Calcium in PDB 2i8t: Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp-Mannose Complex

The structure of Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp-Mannose Complex, PDB code: 2i8t was solved by Y.Zou, C.Li, J.S.Brunzelle, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.41 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.636, 81.586, 98.300, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.4

The binding sites of Calcium atom in the Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp-Mannose Complex (pdb code 2i8t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp-Mannose Complex, PDB code: 2i8t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp-Mannose Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp-Mannose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:9.1 occ:1.00 O2A A:GDD820 2.3 8.0 1.0 O A:GLY50 2.3 7.1 1.0 O2B A:GDD820 2.4 9.9 1.0 O A:HOH965 2.4 9.2 1.0 OE1 A:GLN123 2.4 10.7 1.0 OE2 A:GLU70 2.4 9.6 1.0 CD A:GLU70 3.3 8.1 1.0 CD A:GLN123 3.5 12.8 1.0 PA A:GDD820 3.5 7.0 1.0 C A:GLY50 3.5 6.0 1.0 PB A:GDD820 3.5 9.5 1.0 OE1 A:GLU70 3.6 9.0 1.0 O3A A:GDD820 3.7 10.5 1.0 O A:HOH979 3.7 11.1 1.0 NE2 A:GLN123 3.9 13.3 1.0 O A:HOH953 4.0 10.1 1.0 C11 A:GDD820 4.0 11.7 1.0 O1B A:GDD820 4.1 12.2 1.0 CA A:GLY51 4.1 5.5 1.0 N A:GLY51 4.3 5.5 1.0 C5' A:GDD820 4.4 9.9 1.0 O5' A:GDD820 4.4 9.9 1.0 N A:GLY50 4.4 6.2 1.0 O A:HOH1071 4.4 20.1 1.0 NH1 A:ARG37 4.4 8.8 1.0 CG A:GLU70 4.5 7.4 1.0 O A:HOH1054 4.6 22.8 1.0 CA A:GLY50 4.6 6.0 1.0 O1A A:GDD820 4.7 8.7 1.0 CG A:GLN123 4.8 13.0 1.0 O A:HOH956 4.8 13.7 1.0 O51 A:GDD820 4.8 13.2 1.0 O3B A:GDD820 4.9 14.0 1.0

Calcium binding site 2 out of 2 in the Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp-Mannose Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp-Mannose Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:8.2 occ:1.00 O2A B:GDD800 2.2 6.7 1.0 O2B B:GDD800 2.2 9.7 1.0 O B:GLY50 2.3 7.5 1.0 O B:HOH805 2.3 7.9 1.0 OE2 B:GLU70 2.4 9.8 1.0 OE1 B:GLN123 2.4 8.8 1.0 CD B:GLU70 3.3 8.3 1.0 CD B:GLN123 3.4 9.9 1.0 C B:GLY50 3.5 6.2 1.0 PA B:GDD800 3.5 6.6 1.0 PB B:GDD800 3.5 8.1 1.0 OE1 B:GLU70 3.6 9.3 1.0 O B:HOH835 3.7 10.3 1.0 O3A B:GDD800 3.7 10.6 1.0 NE2 B:GLN123 3.9 11.4 1.0 O B:HOH821 3.9 7.5 1.0 C11 B:GDD800 4.0 14.0 1.0 CA B:GLY51 4.0 5.8 1.0 O1B B:GDD800 4.1 13.2 1.0 N B:GLY51 4.2 5.9 1.0 N B:GLY50 4.4 6.3 1.0 NH1 B:ARG37 4.4 6.0 1.0 O5' B:GDD800 4.4 9.5 1.0 C5' B:GDD800 4.5 8.1 1.0 O3B B:GDD800 4.5 11.5 1.0 CG B:GLU70 4.5 7.8 1.0 CA B:GLY50 4.6 6.2 1.0 O1A B:GDD800 4.6 8.6 1.0 CG B:GLN123 4.8 9.8 1.0 O B:HOH856 4.8 9.7 1.0 O51 B:GDD800 4.8 15.3 1.0 C21 B:GDD800 4.8 14.8 1.0 CB B:GLN123 5.0 9.9 1.0 O21 B:GDD800 5.0 15.5 1.0

Y.Zou, C.Li, J.S.Brunzelle, S.K.Nair. Molecular Basis For Substrate Selectivity and Specificity By An Lps Biosynthetic Enzyme Biochemistry V. 46 4294 2007.
ISSN: ISSN 0006-2960
PubMed: 17371001
DOI: 10.1021/BI061056U