Calcium 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
Potassium	(K)	3 atoms

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the Plant N-Glycan Specific Alpha-1,3-Mannosidase, PDB code: 7zgm:

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca817 b:27.0 occ:1.00 O A:HOH1397 2.2 33.1 1.0 OD2 A:ASP638 2.4 28.2 1.0 OE1 A:GLU596 2.4 19.5 1.0 O A:GLY594 2.4 24.0 1.0 O A:HOH1018 2.7 28.7 1.0 O A:HOH953 3.1 23.8 1.0 O A:HOH1150 3.3 16.6 1.0 CG A:ASP638 3.3 25.1 1.0 HA A:ASN595 3.4 18.3 1.0 CD A:GLU596 3.4 17.0 1.0 OD1 A:ASP638 3.7 33.3 1.0 C A:GLY594 3.7 20.1 1.0 OE2 A:GLU596 3.7 19.1 1.0 H A:GLU596 3.8 15.7 1.0 HZ3 A:TRP351 3.8 15.8 1.0 O A:HOH1432 3.9 31.9 1.0 O A:HOH1205 3.9 36.3 1.0 O A:HOH1421 4.0 37.5 1.0 CA A:ASN595 4.2 17.8 1.0 OD1 A:ASP352 4.4 18.3 1.0 N A:ASN595 4.4 18.3 1.0 O A:HOH901 4.5 40.8 1.0 N A:GLU596 4.5 15.8 1.0 HB2 A:ASN636 4.6 16.3 1.0 CB A:ASP638 4.7 17.7 1.0 CZ3 A:TRP351 4.7 15.5 1.0 OD1 A:ASN595 4.7 23.5 1.0 HB3 A:ASP638 4.7 17.8 1.0 CA A:GLY594 4.8 18.9 1.0 HA2 A:GLY594 4.8 18.9 1.0 HH2 A:TRP351 4.8 16.4 1.0 CG A:GLU596 4.8 16.6 1.0 HA3 A:GLY594 4.9 19.4 1.0 HB2 A:ASP638 4.9 17.5 1.0 HB2 A:GLU596 4.9 16.8 1.0 C A:ASN595 4.9 15.5 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