Calcium in PDB 7l0o: Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis

The structure of Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis, PDB code: 7l0o was solved by N.Schormann, C.Deivanayagam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.59 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.049, 109.14, 204.519, 90, 90, 90
R / Rfree (%)	21.8 / 25.5

The binding sites of Calcium atom in the Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis (pdb code 7l0o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis, PDB code: 7l0o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1501 b:111.8 occ:1.00 OD1 A:ASP1133 2.4 99.8 1.0 O A:TYR1134 2.4 82.8 1.0 OE1 A:GLU1136 2.4 99.9 1.0 O A:LYS1186 2.5 112.6 1.0 O A:ALA1188 2.6 80.0 1.0 O A:HOH1608 3.0 60.7 1.0 C A:TYR1134 3.4 68.3 1.0 CD A:GLU1136 3.5 102.4 1.0 CG A:ASP1133 3.6 81.1 1.0 N A:ALA1188 3.6 88.5 1.0 C A:ALA1188 3.6 75.7 1.0 C A:LYS1186 3.7 100.2 1.0 N A:TYR1134 3.8 73.5 1.0 OE2 A:GLU1136 4.0 104.1 1.0 C A:ASP1133 4.0 78.0 1.0 CA A:ALA1188 4.1 75.5 1.0 N A:GLU1136 4.1 74.1 1.0 CA A:TYR1134 4.3 64.8 1.0 C A:GLY1187 4.3 93.4 1.0 N A:PRO1135 4.3 58.9 1.0 OD2 A:ASP1133 4.3 87.5 1.0 CA A:PRO1135 4.4 60.3 1.0 O A:ASP1133 4.4 85.6 1.0 CA A:ASP1133 4.4 67.2 1.0 N A:GLY1187 4.6 98.7 1.0 CA A:GLY1187 4.6 87.5 1.0 CA A:LYS1186 4.6 103.1 1.0 CB A:ASP1133 4.6 61.9 1.0 CB A:LYS1186 4.6 107.6 1.0 CB A:ALA1188 4.7 64.9 1.0 CG A:GLU1136 4.7 92.2 1.0 CB A:GLU1136 4.8 72.7 1.0 N A:LYS1186 4.8 98.2 1.0 N A:PHE1189 4.8 61.6 1.0 C A:PRO1135 4.8 83.2 1.0

Calcium binding site 2 out of 4 in the Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1502 b:122.2 occ:1.00 O A:TYR1309 2.3 69.1 1.0 O A:ASN1354 2.3 85.7 1.0 OE1 A:GLN1311 2.6 115.8 1.0 OD1 A:ASP1308 3.0 90.7 1.0 CD A:GLN1311 3.3 108.5 1.0 O A:GLY1355 3.3 73.1 1.0 NE2 A:GLN1311 3.4 111.1 1.0 C A:ASN1354 3.5 78.7 1.0 C A:TYR1309 3.5 69.6 1.0 CA A:GLY1355 3.7 77.9 1.0 C A:GLY1355 3.9 82.6 1.0 CG A:ASP1308 4.0 73.9 1.0 N A:GLY1355 4.0 72.2 1.0 N A:GLN1311 4.2 88.3 1.0 CA A:ASP1310 4.2 99.5 1.0 N A:ASP1310 4.3 69.8 1.0 N A:TYR1309 4.3 85.7 1.0 OD2 A:ASP1308 4.4 68.1 1.0 C A:ASP1308 4.5 77.0 1.0 CA A:TYR1309 4.5 83.2 1.0 CG A:GLN1311 4.6 97.2 1.0 CA A:ASN1354 4.7 71.5 1.0 C A:ASP1310 4.7 86.0 1.0 O A:ASP1308 4.9 82.9 1.0 CB A:GLN1311 4.9 86.4 1.0 CA A:ASP1308 5.0 68.0 1.0

Calcium binding site 3 out of 4 in the Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1501 b:135.4 occ:1.00 O B:TYR1134 2.3 76.9 1.0 O B:LYS1186 2.4 104.2 1.0 OD1 B:ASP1133 2.4 100.9 1.0 O B:ALA1188 2.4 101.1 1.0 O B:HOH1601 2.7 73.2 1.0 OE1 B:GLU1136 3.2 112.2 1.0 C B:TYR1134 3.3 65.0 1.0 C B:ALA1188 3.5 94.7 1.0 N B:ALA1188 3.5 85.2 1.0 C B:LYS1186 3.5 96.8 1.0 CG B:ASP1133 3.6 89.3 1.0 N B:TYR1134 3.6 69.7 1.0 C B:ASP1133 3.9 73.5 1.0 CD B:GLU1136 4.0 110.6 1.0 CA B:ALA1188 4.0 90.7 1.0 CA B:TYR1134 4.1 63.0 1.0 C B:GLY1187 4.2 101.4 1.0 N B:PRO1135 4.2 56.6 1.0 O B:ASP1133 4.3 74.2 1.0 OE2 B:GLU1136 4.3 111.4 1.0 N B:GLU1136 4.3 86.6 1.0 CA B:ASP1133 4.3 69.3 1.0 CB B:LYS1186 4.4 115.8 1.0 CA B:PRO1135 4.4 70.1 1.0 CA B:LYS1186 4.4 101.8 1.0 OD2 B:ASP1133 4.4 92.6 1.0 N B:GLY1187 4.5 89.8 1.0 CA B:GLY1187 4.5 99.6 1.0 CB B:ASP1133 4.6 76.3 1.0 N B:LYS1186 4.6 97.7 1.0 CB B:ALA1188 4.6 88.3 1.0 N B:PHE1189 4.7 82.7 1.0 C B:PRO1135 4.9 81.6 1.0 O B:GLY1187 5.0 109.5 1.0

Calcium binding site 4 out of 4 in the Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Streptococcus Gordonii C123 Domain(S)-Structural and Functional Analysis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1502 b:133.7 occ:1.00 O B:TYR1309 2.3 75.4 1.0 O B:ASN1354 2.4 94.9 1.0 OD1 B:ASP1308 2.4 101.1 1.0 O B:GLY1355 3.3 88.5 1.0 CG B:ASP1308 3.4 88.2 1.0 C B:TYR1309 3.4 80.8 1.0 C B:ASN1354 3.6 98.4 1.0 OD2 B:ASP1308 3.9 88.0 1.0 CA B:GLY1355 4.0 80.8 1.0 C B:GLY1355 4.0 82.4 1.0 N B:TYR1309 4.0 89.9 1.0 C B:ASP1308 4.1 75.5 1.0 N B:GLY1355 4.3 93.0 1.0 N B:ASP1310 4.3 87.6 1.0 CA B:TYR1309 4.3 86.6 1.0 O B:ASP1308 4.4 67.8 1.0 CA B:ASP1310 4.4 90.1 1.0 CA B:ASP1308 4.5 70.1 1.0 CB B:ASP1308 4.5 72.0 1.0 NE2 B:GLN1311 4.6 103.9 1.0 CA B:ASN1354 4.7 93.7 1.0 N B:GLN1311 4.8 84.6 1.0 CG B:GLN1311 5.0 86.5 1.0

N.Schormann, S.Purushotham, J.L.Mieher, M.Patel, H.Wu, C.Deivanayagam. Structural and Functional Analysis of the C-Terminal Region of Streptococcus Gordonii Sspb Acta Crystallogr.,Sect.D V. D77 2021.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798321008135