Calcium in PDB 2i8u: Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp Product Complex

The structure of Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp Product Complex, PDB code: 2i8u 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)	38.84 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.588, 81.151, 97.982, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 16.4

The binding sites of Calcium atom in the Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp Product Complex (pdb code 2i8u). 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 Product Complex, PDB code: 2i8u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp Product 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 Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:7.2 occ:1.00 O A:GLY50 2.2 7.9 1.0 O2B A:GDP820 2.2 7.9 1.0 O2A A:GDP820 2.3 6.9 1.0 OE1 A:GLN123 2.3 8.8 1.0 OE2 A:GLU70 2.3 9.6 1.0 O A:HOH1049 2.3 9.0 1.0 CD A:GLU70 3.3 8.6 1.0 CD A:GLN123 3.3 10.3 1.0 C A:GLY50 3.5 6.4 1.0 PA A:GDP820 3.5 7.2 1.0 PB A:GDP820 3.5 7.6 1.0 OE1 A:GLU70 3.6 9.4 1.0 O3A A:GDP820 3.7 9.6 1.0 O A:HOH857 3.7 12.3 1.0 NE2 A:GLN123 3.7 11.5 1.0 O A:HOH1047 4.0 6.6 1.0 CA A:GLY51 4.1 6.0 1.0 O A:HOH1051 4.1 8.0 1.0 N A:GLY51 4.2 6.0 1.0 N A:GLY50 4.2 6.3 1.0 O3B A:GDP820 4.4 8.3 1.0 NH1 A:ARG37 4.5 7.7 1.0 C5' A:GDP820 4.5 9.1 1.0 CA A:GLY50 4.5 6.3 1.0 CG A:GLU70 4.5 7.8 1.0 O1B A:GDP820 4.5 10.4 1.0 O5' A:GDP820 4.5 9.2 1.0 O1A A:GDP820 4.6 8.1 1.0 CG A:GLN123 4.7 10.3 1.0 O A:HOH1048 4.8 7.4 1.0 CB A:GLN123 4.9 10.3 1.0

Calcium binding site 2 out of 2 in the Gdp-Mannose Mannosyl Hydrolase-Calcium-Gdp Product 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 Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:6.8 occ:1.00 O B:GLY50 2.2 8.0 1.0 O2A B:GDP800 2.3 6.8 1.0 O2B B:GDP800 2.3 7.4 1.0 OE2 B:GLU70 2.3 9.2 1.0 O B:HOH1039 2.3 7.6 1.0 OE1 B:GLN123 2.4 8.4 1.0 CD B:GLU70 3.2 8.5 1.0 CD B:GLN123 3.4 8.9 1.0 C B:GLY50 3.5 6.6 1.0 PA B:GDP800 3.5 6.9 1.0 PB B:GDP800 3.5 6.8 1.0 OE1 B:GLU70 3.6 9.2 1.0 O3A B:GDP800 3.7 9.4 1.0 O B:HOH1043 3.7 11.6 1.0 NE2 B:GLN123 3.8 10.1 1.0 O B:HOH1040 3.9 7.3 1.0 CA B:GLY51 4.0 6.1 1.0 O B:HOH817 4.0 7.1 1.0 N B:GLY51 4.2 6.1 1.0 N B:GLY50 4.3 6.6 1.0 O3B B:GDP800 4.4 7.5 1.0 NH1 B:ARG37 4.4 6.6 1.0 CG B:GLU70 4.5 8.2 1.0 C5' B:GDP800 4.5 8.3 1.0 CA B:GLY50 4.5 6.4 1.0 O5' B:GDP800 4.5 9.1 1.0 O1B B:GDP800 4.5 9.8 1.0 O1A B:GDP800 4.6 7.7 1.0 CG B:GLN123 4.7 8.5 1.0 O B:HOH1046 4.8 14.1 1.0 O B:HOH811 4.8 7.0 1.0 CB B:GLN123 4.9 8.6 1.0 O B:HOH1041 5.0 9.1 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