Calcium in PDB 3c1v: The 1.5 A Crystal Structure of CA2+-Bound S100A4

The structure of The 1.5 A Crystal Structure of CA2+-Bound S100A4, PDB code: 3c1v was solved by A.R.Gingras, I.L.Barsukov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.31 / 1.50
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	52.320, 52.320, 139.140, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 21.8

The binding sites of Calcium atom in the The 1.5 A Crystal Structure of CA2+-Bound S100A4 (pdb code 3c1v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The 1.5 A Crystal Structure of CA2+-Bound S100A4, PDB code: 3c1v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the The 1.5 A Crystal Structure of CA2+-Bound S100A4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The 1.5 A Crystal Structure of CA2+-Bound S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:11.8 occ:1.00 O A:ASP25 2.3 14.1 1.0 O A:GLU23 2.3 15.8 1.0 O A:HOH114 2.4 14.3 1.0 O A:LYS28 2.4 13.0 1.0 O A:SER20 2.4 12.4 1.0 OE1 A:GLU33 2.4 12.2 1.0 OE2 A:GLU33 2.6 11.7 1.0 CD A:GLU33 2.9 12.3 1.0 C A:ASP25 3.4 14.3 1.0 C A:SER20 3.5 12.6 1.0 C A:GLU23 3.5 15.9 1.0 C A:LYS28 3.6 13.1 1.0 CA A:SER20 4.0 12.4 1.0 N A:GLU23 4.1 15.9 1.0 N A:ASP25 4.1 14.6 1.0 OE1 A:GLU69 4.2 19.2 1.0 C A:GLY24 4.3 14.8 1.0 CA A:ASP25 4.3 14.4 1.0 N A:LYS26 4.3 14.1 1.0 CA A:GLU23 4.3 16.4 1.0 CA A:LYS26 4.4 14.4 1.0 CG A:GLU33 4.4 13.0 1.0 N A:LYS28 4.4 13.4 1.0 N A:ASN30 4.4 13.4 1.0 CA A:LEU29 4.5 12.8 1.0 N A:LEU29 4.5 12.9 1.0 O A:GLY24 4.5 14.8 1.0 N A:GLY24 4.6 15.6 1.0 CA A:LYS28 4.6 13.3 1.0 N A:GLY21 4.6 13.1 1.0 CB A:SER20 4.6 12.2 1.0 C A:LYS26 4.7 14.0 1.0 CA A:GLY24 4.7 15.1 1.0 CB A:GLU23 4.7 16.3 1.0 CB A:ASP25 4.8 14.6 1.0 O A:TYR19 4.8 12.2 1.0 N A:LYS22 4.9 14.8 1.0 C A:LEU29 4.9 13.0 1.0 ND2 A:ASN30 4.9 14.2 1.0 O A:HOH115 4.9 22.8 1.0 CA A:GLY21 5.0 13.8 1.0

Calcium binding site 2 out of 8 in the The 1.5 A Crystal Structure of CA2+-Bound S100A4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The 1.5 A Crystal Structure of CA2+-Bound S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:10.3 occ:1.00 OD1 A:ASP63 2.3 10.5 1.0 O A:GLU69 2.3 13.6 1.0 OD1 A:ASN65 2.3 14.3 1.0 O A:HOH108 2.4 12.6 1.0 OD1 A:ASP67 2.4 15.7 1.0 OE1 A:GLU74 2.4 10.6 1.0 OE2 A:GLU74 2.6 10.6 1.0 CD A:GLU74 2.8 10.3 1.0 CG A:ASP67 3.3 16.3 1.0 CG A:ASN65 3.4 15.1 1.0 CG A:ASP63 3.4 10.8 1.0 C A:GLU69 3.5 13.9 1.0 OD2 A:ASP67 3.7 16.2 1.0 CA A:ASP63 4.0 11.3 1.0 ND2 A:ASN65 4.1 15.4 1.0 CB A:ASP63 4.1 11.1 1.0 N A:ASP67 4.2 17.3 1.0 N A:GLU69 4.3 15.5 1.0 CG A:GLU74 4.3 9.7 1.0 CA A:VAL70 4.4 12.0 1.0 N A:VAL70 4.4 12.9 1.0 OD2 A:ASP63 4.4 11.3 1.0 N A:ASP71 4.4 11.1 1.0 N A:ASN65 4.4 14.1 1.0 C A:ASP63 4.4 11.8 1.0 CA A:GLU69 4.5 14.8 1.0 CB A:ASP67 4.5 16.8 1.0 OD2 A:ASP71 4.5 11.5 1.0 CB A:ASN65 4.5 15.2 1.0 N A:ARG66 4.6 17.0 1.0 N A:SER64 4.7 12.3 1.0 CA A:ASP67 4.7 16.9 1.0 CA A:ASN65 4.8 15.3 1.0 CG A:ASP71 4.8 11.0 1.0 C A:ASN65 4.8 16.1 1.0 N A:ASN68 4.8 16.6 1.0 C A:VAL70 4.9 11.6 1.0 C A:ASP67 4.9 16.8 1.0 O A:ASP63 5.0 11.7 1.0

