Calcium in PDB 3bs6: 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc

The structure of 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc, PDB code: 3bs6 was solved by S.Ravaud, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.90 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.150, 55.640, 63.330, 90.00, 101.12, 90.00
R / Rfree (%)	17.8 / 21.3

The binding sites of Calcium atom in the 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc (pdb code 3bs6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc, PDB code: 3bs6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:12.0 occ:1.00 O A:HOH354 2.3 16.6 1.0 OE1 A:GLU231 2.4 20.0 1.0 O A:TYR230 2.4 10.2 1.0 O A:HOH343 2.4 17.2 1.0 CD A:GLU231 3.6 21.0 1.0 C A:TYR230 3.6 11.0 1.0 CA A:CA2 3.8 24.6 1.0 CA A:GLU231 4.0 13.4 1.0 CB A:GLU231 4.1 14.3 1.0 N A:GLU231 4.3 10.7 1.0 O A:GLU228 4.4 15.5 1.0 OE2 A:GLU231 4.4 23.3 1.0 CG A:GLU231 4.5 17.8 1.0 CA A:TYR230 4.7 9.6 1.0 OE1 A:GLU228 4.8 20.6 1.0 N A:TYR230 4.9 10.2 1.0

Calcium binding site 2 out of 5 in the 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:24.6 occ:1.00 O A:HOH485 2.5 33.4 1.0 OE2 A:GLU231 2.6 23.3 1.0 OE1 A:GLU231 2.8 20.0 1.0 CD A:GLU231 3.1 21.0 1.0 CA A:CA1 3.8 12.0 1.0 O A:HOH343 4.4 17.2 1.0 CG A:GLU231 4.6 17.8 1.0

Calcium binding site 3 out of 5 in the 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:22.3 occ:1.00 OE2 A:GLU228 2.5 22.8 1.0 OE1 A:GLU228 2.9 20.6 1.0 CD A:GLU228 3.0 22.6 1.0 CG A:GLU228 4.4 21.1 1.0 O A:HOH354 5.0 16.6 1.0

Calcium binding site 4 out of 5 in the 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4 b:26.1 occ:1.00 OD1 A:ASN125 2.3 16.8 1.0 O A:HOH476 2.5 34.0 1.0 CG A:ASN125 3.5 15.8 1.0 CA A:ASN125 4.3 17.4 1.0 CB A:ASN125 4.4 17.9 1.0 ND2 A:ASN125 4.4 14.9 1.0 O A:HOH421 4.5 23.4 1.0 O A:ARG117 4.6 12.3 1.0 O A:ALA124 4.6 19.2 1.0 CA A:CA5 4.6 28.6 1.0

Calcium binding site 5 out of 5 in the 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 1.8 Angstrom Crystal Structure of the Periplasmic Domain of the Membrane Insertase Yidc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5 b:28.6 occ:1.00 O A:ALA124 2.3 19.2 1.0 O A:HOH370 2.4 16.3 1.0 O A:HOH378 2.5 31.5 1.0 C A:ALA124 3.5 17.7 1.0 CA A:ALA124 4.4 17.3 1.0 O A:HOH417 4.5 34.3 1.0 N A:ASN125 4.5 17.4 1.0 CB A:ALA124 4.6 15.9 1.0 CA A:ASN125 4.6 17.4 1.0 CA A:CA4 4.6 26.1 1.0 C A:ASN125 5.0 20.3 1.0

S.Ravaud, G.Stjepanovic, K.Wild, I.Sinning. The Crystal Structure of the Periplasmic Domain of the Escherichia Coli Membrane Protein Insertase Yidc Contains A Substrate Binding Cleft J.Biol.Chem. V. 283 9350 2008.
ISSN: ISSN 0021-9258
PubMed: 18234665
DOI: 10.1074/JBC.M710493200