Sodium in PDB 2ww2: Structure of the Family GH92 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482

The structure of Structure of the Family GH92 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482, PDB code: 2ww2 was solved by M.D.L.Suits, Y.Zhu, A.Thompson, 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)	34.99 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	154.990, 162.990, 114.860, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 18.7

The binding sites of Sodium atom in the Structure of the Family GH92 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482 (pdb code 2ww2). 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 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482, PDB code: 2ww2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Family GH92 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482


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 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na799 b:11.8 occ:1.00 O A:GLU126 2.3 10.4 1.0 O A:HIS123 2.3 8.7 1.0 O A:HOH2146 2.4 13.2 1.0 O A:HOH2152 2.4 7.9 1.0 O A:HOH2151 2.4 15.6 1.0 O A:HOH2782 2.5 16.2 1.0 C A:GLU126 3.4 9.8 1.0 C A:HIS123 3.5 9.0 1.0 O A:HOH2155 3.7 7.0 1.0 C5 A:MPD759 3.8 34.0 1.0 N A:GLU126 3.9 8.7 1.0 O4 A:MPD759 3.9 28.1 1.0 CA A:GLU126 4.0 9.3 1.0 CB A:GLU126 4.1 9.5 1.0 CA A:HIS123 4.4 9.6 1.0 CA A:GLN124 4.4 8.4 1.0 N A:GLN124 4.4 8.4 1.0 C A:GLN124 4.4 8.4 1.0 C4 A:MPD759 4.5 33.9 1.0 N A:LYS127 4.5 9.8 1.0 OE1 A:GLU126 4.5 11.5 1.0 CB A:HIS123 4.6 10.5 1.0 O A:GLN124 4.6 7.8 1.0 CG A:GLU126 4.8 8.8 1.0 CA A:LYS127 4.8 9.9 1.0 N A:GLN125 4.9 7.1 1.0

Sodium binding site 2 out of 4 in the Structure of the Family GH92 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482


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 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na800 b:13.5 occ:1.00 O A:ASP648 2.3 15.3 1.0 O A:SER40 2.3 21.6 1.0 O A:HOH2677 2.4 12.2 1.0 O A:GLY645 2.4 15.2 1.0 O A:TYR643 2.5 15.5 1.0 O A:HOH2680 2.5 15.8 1.0 C A:ASP648 3.5 16.3 1.0 C A:SER40 3.5 21.5 1.0 C A:GLY645 3.5 16.2 1.0 C A:TYR643 3.7 15.0 1.0 CB A:SER40 3.9 21.0 1.0 C A:CYS644 4.0 14.7 1.0 O A:CYS644 4.0 15.3 1.0 N A:ASP648 4.0 16.9 1.0 CA A:SER40 4.1 21.4 1.0 CA A:ASP648 4.2 16.6 1.0 N A:GLY645 4.2 14.8 1.0 O A:HOH2032 4.2 24.0 1.0 O A:HOH2030 4.3 25.2 1.0 CB A:ASP648 4.3 16.7 1.0 N A:ASP646 4.4 16.5 1.0 CB A:TYR643 4.4 14.4 1.0 C A:ASP646 4.4 17.7 1.0 ND2 A:ASN649 4.4 12.9 1.0 CA A:ASP646 4.4 17.6 1.0 CA A:GLY645 4.4 15.4 1.0 O A:ASP646 4.4 17.4 1.0 O A:HOH2678 4.5 26.4 1.0 OG A:SER40 4.5 21.9 1.0 N A:ASN649 4.5 15.5 1.0 N A:CYS644 4.5 14.8 1.0 CA A:CYS644 4.5 14.4 1.0 N A:THR41 4.6 21.6 1.0 CA A:TYR643 4.7 15.0 1.0 CA A:ASN649 4.7 15.9 1.0 CA A:THR41 4.8 22.3 1.0 N A:GLU647 4.9 17.6 1.0

Sodium binding site 3 out of 4 in the Structure of the Family GH92 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482


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 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na800 b:17.7 occ:1.00 O B:HOH2112 2.3 12.8 1.0 O B:HIS123 2.3 11.3 1.0 O B:GLU126 2.4 10.4 1.0 O B:HOH2106 2.4 19.8 1.0 O B:HOH2104 2.5 20.0 1.0 O B:HOH2114 2.6 22.6 1.0 C B:GLU126 3.5 10.6 1.0 C B:HIS123 3.5 11.4 1.0 O B:HOH2115 3.8 10.6 1.0 O B:HOH2063 3.8 18.3 1.0 N B:GLU126 4.0 10.3 1.0 CD B:LYS127 4.1 13.1 0.5 CA B:GLU126 4.1 10.3 1.0 CB B:GLU126 4.1 10.4 1.0 NZ B:LYS127 4.3 16.3 0.5 CA B:HIS123 4.4 11.9 1.0 N B:GLN124 4.4 10.8 1.0 CA B:GLN124 4.4 11.0 1.0 C B:GLN124 4.4 10.9 1.0 CE B:LYS127 4.4 12.8 0.5 OE1 B:GLU126 4.5 14.4 1.0 CB B:HIS123 4.6 12.3 1.0 N B:LYS127 4.6 10.6 1.0 O B:GLN124 4.6 10.6 1.0 CA B:LYS127 4.8 10.8 0.5 CA B:LYS127 4.8 10.7 0.5 N B:GLN125 4.8 10.0 1.0 CG B:GLU126 4.8 10.9 1.0 O B:HOH2035 4.9 42.1 1.0

Sodium binding site 4 out of 4 in the Structure of the Family GH92 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482


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 Inverting Mannosidase BT2199 From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na800 b:20.1 occ:1.00 O C:GLU126 2.3 13.0 1.0 O C:HIS123 2.4 11.3 1.0 O C:HOH2124 2.4 13.2 1.0 O C:HOH2119 2.4 17.0 1.0 O C:HOH2115 2.5 24.1 1.0 O C:HOH2125 2.5 22.1 1.0 C C:GLU126 3.5 12.9 1.0 C C:HIS123 3.5 12.4 1.0 O C:HOH2128 3.8 14.3 1.0 O C:HOH2126 3.9 33.2 1.0 N C:GLU126 4.0 11.2 1.0 O C:HOH2064 4.0 23.7 1.0 CA C:GLU126 4.1 12.1 1.0 CB C:GLU126 4.2 11.7 1.0 CA C:HIS123 4.4 13.1 1.0 C C:GLN124 4.4 10.9 1.0 CA C:GLN124 4.4 10.8 1.0 N C:GLN124 4.4 11.4 1.0 OE1 C:GLU126 4.5 16.0 1.0 O C:GLN124 4.5 10.5 1.0 CB C:HIS123 4.5 14.2 1.0 N C:LYS127 4.6 12.1 1.0 CG C:GLU126 4.8 13.3 1.0 CA C:LYS127 4.9 13.0 1.0 N C:GLN125 4.9 10.1 1.0

Y.Zhu, M.D.L.Suits, A.Thompson, S.Chavan, Z.Dinev, C.Dumon, N.Smith, K.W.Moremen, Y.Xiang, A.Siriwardena, S.J.Williams, H.J.Gilbert, G.J.Davies. Mechanistic Insights Into A CA2+-Dependent Family of A-Mannosidases in A Human Gut Symbiont. Nat.Chem.Biol. V. 6 125 2010.
ISSN: ISSN 1552-4450
PubMed: 20081828
DOI: 10.1038/NCHEMBIO.278