Potassium in PDB 7zgm: Plant N-Glycan Specific Alpha-1,3-Mannosidase

The structure of Plant N-Glycan Specific Alpha-1,3-Mannosidase, PDB code: 7zgm was solved by A.Basle, L.Crouch, D.Bolam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.29 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.941, 84.335, 132.581, 90, 90, 90
R / Rfree (%)	13.3 / 17.3

The structure of Plant N-Glycan Specific Alpha-1,3-Mannosidase also contains other interesting chemical elements:

Sodium	(Na)	13 atoms
Calcium	(Ca)	1 atom

The binding sites of Potassium atom in the Plant N-Glycan Specific Alpha-1,3-Mannosidase (pdb code 7zgm). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Plant N-Glycan Specific Alpha-1,3-Mannosidase, PDB code: 7zgm:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:K801 b:23.6 occ:1.00 O A:HOH1326 2.5 71.1 1.0 O A:HOH1241 2.7 22.4 1.0 OD1 A:ASP99 2.7 20.2 1.0 O A:LEU97 2.7 18.0 1.0 OE1 A:GLN210 2.8 27.5 1.0 O A:HOH1188 3.0 24.2 1.0 HA A:LEU97 3.4 15.7 1.0 OD1 A:ASN204 3.4 44.5 1.0 ND2 A:ASN204 3.5 43.7 1.0 CG A:ASP99 3.6 18.5 1.0 HD2 A:PRO174 3.6 17.1 1.0 CD A:GLN210 3.6 21.6 1.0 CG A:ASN204 3.6 34.8 1.0 C A:LEU97 3.6 16.4 1.0 NA A:NA808 3.6 26.4 1.0 HD22 A:ASN204 3.6 41.5 1.0 HD21 A:ASN204 3.6 40.7 1.0 OD2 A:ASP99 3.8 17.9 1.0 HE22 A:GLN210 3.9 18.7 1.0 NE2 A:GLN210 3.9 18.2 1.0 CA A:LEU97 4.0 15.5 1.0 O A:HOH1185 4.0 25.9 1.0 HD21 A:LEU97 4.3 20.1 1.0 HA3 A:GLY173 4.4 16.1 1.0 CD A:PRO174 4.5 17.1 1.0 HE21 A:GLN210 4.5 18.7 1.0 HB3 A:LEU97 4.5 16.4 1.0 HA A:ASP99 4.5 15.1 1.0 HD3 A:PRO174 4.6 16.8 1.0 HE2 A:TYR212 4.6 22.5 1.0 HB2 A:ASN204 4.7 37.5 1.0 HB3 A:GLN210 4.7 20.1 1.0 O A:ASP96 4.8 17.6 1.0 N A:GLY98 4.8 16.6 1.0 CB A:ASN204 4.8 39.7 1.0 HG2 A:PRO174 4.8 18.0 1.0 C A:GLY98 4.8 17.5 1.0 CB A:ASP99 4.9 17.4 1.0 CB A:LEU97 4.9 16.0 1.0 CG A:GLN210 4.9 20.9 1.0 O A:HOH904 4.9 39.6 1.0 N A:ASP99 4.9 15.9 1.0 HA2 A:GLY173 4.9 16.8 1.0 O A:GLY98 5.0 17.9 1.0 O A:HOH1120 5.0 35.0 1.0

