Calcium in PDB 2wza: Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain

The structure of Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain, PDB code: 2wza was solved by N.Forsgren, R.J.Lamont, K.Persson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.58 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.750, 80.150, 87.430, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 25.5

The binding sites of Calcium atom in the Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain (pdb code 2wza). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain, PDB code: 2wza:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2414 b:21.8 occ:1.00 O A:LYS1186 2.3 21.6 1.0 OE1 A:GLU1136 2.3 27.6 1.0 O A:ALA1188 2.4 27.1 1.0 O A:TYR1134 2.4 21.9 1.0 O A:HOH2040 2.4 26.7 1.0 OD1 A:ASP1133 2.5 24.2 1.0 CD A:GLU1136 3.4 32.7 1.0 C A:ALA1188 3.5 25.5 1.0 C A:LYS1186 3.5 25.5 1.0 C A:TYR1134 3.5 28.1 1.0 N A:ALA1188 3.6 24.7 1.0 CG A:ASP1133 3.7 23.6 1.0 OE2 A:GLU1136 3.8 38.2 1.0 C A:GLY1187 4.0 24.6 1.0 N A:TYR1134 4.1 24.0 1.0 CA A:ALA1188 4.1 26.6 1.0 C A:ASP1133 4.1 22.9 1.0 N A:GLU1136 4.3 28.4 1.0 OD2 A:ASP1133 4.3 26.6 1.0 O A:ASP1133 4.4 20.7 1.0 O A:HOH2029 4.4 21.6 1.0 CA A:LYS1186 4.4 25.7 1.0 N A:PRO1135 4.4 26.6 1.0 CA A:GLY1187 4.4 25.4 1.0 N A:GLY1187 4.4 24.4 1.0 CA A:TYR1134 4.4 23.4 1.0 CA A:PRO1135 4.4 24.1 1.0 N A:LYS1186 4.5 28.6 1.0 CB A:LYS1186 4.5 33.3 1.0 O A:GLY1187 4.5 32.4 1.0 CA A:ASP1133 4.5 20.6 1.0 N A:PHE1189 4.6 22.8 1.0 CB A:ASP1133 4.7 17.1 1.0 CG A:GLU1136 4.7 26.6 1.0 CB A:ALA1188 4.8 25.3 1.0 CB A:GLU1136 4.9 29.1 1.0 C A:PRO1135 4.9 29.7 1.0 CA A:PHE1189 5.0 22.0 1.0

Calcium binding site 2 out of 3 in the Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2415 b:19.5 occ:1.00 OD1 A:ASP1308 2.3 20.7 1.0 O A:ASN1354 2.4 26.6 1.0 O A:TYR1309 2.5 12.1 1.0 O A:HOH2118 2.5 24.5 1.0 OE1 A:GLN1311 2.5 19.8 1.0 O A:GLY1355 2.6 16.9 1.0 C A:ASN1354 3.5 26.1 1.0 C A:GLY1355 3.5 18.8 1.0 CG A:ASP1308 3.6 24.5 1.0 C A:TYR1309 3.6 16.8 1.0 CD A:GLN1311 3.6 24.2 1.0 CA A:GLY1355 3.8 19.4 1.0 N A:TYR1309 3.8 13.2 1.0 C A:ASP1308 4.0 16.3 1.0 N A:GLY1355 4.0 21.3 1.0 NE2 A:GLN1311 4.1 20.4 1.0 OD2 A:ASP1308 4.3 30.4 1.0 N A:GLN1311 4.3 15.7 1.0 CA A:TYR1309 4.4 14.4 1.0 O A:ASP1308 4.4 13.0 1.0 CA A:ASP1308 4.4 16.4 1.0 CG1 A:ILE1356 4.5 22.7 1.0 CB A:ASP1308 4.6 16.3 1.0 N A:ASP1310 4.6 14.4 1.0 O A:HOH2087 4.6 29.5 1.0 N A:ILE1356 4.7 17.9 1.0 CA A:ASP1310 4.7 18.0 1.0 CA A:ASN1354 4.7 28.7 1.0 CG A:GLN1311 4.9 18.0 1.0 CB A:GLN1311 4.9 19.0 1.0 O A:HOH2091 5.0 32.5 1.0

Calcium binding site 3 out of 3 in the Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2416 b:16.8 occ:1.00 O A:TYR1077 2.4 18.2 1.0 OD2 A:ASP1110 2.5 15.6 1.0 OD1 A:ASP1112 2.5 22.4 1.0 OE1 A:GLN1113 2.5 18.1 1.0 O A:HOH2005 2.6 21.8 1.0 OD1 A:ASP1110 2.7 20.5 1.0 O A:HOH2022 2.7 17.9 1.0 CG A:ASP1110 2.9 18.4 1.0 CG A:ASP1112 3.5 22.4 1.0 CD A:GLN1113 3.6 18.0 1.0 C A:TYR1077 3.6 20.8 1.0 OD2 A:ASP1112 3.8 25.6 1.0 CB A:GLN1113 4.1 19.8 1.0 N A:GLN1113 4.2 20.9 1.0 O A:HOH2021 4.3 27.4 1.0 CG A:GLN1113 4.3 18.5 1.0 CB A:ASP1110 4.5 16.2 1.0 CA A:ILE1078 4.5 21.7 1.0 N A:ILE1078 4.5 18.5 1.0 CA A:TYR1077 4.6 26.7 1.0 N A:ASN1076 4.6 26.4 1.0 NE2 A:GLN1113 4.7 16.2 1.0 N A:LYS1079 4.7 14.7 1.0 CA A:GLN1113 4.7 20.1 1.0 N A:ASP1112 4.8 22.6 1.0 CB A:ASP1112 4.9 18.8 1.0

N.Forsgren, R.J.Lamont, K.Persson. Two Intramolecular Isopeptide Bonds Are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain. J.Mol.Biol. V. 397 740 2010.
ISSN: ISSN 0022-2836
PubMed: 20138058
DOI: 10.1016/J.JMB.2010.01.065