Calcium in PDB 2y3c: Treponema Denticola Variable Protein 1

The structure of Treponema Denticola Variable Protein 1, PDB code: 2y3c was solved by J.Le Coq, P.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.58 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.393, 77.629, 88.917, 90.00, 90.00, 90.00
R / Rfree (%)	14.619 / 17.24

The structure of Treponema Denticola Variable Protein 1 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Treponema Denticola Variable Protein 1 (pdb code 2y3c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Treponema Denticola Variable Protein 1, PDB code: 2y3c:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Treponema Denticola Variable Protein 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Treponema Denticola Variable Protein 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1340 b:8.9 occ:0.15 CA A:CA1341 1.1 14.2 0.8 OE2 A:GLU101 2.2 11.6 1.0 O A:ASP255 2.4 9.1 1.0 O A:VAL260 2.4 7.7 1.0 O A:GLY258 2.4 8.8 1.0 OE2 A:GLU262 2.5 9.1 1.0 CD A:GLU262 3.4 8.3 1.0 CD A:GLU101 3.5 10.1 1.0 C A:VAL260 3.6 7.5 1.0 C A:ASP255 3.6 9.1 1.0 C A:GLY258 3.6 8.1 1.0 O A:ILE256 3.7 11.7 1.0 CG A:GLU262 3.8 8.2 1.0 N A:VAL260 3.9 7.2 1.0 C A:ILE256 4.0 10.7 1.0 O A:GLY295 4.0 10.0 1.0 N A:GLY258 4.1 9.1 1.0 CG A:GLU101 4.2 10.1 1.0 C A:ALA257 4.3 9.3 1.0 CA A:VAL260 4.3 7.5 1.0 CB A:ASP255 4.4 8.8 1.0 CA A:ILE256 4.4 10.9 1.0 OE1 A:GLU101 4.4 12.9 1.0 NH2 A:ARG324 4.4 7.9 1.0 OE1 A:GLU262 4.4 8.4 1.0 CA A:GLY258 4.4 8.9 1.0 N A:ILE256 4.5 9.7 1.0 N A:ALA261 4.6 7.6 1.0 CA A:ASP255 4.6 8.8 1.0 CB A:ASN259 4.6 8.1 1.0 O A:ALA257 4.6 9.5 1.0 N A:ALA257 4.6 10.3 1.0 N A:ASN259 4.6 8.2 1.0 CG2 A:VAL260 4.7 7.9 1.0 O A:GLY294 4.7 10.0 1.0 CA A:ALA261 4.8 7.8 1.0 C A:ASN259 4.8 7.9 1.0 CA A:ASN259 4.9 8.0 1.0 CA A:ALA257 4.9 9.8 1.0 C A:ALA261 5.0 8.0 1.0

Calcium binding site 2 out of 2 in the Treponema Denticola Variable Protein 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Treponema Denticola Variable Protein 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1341 b:14.2 occ:0.85 CA A:CA1340 1.1 8.9 0.1 O A:GLY258 2.6 8.8 1.0 O A:VAL260 2.6 7.7 1.0 O A:ASP255 2.8 9.1 1.0 O A:ILE256 3.0 11.7 1.0 OE2 A:GLU262 3.0 9.1 1.0 OE2 A:GLU101 3.3 11.6 1.0 O A:GLY295 3.4 10.0 1.0 C A:ILE256 3.5 10.7 1.0 N A:GLY258 3.5 9.1 1.0 C A:GLY258 3.6 8.1 1.0 O A:GLY294 3.7 10.0 1.0 C A:VAL260 3.7 7.5 1.0 CD A:GLU262 3.7 8.3 1.0 C A:ALA257 3.8 9.3 1.0 C A:ASP255 3.9 9.1 1.0 C A:GLY294 3.9 9.6 1.0 CA A:GLY258 4.1 8.9 1.0 CG A:GLU262 4.1 8.2 1.0 N A:ALA257 4.1 10.3 1.0 CA A:GLY294 4.1 9.6 1.0 CA A:ALA257 4.2 9.8 1.0 CA A:ILE256 4.2 10.9 1.0 N A:VAL260 4.3 7.2 1.0 O A:ALA257 4.4 9.5 1.0 O A:ARG293 4.4 9.6 1.0 C A:GLY295 4.4 9.4 1.0 CA A:ALA261 4.5 7.8 1.0 N A:ALA261 4.5 7.6 1.0 CD A:GLU101 4.6 10.1 1.0 N A:ILE256 4.6 9.7 1.0 OE1 A:GLU262 4.6 8.4 1.0 N A:GLY295 4.7 9.5 1.0 CA A:VAL260 4.7 7.5 1.0 N A:ASN259 4.8 8.2 1.0 C A:ALA261 4.9 8.0 1.0 NH2 A:ARG324 5.0 7.9 1.0

J.Le Coq, P.Ghosh. Conservation of the C-Type Lectin Fold For Massive Sequence Variation in A Treponema Diversity-Generating Retroelement. Proc.Natl.Acad.Sci.Usa V. 108 14649 2011.
ISSN: ISSN 0027-8424
PubMed: 21873231
DOI: 10.1073/PNAS.1105613108