Potassium binding site 2 out of 3 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:K802 b:20.2 occ:1.00 O A:ARG71 2.7 16.4 1.0 O A:HOH1468 2.7 24.4 1.0 O A:HOH1217 2.7 24.5 1.0 O A:THR175 2.7 16.7 1.0 O A:HOH1412 2.9 18.7 1.0 O A:HOH1462 2.9 27.1 1.0 HE1 A:TRP70 3.3 18.1 1.0 H A:THR175 3.4 15.8 1.0 NE1 A:TRP70 3.6 18.3 1.0 O A:TYR72 3.7 16.7 1.0 C A:ARG71 3.9 16.1 1.0 C A:THR175 3.9 17.1 1.0 O A:HOH1099 3.9 20.9 1.0 C A:TYR72 4.0 16.4 1.0 HA A:TRP176 4.0 17.2 1.0 N A:THR175 4.0 15.2 1.0 HA A:PRO174 4.1 16.4 1.0 HB3 A:ARG71 4.2 15.8 1.0 O A:HOH1275 4.2 25.2 1.0 CD1 A:TRP70 4.2 19.9 1.0 CE2 A:TRP70 4.3 17.3 1.0 HA A:CYS73 4.4 15.1 1.0 HD1 A:TRP70 4.4 19.3 1.0 HZ2 A:TRP70 4.4 16.9 1.0 HA A:TYR72 4.4 16.7 1.0 N A:CYS73 4.4 14.8 1.0 O A:HOH1350 4.5 25.0 1.0 H A:ARG71 4.6 17.6 1.0 CA A:TYR72 4.6 16.9 1.0 CZ2 A:TRP70 4.6 17.2 1.0 CA A:THR175 4.6 16.3 1.0 O A:HOH941 4.6 25.2 1.0 N A:TYR72 4.7 16.0 1.0 O A:HOH1503 4.7 27.3 1.0 CA A:ARG71 4.8 17.4 1.0 N A:TRP176 4.8 17.7 1.0 CA A:TRP176 4.8 17.1 1.0 CA A:CYS73 4.8 14.9 1.0 N A:ARG71 4.9 17.6 1.0 CA A:PRO174 4.9 16.6 1.0 H A:CYS73 4.9 14.8 1.0 C A:PRO174 4.9 16.6 1.0 CB A:ARG71 4.9 15.9 1.0 O A:SER74 4.9 16.9 1.0 HG2 A:ARG71 4.9 15.5 1.0

Potassium binding site 3 out of 3 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:K803 b:26.7 occ:1.00 O A:LYS122 2.7 22.2 1.0 O A:GLU125 2.8 17.0 1.0 O A:HOH1138 2.9 21.8 1.0 O A:HOH1373 2.9 44.7 1.0 HB3 A:GLU125 3.6 15.7 1.0 C A:GLU125 3.8 15.2 1.0 C A:LYS122 3.8 21.6 1.0 H A:GLU125 3.9 16.5 1.0 HB3 A:LYS122 4.1 25.7 1.0 HA A:LYS123 4.2 21.0 1.0 O A:LYS123 4.3 28.4 1.0 HA A:ALA126 4.3 14.1 1.0 N A:GLU125 4.4 15.4 1.0 CB A:GLU125 4.4 16.0 1.0 O A:HOH1249 4.4 40.5 1.0 CA A:GLU125 4.4 15.0 1.0 C A:LYS123 4.5 20.7 1.0 HD3 A:LYS122 4.5 26.5 1.0 O A:HOH1272 4.5 24.2 1.0 HA A:LYS122 4.5 21.8 1.0 CA A:LYS123 4.7 21.2 1.0 CA A:LYS122 4.7 21.2 1.0 N A:LYS123 4.7 20.7 1.0 N A:ALA126 4.9 13.8 1.0 CB A:LYS122 4.9 26.3 1.0 OE1 A:GLU125 4.9 15.6 1.0 HD2 A:LYS122 4.9 26.1 1.0 HG2 A:GLU125 4.9 14.6 1.0 O A:HOH1443 5.0 28.7 1.0 HB2 A:ALA126 5.0 16.2 1.0

L.I.Crouch, P.A.Urbanowicz, A.Basle, Z.P.Cai, L.Liu, J.Voglmeir, J.M.Melo Diaz, S.T.Benedict, D.I.R.Spencer, D.N.Bolam. Plant N -Glycan Breakdown By Human Gut Bacteroides. Proc.Natl.Acad.Sci.Usa V. 119 68119 2022.
ISSN: ESSN 1091-6490
PubMed: 36122227
DOI: 10.1073/PNAS.2208168119