Calcium in PDB 1jl5: Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis

The structure of Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis, PDB code: 1jl5 was solved by A.G.Evdokimov, D.E.Anderson, K.M.Routzahn, D.S.Waugh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.89 / 2.10
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	149.430, 149.430, 191.180, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 24

The binding sites of Calcium atom in the Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis (pdb code 1jl5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis, PDB code: 1jl5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:18.8 occ:1.00 OD2 A:ASP1266 2.0 18.0 1.0 OD1 A:ASN1246 2.0 18.5 1.0 O A:HOH5 2.2 20.0 1.0 O A:HOH28 2.2 24.9 1.0 O A:HOH9 2.3 22.4 1.0 CG A:ASP1266 3.1 17.4 1.0 CG A:ASN1246 3.2 18.3 1.0 CB A:ASP1266 3.7 16.2 1.0 O A:HOH198 3.7 49.4 1.0 ND2 A:ASN1246 3.9 17.9 1.0 OE1 A:GLU1286 3.9 29.2 1.0 O A:HOH1 4.0 15.3 1.0 OD1 A:ASP1266 4.2 18.7 1.0 CB A:ASN1246 4.3 16.8 1.0 O A:HOH31 4.3 36.4 1.0 O A:HOH304 4.6 50.6 1.0 CD A:GLU1286 4.8 26.5 1.0 CA A:ASN1246 4.8 18.6 1.0 OE2 A:GLU1286 4.9 35.1 1.0

Calcium binding site 2 out of 5 in the Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:19.2 occ:1.00 OD1 A:ASP1266 2.2 18.7 1.0 O A:HOH8 2.3 19.1 1.0 O A:HOH1 2.4 15.3 1.0 O A:HOH2 2.5 22.4 1.0 O A:HOH18 2.8 37.1 1.0 CG A:ASP1266 3.3 17.4 1.0 OD2 A:ASP1266 3.7 18.0 1.0 O A:GLU1286 4.3 19.2 1.0 CB A:ASP1266 4.5 16.2 1.0 OE1 A:GLU1286 4.6 29.2 1.0 CA A:ASP1266 4.6 15.6 1.0 O A:ASN1267 4.6 17.7 1.0 C A:ASP1266 4.6 16.8 1.0 N A:ASN1267 4.9 16.1 1.0

Calcium binding site 3 out of 5 in the Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:70.3 occ:1.00 O A:HOH189 2.4 52.4 1.0 OD1 A:ASN1162 2.4 47.7 1.0 O A:HOH27 2.5 59.6 1.0 O A:HOH316 2.9 63.2 1.0 CG A:ASN1162 3.4 43.5 1.0 OD1 A:ASN1182 3.4 41.3 1.0 ND2 A:ASN1162 3.8 49.8 1.0 O A:HOH261 4.0 87.6 1.0 CG A:ASN1182 4.0 39.1 1.0 O A:HOH306 4.2 61.3 1.0 ND2 A:ASN1182 4.2 39.9 1.0 CB A:ASN1162 4.6 36.8 1.0 CA A:ASN1162 4.6 31.6 1.0 O A:ASN1182 4.7 28.7 1.0 C A:ASN1162 4.7 30.3 1.0 O A:ASN1163 4.9 27.3 1.0 O A:HOH278 4.9 57.9 1.0 O A:HOH113 4.9 48.9 1.0

Calcium binding site 4 out of 5 in the Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:62.8 occ:1.00 OE1 A:GLU1294 2.2 53.6 1.0 OE1 A:GLU1274 2.4 29.9 1.0 O A:HOH232 2.4 63.0 1.0 OE2 A:GLU1294 2.4 55.6 1.0 CD A:GLU1294 2.6 51.6 1.0 O A:HOH392 2.6 63.4 1.0 OE2 A:GLU1274 2.8 34.0 1.0 CD A:GLU1274 2.9 28.7 1.0 O A:HOH333 3.5 73.0 1.0 O A:HOH56 3.5 31.3 1.0 CG A:GLU1294 4.0 47.6 1.0 CG A:GLU1274 4.4 27.3 1.0 CB A:GLU1294 4.5 38.6 1.0 O A:HOH163 4.9 64.8 1.0

Calcium binding site 5 out of 5 in the Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Novel Molecular Architecture of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:78.9 occ:1.00 OE2 A:GLU1059 3.1 48.4 1.0 OE1 A:GLU1059 3.7 49.8 1.0 CD A:GLU1059 3.8 45.1 1.0 O A:HOH276 4.0 67.4 0.5

A.G.Evdokimov, D.E.Anderson, K.M.Routzahn, D.S.Waugh. Unusual Molecular Architecture of the Yersinia Pestis Cytotoxin Yopm: A Leucine-Rich Repeat Protein with the Shortest Repeating Unit. J.Mol.Biol. V. 312 807 2001.
ISSN: ISSN 0022-2836
PubMed: 11575934
DOI: 10.1006/JMBI.2001.4973