Calcium in PDB 4mkm: Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147

The structure of Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147, PDB code: 4mkm was solved by H.Kwon, C.J.Squire, P.G.Young, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.62 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.188, 63.448, 104.984, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.9

The binding sites of Calcium atom in the Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147 (pdb code 4mkm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147, PDB code: 4mkm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:38.9 occ:1.00 OD1 A:ASP120 2.1 47.3 1.0 O A:GLU124 2.2 44.6 1.0 OD2 A:ASP126 2.2 45.1 1.0 OD1 A:ASP118 2.3 46.5 1.0 OD1 A:ASN122 2.5 45.5 1.0 CG A:ASP120 3.3 53.6 1.0 CG A:ASN122 3.3 52.0 1.0 CG A:ASP126 3.4 45.8 1.0 C A:GLU124 3.4 47.4 1.0 CG A:ASP118 3.5 47.6 1.0 ND2 A:ASN122 3.5 49.1 1.0 OD2 A:ASP120 3.8 62.8 1.0 CB A:ASP126 3.9 39.6 1.0 N A:GLU124 4.1 48.1 1.0 CA A:GLU124 4.2 46.5 1.0 N A:ASP120 4.2 55.6 1.0 CB A:GLU124 4.2 49.3 1.0 CA A:ASP118 4.2 43.0 1.0 CB A:ASP118 4.3 45.3 1.0 OD2 A:ASP118 4.3 48.6 1.0 N A:THR119 4.3 49.5 1.0 OD1 A:ASP126 4.4 48.0 1.0 N A:ASP126 4.4 36.1 1.0 CB A:ASP120 4.4 58.4 1.0 N A:LEU125 4.5 44.0 1.0 N A:ASN122 4.6 49.6 1.0 CB A:ASN122 4.6 50.8 1.0 C A:LEU125 4.6 44.1 1.0 C A:ASP118 4.7 50.3 1.0 CA A:ASP120 4.7 56.9 1.0 CA A:LEU125 4.7 42.2 1.0 C A:ASP120 4.8 60.8 1.0 CA A:ASP126 4.9 37.2 1.0 N A:ASN121 5.0 56.4 1.0 CA A:ASN122 5.0 50.5 1.0

Calcium binding site 2 out of 4 in the Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:30.0 occ:1.00 O A:HOH553 1.9 41.7 1.0 O A:GLY185 2.2 47.3 1.0 OD2 A:ASP165 2.3 56.3 1.0 O A:HOH559 2.3 37.3 1.0 O A:ASN181 2.4 52.6 1.0 OD1 A:ASP184 2.6 52.6 1.0 OD1 A:ASP165 2.7 47.3 1.0 CG A:ASP165 2.8 48.2 1.0 C A:ASN181 3.4 52.3 1.0 C A:GLY185 3.5 47.8 1.0 CG A:ASP184 3.6 59.0 1.0 CA A:VAL186 4.1 40.4 1.0 CA A:ASN181 4.1 50.7 1.0 OD2 A:ASP184 4.1 65.9 1.0 CB A:ASP165 4.2 46.0 1.0 N A:VAL186 4.2 42.8 1.0 C A:ASP184 4.3 54.7 1.0 N A:GLY185 4.4 47.1 1.0 N A:SER182 4.4 48.0 1.0 CB A:ASN181 4.4 53.9 1.0 O A:ASP184 4.4 56.0 1.0 OD1 A:ASN181 4.5 61.0 1.0 CA A:GLY185 4.5 45.7 1.0 CA A:SER182 4.6 47.8 1.0 N A:ASP187 4.7 41.4 1.0 OD2 A:ASP187 4.7 62.5 1.0 N A:ASP184 4.8 53.6 1.0 CB A:ASP184 4.8 56.6 1.0 C A:SER182 4.8 53.5 1.0 CG A:ASN181 4.9 66.1 1.0 CA A:ASP184 4.9 53.4 1.0 C A:VAL186 4.9 42.4 1.0

