Calcium in PDB 3cga: Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form

The structure of Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form, PDB code: 3cga was solved by P.Pathuri, H.Luecke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.03
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	47.107, 47.107, 176.200, 90.00, 90.00, 120.00
R / Rfree (%)	25.5 / 33.1

The binding sites of Calcium atom in the Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form (pdb code 3cga). 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 of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form, PDB code: 3cga:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:6.2 occ:1.00 OD1 A:ASN65 2.1 33.6 1.0 OE1 A:GLU74 2.3 38.0 1.0 O A:GLU69 2.3 26.1 1.0 OD1 A:ASP63 2.3 33.1 1.0 OE2 A:GLU74 2.6 39.1 1.0 OD1 A:ASP67 2.7 33.1 1.0 CD A:GLU74 2.8 27.0 1.0 CG A:ASN65 3.3 26.4 1.0 CG A:ASP67 3.4 44.3 1.0 OD2 A:ASP67 3.4 48.8 1.0 C A:GLU69 3.5 22.5 1.0 CG A:ASP63 3.5 35.7 1.0 ND2 A:ASN65 4.0 30.9 1.0 CA A:ASP63 4.2 30.6 1.0 CB A:ASP63 4.2 27.0 1.0 N A:ASN65 4.3 37.6 1.0 CG A:GLU74 4.3 27.5 1.0 N A:ASP71 4.3 37.3 1.0 CB A:ASN65 4.3 35.8 1.0 N A:VAL70 4.3 29.7 1.0 CA A:VAL70 4.4 34.8 1.0 OD2 A:ASP63 4.5 39.6 1.0 N A:GLU69 4.5 33.2 1.0 OD1 A:ASP71 4.5 59.8 1.0 N A:ASP67 4.5 42.8 1.0 CG A:ASP71 4.5 51.1 1.0 CA A:GLU69 4.5 26.8 1.0 C A:ASP63 4.6 27.7 1.0 N A:ARG66 4.6 48.2 1.0 CA A:ASN65 4.7 40.8 1.0 CB A:ASP67 4.7 43.1 1.0 N A:SER64 4.8 35.8 1.0 OD2 A:ASP71 4.8 64.7 1.0 CB A:ASP71 4.8 47.1 1.0 C A:VAL70 4.8 33.8 1.0 CB A:GLU74 4.9 29.1 1.0 CB A:GLU69 4.9 35.6 1.0 C A:ASN65 4.9 46.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:2.4 occ:1.00 O A:ASP25 2.2 41.2 1.0 O A:HOH124 2.4 26.3 1.0 OE2 A:GLU33 2.4 36.2 1.0 O A:SER20 2.5 41.4 1.0 O A:GLU23 2.5 53.7 1.0 O A:LYS28 2.6 27.8 1.0 OE1 A:GLU33 2.8 29.8 1.0 CD A:GLU33 2.9 43.0 1.0 C A:ASP25 3.4 34.3 1.0 C A:SER20 3.6 33.3 1.0 C A:GLU23 3.7 42.3 1.0 C A:LYS28 3.8 30.1 1.0 N A:GLU23 3.9 49.9 1.0 CA A:SER20 4.2 21.0 1.0 CA A:LYS26 4.3 31.1 1.0 N A:ASP25 4.3 33.2 1.0 CA A:GLU23 4.3 44.1 1.0 C A:GLY24 4.3 37.5 1.0 OE1 A:GLU69 4.3 48.8 1.0 N A:LYS26 4.3 32.6 1.0 CA A:ASP25 4.4 36.2 1.0 O A:GLY24 4.4 38.6 1.0 N A:LYS22 4.4 47.0 1.0 CG A:GLU33 4.4 48.5 1.0 N A:LYS28 4.5 40.7 1.0 N A:ASN30 4.5 36.5 1.0 CA A:LEU29 4.6 33.8 1.0 CA A:LYS28 4.6 30.6 1.0 C A:LYS26 4.6 23.9 1.0 N A:GLY21 4.6 37.2 1.0 N A:LEU29 4.7 29.7 1.0 N A:GLY24 4.7 39.5 1.0 CB A:SER20 4.8 24.6 1.0 CB A:ASP25 4.9 33.4 1.0 CA A:GLY21 4.9 42.6 1.0 C A:LEU29 4.9 33.7 1.0 CB A:GLU23 4.9 37.2 1.0 C A:LYS22 5.0 50.6 1.0 O A:LYS26 5.0 33.9 1.0 O A:TYR19 5.0 43.0 1.0 CA A:GLY24 5.0 40.