Calcium in PDB 3km5: Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp)

The structure of Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp), PDB code: 3km5 was solved by N.Li, C.A.Collyer, N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.32 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	29.911, 59.858, 85.672, 90.00, 94.23, 90.00
R / Rfree (%)	17.5 / 20.8

The binding sites of Calcium atom in the Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) (pdb code 3km5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp), PDB code: 3km5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2011 b:9.0 occ:1.00 O A:GLN1185 2.3 10.5 1.0 OD1 A:ASP1179 2.3 11.3 1.0 OD1 A:ASP1183 2.4 9.7 1.0 OD1 A:ASP1181 2.4 10.1 1.0 OD1 A:ASN1221 2.4 8.2 1.0 O A:HOH3 2.4 10.0 1.0 OD2 A:ASP1181 2.8 12.7 1.0 CG A:ASP1181 3.0 9.6 1.0 CG A:ASP1183 3.3 13.2 1.0 CG A:ASP1179 3.4 9.4 1.0 CG A:ASN1221 3.5 8.0 1.0 C A:GLN1185 3.5 9.0 1.0 OD2 A:ASP1183 3.7 11.3 1.0 ND2 A:ASN1221 3.8 7.7 1.0 N A:GLN1185 4.1 9.5 1.0 OD2 A:ASP1179 4.2 9.4 1.0 N A:ASP1183 4.2 8.9 1.0 CA A:GLN1185 4.2 8.3 1.0 O A:HOH12 4.3 9.0 1.0 CB A:ASP1179 4.3 10.2 1.0 CA A:ASP1179 4.4 9.7 1.0 CB A:ASP1181 4.5 11.5 1.0 CB A:ASP1183 4.5 10.3 1.0 N A:GLY1186 4.5 8.3 1.0 CB A:GLN1185 4.5 8.9 1.0 N A:ASP1220 4.5 8.6 1.0 N A:GLY1182 4.6 11.1 1.0 CA A:GLY1186 4.6 10.1 1.0 CA A:PRO1219 4.6 10.2 1.0 C A:ASP1179 4.7 9.2 1.0 CA A:ASP1183 4.7 9.1 1.0 N A:GLY1184 4.8 10.3 1.0 N A:ASP1181 4.8 9.6 1.0 CB A:ASN1221 4.8 8.2 1.0 C A:ASP1183 4.9 9.3 1.0 O A:ASP1220 4.9 9.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2012 b:9.2 occ:1.00 O A:HOH8 2.4 11.3 1.0 O A:ASN1205 2.4 8.9 1.0 OE2 A:GLU1164 2.4 10.7 1.0 O A:THR1162 2.4 8.5 1.0 O A:GLY1202 2.5 11.6 1.0 OD1 A:ASP1326 2.5 8.4 1.0 OD2 A:ASP1326 2.6 10.3 1.0 CG A:ASP1326 2.9 7.7 1.0 C A:ASN1205 3.5 10.6 1.0 C A:GLY1202 3.5 10.2 1.0 CD A:GLU1164 3.5 10.9 1.0 C A:THR1162 3.6 8.3 1.0 N A:ASN1205 4.0 9.3 1.0 CG A:GLU1164 4.1 12.9 1.0 CA A:THR1162 4.2 9.4 1.0 N A:GLY1202 4.2 11.8 1.0 CA A:ASN1205 4.2 11.4 1.0 CA A:GLY1202 4.2 11.5 1.0 CB A:THR1162 4.3 12.0 1.0 CB A:ALA1200 4.3 12.8 1.0 CB A:ASP1326 4.4 9.6 1.0 O B:HOH20 4.5 14.7 1.0 N A:GLY1203 4.5 12.9 1.0 OD1 A:ASP1327 4.5 12.1 1.0 CB A:ASN1205 4.5 10.3 1.0 OE1 A:GLU1164 4.6 11.9 1.0 N A:VAL1206 4.6 9.2 1.0 N A:PHE1163 4.7 9.6 1.0 CA A:GLY1203 4.7 12.4 1.0 C A:GLY1203 4.8 10.6 1.0 CB A:PHE1163 4.8 7.7 1.0 N A:SER1204 4.9 10.8 1.0 N A:GLU1164 4.9 9.3 1.0 CA A:VAL1206 4.9 9.