:GLY99 4.2 30.2 1.0 CA C:PRO96 4.2 38.3 1.0 O C:ASP97 4.3 36.5 1.0 CB C:PRO96 4.3 38.9 1.0 O C:TYR100 4.3 26.1 1.0 CA C:GLY99 4.4 29.8 1.0 CE C:LYS87 4.5 45.6 1.0 CB C:ARG101 4.5 25.0 1.0 N C:SER102 4.5 29.7 1.0 NZ C:LYS87 4.5 44.7 1.0 OD2 C:ASP122 4.6 33.0 1.0 OH C:TYR123 4.6 33.3 1.0 OD1 C:ASP97 4.6 46.6 1.0 CA C:SER102 4.8 33.1 1.0 N C:GLN98 4.9 37.1 1.0

Sodium binding site 4 out of 4 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na801 b:16.5 occ:1.00 O D:HOH1469 2.2 18.3 1.0 O D:PRO96 2.2 18.3 1.0 O D:HOH1114 2.3 19.0 1.0 O D:ARG101 2.3 14.2 1.0 O D:GLY99 2.3 15.7 1.0 C D:PRO96 3.2 19.8 1.0 C D:GLY99 3.4 14.9 1.0 C D:ARG101 3.4 13.4 1.0 CA D:ASP97 3.7 20.4 1.0 N D:ASP97 3.8 19.3 1.0 N D:ARG101 3.8 12.5 1.0 C D:TYR100 4.0 12.8 1.0 CA D:ARG101 4.1 12.8 1.0 C D:ASP97 4.2 19.6 1.0 CA D:PRO96 4.2 19.7 1.0 O D:HOH985 4.2 43.9 1.0 CB D:PRO96 4.2 19.9 1.0 N D:TYR100 4.2 13.9 1.0 N D:GLY99 4.2 17.1 1.0 CA D:TYR100 4.3 12.6 1.0 O D:ASP97 4.3 20.5 1.0 CA D:GLY99 4.4 16.4 1.0 CB D:ARG101 4.4 12.9 1.0 O D:TYR100 4.5 12.4 1.0 OD1 D:ASP97 4.5 23.3 1.0 N D:SER102 4.5 13.7 1.0 OD2 D:ASP122 4.5 14.9 1.0 NZ D:LYS87 4.6 30.3 1.0 CA D:SER102 4.8 14.0 1.0 OH D:TYR123 4.9 13.7 1.0 N D:GLN98 4.9 19.0 1.0 CB D:ASP97 5.0 21.3 1.0

A.J.Thompson, R.J.Spears, Y.Zhu, M.D.L.Suits, S.J.Williams, H.J.Gilbert, G.J.Davies. Bacteroides Thetaiotaomicron Generates Diverse Alpha-Mannosidase Activities Through Subtle Evolution of A Distal Substrate-Binding Motif. Acta Crystallogr D Struct V. 74 394 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29717710
DOI: 10.1107/S2059798318002942