Calcium binding site 3 out of 8 in the The 1.5 A Crystal Structure of CA2+-Bound S100A4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The 1.5 A Crystal Structure of CA2+-Bound S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:11.8 occ:1.00 O B:GLU23 2.4 18.7 1.0 O B:SER20 2.4 13.1 1.0 O B:ASP25 2.4 19.1 1.0 O B:LYS28 2.4 13.1 1.0 OE1 B:GLU33 2.4 10.8 1.0 O B:HOH174 2.4 16.5 1.0 OE2 B:GLU33 2.6 11.0 1.0 CD B:GLU33 2.9 10.8 1.0 C B:SER20 3.4 13.2 1.0 C B:ASP25 3.5 19.4 1.0 C B:GLU23 3.5 18.9 1.0 C B:LYS28 3.6 13.4 1.0 CA B:SER20 3.9 12.4 1.0 N B:GLU23 4.2 18.6 1.0 N B:ASP25 4.2 19.2 1.0 C B:GLY24 4.3 19.1 1.0 N B:LYS26 4.3 19.6 1.0 CA B:GLU23 4.3 19.0 1.0 CG B:GLU33 4.4 11.0 1.0 CA B:ASP25 4.4 19.3 1.0 CA B:LYS26 4.4 19.8 1.0 N B:ASN30 4.4 12.1 1.0 N B:LYS28 4.5 15.4 1.0 OE1 B:GLU69 4.5 17.7 1.0 CA B:LEU29 4.5 11.8 1.0 N B:LEU29 4.5 12.4 1.0 CB B:SER20 4.5 12.3 1.0 N B:GLY21 4.5 14.3 1.0 N B:GLY24 4.5 18.9 1.0 O B:GLY24 4.6 19.1 1.0 CA B:LYS28 4.6 14.3 1.0 CA B:GLY24 4.7 19.1 1.0 ND2 B:ASN30 4.7 13.4 1.0 C B:LYS26 4.7 19.4 1.0 O B:TYR19 4.8 11.1 1.0 CB B:GLU23 4.8 19.0 1.0 CB B:ASP25 4.9 19.4 1.0 O B:HOH187 4.9 29.3 1.0 N B:LYS22 4.9 17.6 1.0 C B:LEU29 4.9 11.8 1.0 CG B:ASN30 4.9 12.6 1.0 CA B:GLY21 5.0 15.7 1.0

Calcium binding site 4 out of 8 in the The 1.5 A Crystal Structure of CA2+-Bound S100A4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The 1.5 A Crystal Structure of CA2+-Bound S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:12.0 occ:1.00 OD1 B:ASP63 2.3 13.0 1.0 OD1 B:ASN65 2.3 16.9 1.0 O B:GLU69 2.3 12.8 1.0 O B:HOH107 2.4 15.7 1.0 OD1 B:ASP67 2.4 15.9 1.0 OE1 B:GLU74 2.4 11.0 1.0 OE2 B:GLU74 2.6 11.8 1.0 CD B:GLU74 2.9 11.1 1.0 CG B:ASP67 3.3 16.6 1.0 CG B:ASN65 3.4 17.2 1.0 CG B:ASP63 3.4 13.6 1.0 C B:GLU69 3.5 12.8 1.0 OD2 B:ASP67 3.7 16.7 1.0 ND2 B:ASN65 4.0 17.6 1.0 CA B:ASP63 4.0 13.7 1.0 CB B:ASP63 4.2 13.6 1.0 N B:ASP67 4.2 17.6 1.0 N B:GLU69 4.2 14.3 1.0 OD2 B:ASP63 4.4 14.0 1.0 CG B:GLU74 4.4 10.1 1.0 N B:VAL70 4.4 11.8 1.0 N B:ASN65 4.4 16.3 1.0 N B:ASP71 4.4 10.1 1.0 CA B:VAL70 4.4 11.0 1.0 C B:ASP63 4.4 14.4 1.0 CA B:GLU69 4.4 13.7 1.0 OD2 B:ASP71 4.4 12.4 1.0 CB B:ASP67 4.5 16.8 1.0 CB B:ASN65 4.5 17.1 1.0 N B:ARG66 4.6 18.2 1.0 N B:SER64 4.6 14.9 1.0 CA B:ASP67 4.7 16.9 1.0 CG B:ASP71 4.8 10.7 1.0 CA B:ASN65 4.8 17.1 1.0 N B:ASN68 4.8 15.8 1.0 C B:ASN65 4.9 17.7 1.0 C B:ASP67 4.9 16.4 1.0 C B:VAL70 4.9 10.5 1.0 O B:ASP63 5.0 14.6 1.0

