Calcium in PDB 2ri9: Penicillium Citrinum Alpha-1,2-Mannosidase in Complex with A Substrate Analog

All present enzymatic activity of Penicillium Citrinum Alpha-1,2-Mannosidase in Complex with A Substrate Analog:
3.2.1.113;

The structure of Penicillium Citrinum Alpha-1,2-Mannosidase in Complex with A Substrate Analog, PDB code: 2ri9 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)	49.83 / 1.95
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 (%)	21 / 26

The binding sites of Calcium atom in the Penicillium Citrinum Alpha-1,2-Mannosidase in Complex with A Substrate Analog (pdb code 2ri9). 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 in Complex with A Substrate Analog, PDB code: 2ri9:
Jump to Calcium binding site number: 1; 2;

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


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 in Complex with A Substrate Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1550 b:8.5 occ:1.00 O A:HOH155 2.5 8.1 1.0 O A:HOH154 2.5 6.5 1.0 O A:THR1501 2.5 6.2 1.0 O A:HOH157 2.6 6.4 1.0 O3 A:LDY1900 2.6 8.5 0.8 OG1 A:THR1501 2.6 7.8 1.0 O2 A:LDY1900 2.6 4.8 0.8 O A:HOH156 2.6 8.6 1.0 O2 A:GOL1903 2.7 7.4 0.2 O1 A:GOL1903 2.8 6.1 0.2 C3 A:LDY1900 3.5 10.2 0.8 C A:THR1501 3.5 9.4 1.0 C2 A:LDY1900 3.6 11.3 0.8 C1 A:GOL1903 3.6 7.2 0.2 C2 A:GOL1903 3.7 7.6 0.2 CB A:THR1501 3.7 7.9 1.0 CA A:THR1501 3.9 7.2 1.0 O A:HOH165 4.2 8.0 1.0 OE1 A:GLU1271 4.2 10.5 1.0 OE2 A:GLU1472 4.3 9.1 1.0 CG2 A:THR1501 4.3 1.5 1.0 C1 A:LDY1900 4.3 13.6 0.8 OE2 A:GLU1412 4.4 4.7 1.0 OE1 A:GLU1472 4.5 9.9 1.0 O A:HOH33 4.5 10.7 1.0 O A:HOH158 4.6 12.0 1.0 OE2 A:GLU1271 4.7 6.8 1.0 OE1 A:GLU1409 4.7 8.3 1.0 N A:GLU1502 4.7 8.9 1.0 CD A:GLU1472 4.8 11.1 1.0 C4 A:LDY1900 4.8 12.2 0.8 CD A:GLU1271 4.9 8.3 1.0 C3 A:GOL1903 5.0 8.0 0.2 CG A:GLU1409 5.0 6.8 1.0

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


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 in Complex with A Substrate Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2551 b:15.6 occ:1.00 O B:HOH160 2.6 9.6 1.0 O B:THR2501 2.6 14.1 1.0 O B:HOH161 2.6 20.9 1.0 O3 B:LDY2900 2.7 15.1 0.8 O2 B:LDY2900 2.7 17.6 0.8 OG1 B:THR2501 2.7 16.9 1.0 O B:HOH159 2.7 15.9 1.0 O2 B:GOL2903 2.8 11.6 0.2 O B:HOH187 2.8 20.0 1.0 O1 B:GOL2903 2.8 12.4 0.2 C3 B:LDY2900 3.6 16.8 0.8 C B:THR2501 3.6 16.1 1.0 C2 B:LDY2900 3.6 18.9 0.8 C1 B:GOL2903 3.6 11.9 0.2 C2 B:GOL2903 3.7 11.2 0.2 CB B:THR2501 3.7 16.2 1.0 CA B:THR2501 4.0 16.3 1.0 CG2 B:THR2501 4.2 15.7 1.0 OE1 B:GLU2271 4.3 13.5 1.0 C1 B:LDY2900 4.3 20.8 0.8 O B:HOH162 4.3 19.7 1.0 OE2 B:GLU2472 4.3 18.5 1.0 O B:HOH163 4.4 18.8 1.0 OE2 B:GLU2412 4.4 16.7 1.0 O B:HOH185 4.5 17.9 1.0 OE1 B:GLU2472 4.5 17.6 1.0 OE2 B:GLU2271 4.6 13.8 1.0 OE1 B:GLU2409 4.7 15.9 1.0 N B:GLU2502 4.8 15.8 1.0 CD B:GLU2271 4.9 14.6 1.0 CD B:GLU2472 4.9 17.7 1.0 C4 B:LDY2900 4.9 19.4 0.8

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