Calcium binding site 3 out of 4 in the Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:30.0 occ:1.00 O A:GLY36 2.1 45.5 1.0 O A:HOH550 2.2 43.1 1.0 O A:HOH569 2.2 39.6 1.0 OD1 A:ASP35 2.3 58.7 1.0 O A:ASN32 2.4 47.6 1.0 OD2 A:ASP16 2.4 57.0 1.0 OD1 A:ASP16 3.1 49.5 1.0 CG A:ASP16 3.1 51.5 1.0 C A:GLY36 3.3 46.9 1.0 CG A:ASP35 3.4 63.9 1.0 C A:ASN32 3.5 48.5 1.0 CA A:VAL37 4.0 40.6 1.0 OD2 A:ASP35 4.0 68.3 1.0 N A:VAL37 4.1 41.6 1.0 CA A:ASN32 4.2 48.6 1.0 N A:GLY36 4.2 49.3 1.0 C A:ASP35 4.2 55.4 1.0 CB A:ASN32 4.3 50.0 1.0 CA A:GLY36 4.4 46.3 1.0 O A:ASP35 4.4 56.6 1.0 CB A:ASP16 4.5 47.1 1.0 N A:SER33 4.5 42.2 1.0 CB A:ASP35 4.6 57.1 1.0 N A:ASP35 4.6 53.1 1.0 OD2 A:ASP38 4.6 76.0 1.0 CA A:ASP35 4.7 53.9 1.0 CA A:SER33 4.7 41.3 1.0 N A:ASP38 4.8 40.7 1.0 C A:VAL37 4.8 43.5 1.0 C A:SER33 4.9 47.0 1.0 CG2 A:VAL37 5.0 42.0 1.0

Calcium binding site 4 out of 4 in the Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Repeat Domains 1 & 2 of Clostridium Perfringens CPE0147 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:30.0 occ:1.00 OD1 A:ASP269 2.0 67.7 1.0 OD1 A:ASP267 2.2 49.3 1.0 OD1 A:ASP271 2.2 64.0 1.0 O A:HOH676 2.2 41.7 1.0 O A:ASN273 2.2 53.3 1.0 OD2 A:ASP275 2.4 43.0 1.0 CG A:ASP269 3.1 69.6 1.0 CG A:ASP271 3.1 62.6 1.0 CG A:ASP267 3.3 50.8 1.0 C A:ASN273 3.4 55.7 1.0 CG A:ASP275 3.5 49.2 1.0 OD2 A:ASP269 3.5 76.8 1.0 OD2 A:ASP271 3.6 66.9 1.0 N A:ASN273 3.9 56.5 1.0 CA A:ASP267 4.0 43.8 1.0 CB A:ASP275 4.0 50.4 1.0 CB A:ASP267 4.0 47.1 1.0 N A:ASP269 4.0 54.9 1.0 CA A:ASN273 4.1 55.4 1.0 OD2 A:ASP267 4.2 50.0 1.0 N A:ASP271 4.2 56.7 1.0 N A:THR268 4.3 48.6 1.0 CB A:ASP271 4.3 60.3 1.0 CB A:ASP269 4.3 60.8 1.0 CB A:ASN273 4.3 55.7 1.0 C A:ASP267 4.5 49.3 1.0 N A:LEU274 4.5 49.6 1.0 OD1 A:ASP275 4.5 47.4 1.0 CA A:ASP269 4.5 57.4 1.0 N A:ASP275 4.5 49.4 1.0 C A:ASP269 4.6 62.4 1.0 N A:TYR272 4.6 55.8 1.0 CA A:ASP271 4.7 57.9 1.0 N A:LYS270 4.7 58.5 1.0 C A:ASP271 4.8 59.9 1.0 C A:LEU274 4.8 52.9 1.0 CA A:LEU274 4.8 47.8 1.0 CA A:ASP275 5.0 48.9 1.0 C A:TYR272 5.0 59.4 1.0

H.Kwon, C.J.Squire, P.G.Young, E.N.Baker. Autocatalytically Generated Thr-Gln Ester Bond Cross-Links Stabilize the Repetitive Ig-Domain Shaft of A Bacterial Cell Surface Adhesin. Proc.Natl.Acad.Sci.Usa V. 111 1367 2014.
ISSN: ISSN 0027-8424
PubMed: 24344302
DOI: 10.1073/PNAS.1316855111