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2011 b:8.7 occ:1.00 O B:GLN1185 2.2 10.5 1.0 OD1 B:ASP1179 2.3 9.4 1.0 OD1 B:ASP1183 2.4 10.4 1.0 O B:HOH116 2.4 8.5 1.0 OD1 B:ASN1221 2.4 8.7 1.0 OD1 B:ASP1181 2.4 8.9 1.0 OD2 B:ASP1181 2.7 11.2 1.0 CG B:ASP1181 3.0 8.7 1.0 CG B:ASP1183 3.3 10.9 1.0 CG B:ASP1179 3.4 12.0 1.0 C B:GLN1185 3.5 9.6 1.0 CG B:ASN1221 3.5 7.6 1.0 OD2 B:ASP1183 3.7 10.9 1.0 ND2 B:ASN1221 3.8 8.3 1.0 N B:GLN1185 4.1 9.2 1.0 OD2 B:ASP1179 4.2 10.9 1.0 CA B:GLN1185 4.2 8.2 1.0 N B:ASP1183 4.2 10.6 1.0 CB B:ASP1179 4.3 7.4 1.0 O B:HOH136 4.3 8.1 1.0 CA B:ASP1179 4.4 10.5 1.0 CB B:ASP1181 4.4 8.8 1.0 CB B:ASP1183 4.5 10.8 1.0 CB B:GLN1185 4.5 10.3 1.0 N B:GLY1186 4.5 9.1 1.0 N B:ASP1220 4.5 8.3 1.0 CA B:PRO1219 4.6 9.1 1.0 N B:GLY1182 4.6 10.3 1.0 CA B:GLY1186 4.7 9.2 1.0 CA B:ASP1183 4.7 10.4 1.0 N B:ASP1181 4.8 9.7 1.0 C B:ASP1179 4.8 11.3 1.0 N B:GLY1184 4.8 9.8 1.0 CB B:ASN1221 4.8 9.3 1.0 C B:ASP1183 4.9 9.9 1.0 O B:ASP1220 5.0 10.2 1.0 CA B:ASP1181 5.0 10.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2012 b:9.6 occ:1.00 O B:ASN1205 2.4 9.5 1.0 O B:HOH2 2.4 11.6 1.0 OE2 B:GLU1164 2.4 12.1 1.0 O B:GLY1202 2.4 10.6 1.0 OD1 B:ASP1326 2.4 9.1 1.0 O B:THR1162 2.4 9.4 1.0 OD2 B:ASP1326 2.6 8.3 1.0 CG B:ASP1326 2.9 8.3 1.0 C B:GLY1202 3.4 12.3 1.0 C B:ASN1205 3.5 7.5 1.0 C B:THR1162 3.6 8.3 1.0 CD B:GLU1164 3.6 12.1 1.0 N B:ASN1205 4.0 9.9 1.0 N B:GLY1202 4.1 12.5 1.0 CA B:GLY1202 4.1 13.0 1.0 CA B:THR1162 4.2 8.3 1.0 CG B:GLU1164 4.2 12.0 1.0 CA B:ASN1205 4.2 9.5 1.0 CB B:THR1162 4.3 10.5 1.0 OD1 B:ASP1327 4.4 11.5 1.0 CB B:ASP1326 4.4 9.1 1.0 CB B:ALA1200 4.4 11.7 1.0 N B:GLY1203 4.4 13.4 1.0 CB B:ASN1205 4.6 9.1 1.0 N B:VAL1206 4.6 8.4 1.0 OE1 B:GLU1164 4.6 13.5 1.0 CA B:GLY1203 4.6 14.7 1.0 N B:PHE1163 4.7 8.2 1.0 CB B:PHE1163 4.8 8.7 1.0 C B:GLY1203 4.8 13.1 1.0 OD2 B:ASP1327 4.8 16.6 1.0 CG B:ASP1327 4.8 15.0 1.0 N B:SER1204 4.8 12.1 1.0 CA B:VAL1206 4.9 9.3 1.0 N B:GLU1164 5.0 10.2 1.0

N.Li, P.Yun, M.A.Nadkarni, N.B.Ghadikolaee, K.-A.Nguyen, M.Lee, N.Hunter, C.A.Collyer. Structure Determination and Analysis of A Haemolytic Gingipain Adhesin Domain From Porphyromonas Gingivalis Mol.Microbiol. V. 76 861 2010.
ISSN: ISSN 0950-382X
PubMed: 20233299
DOI: 10.1111/J.1365-2958.2010.07123.X