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:8.2 occ:1.00 OE1 B:GLU33 2.2 39.7 1.0 O B:SER20 2.3 27.5 1.0 O B:GLU23 2.3 36.9 1.0 O B:ASP25 2.4 30.4 1.0 O B:LYS28 2.5 35.1 1.0 OE2 B:GLU33 2.7 39.2 1.0 CD B:GLU33 2.8 37.3 1.0 ND2 B:ASN30 3.1 70.0 1.0 C B:SER20 3.3 44.1 1.0 C B:GLU23 3.5 36.2 1.0 C B:ASP25 3.5 36.0 1.0 C B:LYS28 3.7 36.5 1.0 CA B:SER20 3.8 37.6 1.0 N B:ASP25 4.0 45.9 1.0 C B:GLY24 4.2 53.0 1.0 CG B:ASN30 4.2 50.8 1.0 OE1 B:GLU69 4.2 43.5 1.0 CA B:ASP25 4.3 37.6 1.0 CG B:GLU33 4.3 31.4 1.0 N B:GLU23 4.3 37.0 1.0 CA B:GLU23 4.4 32.3 1.0 N B:GLY21 4.4 49.3 1.0 N B:ASN30 4.4 46.8 1.0 N B:GLY24 4.4 39.1 1.0 OE2 B:GLU69 4.5 54.1 1.0 CB B:SER20 4.5 33.9 1.0 CA B:LEU29 4.5 35.3 1.0 O B:GLY24 4.5 57.6 1.0 N B:LYS26 4.5 30.6 1.0 N B:LEU29 4.5 36.2 1.0 CA B:GLY24 4.6 43.2 1.0 N B:LYS28 4.6 34.8 1.0 CA B:LYS26 4.6 34.2 1.0 O B:TYR19 4.7 45.4 1.0 CA B:LYS28 4.7 35.1 1.0 OD1 B:ASN30 4.7 48.6 1.0 CB B:ASP25 4.8 43.5 1.0 CB B:GLU23 4.8 37.0 1.0 CD B:GLU69 4.8 41.1 1.0 CA B:GLY21 4.8 53.3 1.0 C B:LEU29 4.8 39.7 1.0 CB B:GLU33 5.0 32.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Metastasis-Associated Protein S100A4 in the Active, Calcium-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:4.6 occ:1.00 OE2 B:GLU74 2.2 33.6 1.0 O B:GLU69 2.3 32.1 1.0 OD1 B:ASN65 2.4 31.9 1.0 OD1 B:ASP63 2.5 38.8 1.0 OE1 B:GLU74 2.5 31.8 1.0 ND2 B:ASN65 2.6 48.0 1.0 CG B:ASN65 2.7 44.9 1.0 CD B:GLU74 2.7 32.2 1.0 OD1 B:ASP67 2.8 43.2 1.0 C B:GLU69 3.5 30.1 1.0 CG B:ASP67 3.5 48.6 1.0 CG B:ASP63 3.5 40.7 1.0 OD2 B:ASP67 3.9 52.2 1.0 CB B:ASN65 3.9 46.6 1.0 N B:ASN65 4.1 54.5 1.0 CA B:ASP63 4.1 44.3 1.0 CG B:GLU74 4.2 22.4 1.0 C B:ASP63 4.2 45.1 1.0 N B:GLU69 4.3 36.5 1.0 CA B:VAL70 4.3 30.8 1.0 CB B:ASP63 4.3 41.8 1.0 OD2 B:ASP63 4.4 42.0 1.0 N B:VAL70 4.4 30.6 1.0 N B:ASP67 4.4 41.3 1.0 CA B:GLU69 4.4 38.9 1.0 N B:ASP71 4.4 32.0 1.0 O B:ASP63 4.4 42.8 1.0 CA B:ASN65 4.5 50.8 1.0 N B:ARG66 4.5 55.3 1.0 OD2 B:ASP71 4.6 50.7 1.0 CB B:ASP67 4.6 40.1 1.0 N B:SER64 4.7 49.2 1.0 CA B:ASP67 4.9 40.6 1.0 C B:VAL70 4.9 28.4 1.0 C B:ASP67 4.9 36.4 1.0 C B:ASN65 5.0 56.6 1.0 CB B:GLU69 5.0 45.1 1.0 CG B:ASP71 5.0 43.8 1.0

P.Pathuri, L.Vogeley, H.Luecke. Crystal Structure of Metastasis-Associated Protein S100A4 in the Active Calcium-Bound Form J.Mol.Biol. V. 383 62 2008.
ISSN: ISSN 0022-2836
PubMed: 18783790
DOI: 10.1016/J.JMB.2008.04.076