Calcium in PDB 2ri8: Penicillium Citrinum Alpha-1,2-Mannosidase Complex with Glycerol

All present enzymatic activity of Penicillium Citrinum Alpha-1,2-Mannosidase Complex with Glycerol:
3.2.1.113;

The structure of Penicillium Citrinum Alpha-1,2-Mannosidase Complex with Glycerol, PDB code: 2ri8 was solved by Y.D.Lobsanov, T.Yoshida, T.Desmet, W.Nerinckx, P.Yip, M.Claeyssens, A.Herscovics, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.32 / 2.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.487, 110.997, 86.235, 90.00, 99.17, 90.00
R / Rfree (%)	20.6 / 27.4

The binding sites of Calcium atom in the Penicillium Citrinum Alpha-1,2-Mannosidase Complex with Glycerol (pdb code 2ri8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Penicillium Citrinum Alpha-1,2-Mannosidase Complex with Glycerol, PDB code: 2ri8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Penicillium Citrinum Alpha-1,2-Mannosidase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Penicillium Citrinum Alpha-1,2-Mannosidase Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1550 b:12.4 occ:1.00 O A:THR1501 2.5 11.6 1.0 O A:HOH158 2.6 12.1 1.0 O A:HOH159 2.6 15.9 1.0 O1 A:GOL1901 2.6 10.8 1.0 O2 A:GOL1901 2.6 11.4 1.0 OG1 A:THR1501 2.6 16.6 1.0 O A:HOH161 2.7 12.2 1.0 O A:HOH162 2.8 16.4 1.0 C1 A:GOL1901 3.4 12.8 1.0 C2 A:GOL1901 3.5 11.6 1.0 C A:THR1501 3.5 12.7 1.0 CB A:THR1501 3.7 14.9 1.0 CA A:THR1501 3.9 12.4 1.0 OE2 A:GLU1472 4.1 12.5 1.0 O A:HOH175 4.1 5.8 1.0 CG2 A:THR1501 4.3 12.6 1.0 OE1 A:GLU1271 4.3 16.6 1.0 OE1 A:GLU1472 4.4 15.9 1.0 OE1 A:GLU1412 4.4 5.2 1.0 O A:HOH163 4.6 8.4 1.0 OE2 A:GLU1271 4.6 11.6 1.0 O A:HOH33 4.6 13.6 1.0 CD A:GLU1472 4.7 13.3 1.0 N A:GLU1502 4.7 9.8 1.0 O A:HOH496 4.7 45.8 1.0 OE1 A:GLU1409 4.8 10.8 1.0 C3 A:GOL1901 4.8 11.8 1.0 CD A:GLU1271 4.9 14.9 1.0 CG A:GLU1409 5.0 9.0 1.0

Calcium binding site 2 out of 2 in the Penicillium Citrinum Alpha-1,2-Mannosidase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Penicillium Citrinum Alpha-1,2-Mannosidase Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1551 b:15.0 occ:1.00 O B:THR2501 2.5 12.7 1.0 O2 B:GOL2901 2.6 13.4 1.0 O B:HOH166 2.6 18.4 1.0 O B:HOH209 2.7 8.8 1.0 O1 B:GOL2901 2.7 13.4 1.0 O B:HOH167 2.7 23.0 1.0 OG1 B:THR2501 2.7 13.3 1.0 O B:HOH165 2.8 12.8 1.0 C2 B:GOL2901 3.5 15.5 1.0 C1 B:GOL2901 3.5 14.4 1.0 C B:THR2501 3.5 16.0 1.0 CB B:THR2501 3.8 14.7 1.0 CA B:THR2501 3.9 16.1 1.0 CG2 B:THR2501 4.3 15.6 1.0 OE1 B:GLU2271 4.3 20.6 1.0 OE2 B:GLU2472 4.3 15.9 1.0 O B:HOH170 4.4 15.4 1.0 O B:HOH169 4.4 13.7 1.0 OE2 B:GLU2412 4.4 14.2 1.0 OE1 B:GLU2472 4.5 16.6 1.0 OE2 B:GLU2271 4.6 19.9 1.0 O B:HOH205 4.7 26.7 1.0 N B:GLU2502 4.8 15.6 1.0 OE1 B:GLU2409 4.9 15.1 1.0 CD B:GLU2472 4.9 13.0 1.0 C3 B:GOL2901 4.9 15.1 1.0 CD B:GLU2271 4.9 20.1 1.0 CG B:GLU2409 5.0 12.7 1.0

Y.D.Lobsanov, T.Yoshida, T.Desmet, W.Nerinckx, P.Yip, M.Claeyssens, A.Herscovics, P.L.Howell. Modulation of Activity By ARG407: Structure of A Fungal Alpha-1,2-Mannosidase in Complex with A Substrate Analogue. Acta Crystallogr.,Sect.D V. 64 227 2008.
ISSN: ISSN 0907-4449
PubMed: 18323617
DOI: 10.1107/S0907444907065572