Calcium in PDB 4itc: Crystal Structure Analysis of the K1 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83

All present enzymatic activity of Crystal Structure Analysis of the K1 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83:
3.4.22.47;

The structure of Crystal Structure Analysis of the K1 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83, PDB code: 4itc was solved by L.A.Ganuelas, N.Li, N.Hunter, C.A.Collyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.74 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.034, 33.321, 67.245, 90.00, 93.96, 90.00
R / Rfree (%)	15.3 / 18.1

The binding sites of Calcium atom in the Crystal Structure Analysis of the K1 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 (pdb code 4itc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure Analysis of the K1 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83, PDB code: 4itc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure Analysis of the K1 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


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 K1 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1201 b:8.6 occ:1.00 OD1 A:ASP1001 2.3 10.8 1.0 O A:HIS1007 2.3 11.0 1.0 OD1 A:ASP1003 2.4 9.6 1.0 OD1 A:ASN1043 2.4 7.0 1.0 OD1 A:ASP1005 2.4 10.4 1.0 O A:HOH1301 2.4 9.7 1.0 OD2 A:ASP1003 2.7 11.1 1.0 CG A:ASP1003 2.9 10.9 1.0 CG A:ASP1005 3.3 11.4 1.0 CG A:ASP1001 3.3 12.2 1.0 CG A:ASN1043 3.5 6.9 1.0 C A:HIS1007 3.5 10.9 1.0 OD2 A:ASP1005 3.7 11.4 1.0 ND2 A:ASN1043 3.9 6.8 1.0 OD2 A:ASP1001 4.1 13.6 1.0 N A:HIS1007 4.1 11.4 1.0 CA A:HIS1007 4.2 11.7 1.0 N A:ASP1005 4.2 11.1 1.0 O A:HOH1302 4.3 8.1 1.0 CB A:ASP1001 4.3 10.7 1.0 CB A:ASP1003 4.4 10.8 1.0 CB A:HIS1007 4.4 12.8 1.0 CA A:PRO1041 4.4 8.7 1.0 CA A:ASP1001 4.5 9.9 1.0 CB A:ASP1005 4.5 11.0 1.0 N A:ASP1042 4.5 8.8 1.0 N A:GLY1008 4.5 10.2 1.0 N A:GLY1004 4.6 11.7 1.0 CA A:GLY1008 4.7 10.2 1.0 N A:ASP1003 4.7 10.6 1.0 CA A:ASP1005 4.8 11.3 1.0 C A:ASP1001 4.8 10.3 1.0 N A:GLY1006 4.8 12.3 1.0 CB A:ASN1043 4.8 6.7 1.0 CB A:PRO1041 4.9 8.9 1.0 O A:ASP1042 4.9 8.3 1.0 CA A:ASP1003 5.0 11.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure Analysis of the K1 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


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 K1 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1202 b:9.2 occ:1.00 OE2 A:GLU990 2.3 14.4 1.0 O A:GLY1024 2.3 10.6 1.0 O A:SER988 2.3 10.4 1.0 OE1 A:GLU1147 2.4 12.1 1.0 OD1 A:ASP1146 2.4 8.7 1.0 OG A:SER1022 2.4 12.3 1.0 OD2 A:ASP1146 2.5 10.1 1.0 CG A:ASP1146 2.8 9.4 1.0 C A:GLY1024 3.5 10.6 1.0 CB A:SER1022 3.5 12.8 1.0 C A:SER988 3.5 9.6 1.0 CD A:GLU990 3.5 14.4 1.0 CD A:GLU1147 3.5 12.3 1.0 CA A:SER988 4.1 11.1 1.0 CG A:GLU1147 4.1 11.7 1.0 CB A:SER988 4.2 11.1 1.0 N A:GLY1024 4.2 11.4 1.0 CA A:GLY1024 4.3 11.0 1.0 OE1 A:GLU990 4.3 17.1 1.0 CB A:ASP1146 4.3 8.3 1.0 CG A:GLU990 4.4 12.8 1.0 N A:CYS1025 4.5 9.9 1.0 OE2 A:GLU1147 4.6 13.0 1.0 N A:PHE989 4.6 9.7 1.0 O A:TYR1020 4.6 12.8 1.0 CA A:CYS1025 4.6 9.5 1.0 CA A:GLY1019 4.6 11.9 1.0 C A:PHE989 4.6 11.2 1.0 CA A:SER1022 4.7 13.0 1.0 N A:TYR1020 4.7 10.8 1.0 N A:GLU1147 4.8 9.3 1.0 C A:SER1022 4.8 13.3 1.0 O A:PHE989 4.8 12.4 1.0 CB A:PHE989 4.8 11.2 1.0 N A:GLU990 4.8 11.2 1.0 CA A:PHE989 4.9 10.5 1.0 N A:ASN1023 4.9 14.5 0.5 CB A:CYS1025 4.9 10.3 1.0

L.A.Ganuelas, N.Li, P.Yun, N.Hunter, C.A.Collyer. The Lysine Gingipain Adhesin Domains From Porphyromonas Gingivalis Interact with Erythrocytes and Albumin: Structures Correlate to Function. Eur J Microbiol Immunol (Bp) V. 3 152 2013.
ISSN: ISSN 2062-509X
PubMed: 24265933
DOI: 10.1556/EUJMI.3.2013.3.2