Calcium binding site 5 out of 8 in the The 1.5 A Crystal Structure of CA2+-Bound S100A4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The 1.5 A Crystal Structure of CA2+-Bound S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca102 b:11.6 occ:1.00 O C:ASP25 2.3 13.7 1.0 O C:GLU23 2.3 15.2 1.0 O C:SER20 2.4 13.1 1.0 O C:LYS28 2.4 12.8 1.0 O C:HOH151 2.4 15.6 1.0 OE1 C:GLU33 2.4 12.1 1.0 OE2 C:GLU33 2.6 12.0 1.0 CD C:GLU33 2.9 12.5 1.0 C C:SER20 3.4 13.1 1.0 C C:ASP25 3.5 13.9 1.0 C C:GLU23 3.5 15.4 1.0 C C:LYS28 3.6 12.9 1.0 CA C:SER20 4.0 12.9 1.0 N C:GLU23 4.1 15.6 1.0 N C:ASP25 4.2 14.3 1.0 C C:GLY24 4.3 14.5 1.0 CA C:GLU23 4.3 15.9 1.0 N C:LYS26 4.3 13.8 1.0 CA C:ASP25 4.3 14.1 1.0 CA C:LYS26 4.4 14.0 1.0 CG C:GLU33 4.4 13.4 1.0 OE1 C:GLU69 4.4 18.6 1.0 N C:LYS28 4.4 13.1 1.0 N C:ASN30 4.4 13.7 1.0 N C:LEU29 4.5 12.8 1.0 CA C:LEU29 4.5 12.8 1.0 N C:GLY21 4.5 13.5 1.0 O C:GLY24 4.6 14.4 1.0 CA C:LYS28 4.6 13.0 1.0 N C:GLY24 4.6 15.2 1.0 CB C:SER20 4.6 12.8 1.0 C C:LYS26 4.7 13.8 1.0 CB C:GLU23 4.7 15.8 1.0 CA C:GLY24 4.7 14.8 1.0 O C:TYR19 4.8 12.5 1.0 CB C:ASP25 4.8 14.3 1.0 N C:LYS22 4.8 14.8 1.0 C C:LEU29 4.9 13.2 1.0 CA C:GLY21 4.9 14.0 1.0 O C:HOH163 5.0 25.5 1.0 ND2 C:ASN30 5.0 14.7 1.0

Calcium binding site 6 out of 8 in the The 1.5 A Crystal Structure of CA2+-Bound S100A4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The 1.5 A Crystal Structure of CA2+-Bound S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca103 b:10.3 occ:1.00 OD1 C:ASP63 2.3 10.7 1.0 O C:GLU69 2.3 13.6 1.0 OD1 C:ASN65 2.4 14.7 1.0 O C:HOH106 2.4 11.8 1.0 OE1 C:GLU74 2.4 9.1 1.0 OD1 C:ASP67 2.4 15.2 1.0 OE2 C:GLU74 2.6 9.3 1.0 CD C:GLU74 2.8 9.2 1.0 CG C:ASP67 3.3 16.1 1.0 CG C:ASP63 3.4 11.0 1.0 CG C:ASN65 3.4 15.1 1.0 C C:GLU69 3.5 13.8 1.0 OD2 C:ASP67 3.7 16.2 1.0 CA C:ASP63 4.0 11.5 1.0 ND2 C:ASN65 4.1 15.6 1.0 CB C:ASP63 4.1 11.3 1.0 N C:ASP67 4.2 16.8 1.0 N C:GLU69 4.3 15.5 1.0 N C:VAL70 4.4 12.8 1.0 CG C:GLU74 4.4 9.3 1.0 CA C:VAL70 4.4 11.8 1.0 OD2 C:ASP63 4.4 11.5 1.0 N C:ASN65 4.4 13.9 1.0 C C:ASP63 4.4 11.9 1.0 N C:ASP71 4.4 10.8 1.0 CA C:GLU69 4.5 15.0 1.0 OD2 C:ASP71 4.5 10.8 1.0 CB C:ASP67 4.5 16.4 1.0 CB C:ASN65 4.5 14.9 1.0 N C:ARG66 4.5 16.3 1.0 N C:SER64 4.7 12.4 1.0 CA C:ASP67 4.7 16.5 1.0 CA C:ASN65 4.8 14.9 1.0 CG C:ASP71 4.8 10.5 1.0 C C:ASN65 4.8 15.7 1.0 N C:ASN68 4.8 16.4 1.0 C C:ASP67 4.9 16.5 1.0 C C:VAL70 4.9 11.2 1.0 O C:ASP63 4.9 11.7 1.0

Calcium binding site 7 out of 8 in the The 1.5 A Crystal Structure of CA2+-Bound S100A4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The 1.5 A Crystal Structure of CA2+-Bound S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:11.7 occ:1.00 OD1 D:ASN65 2.3 17.3 1.0 OD1 D:ASP63 2.3 12.2 1.0 O D:GLU69 2.3 13.0 1.0 O D:HOH109 2.3 16.1 1.0 OD1 D:ASP67 2.4 16.1 1.0 OE1 D:GLU74 2.4 10.8 1.0 OE2 D:GLU74 2.7 11.1 1.0 CD D:GLU74 2.9 10.7 1.0 CG D:ASP67 3.3 16.7 1.0 CG D:ASN65 3.4 17.4 1.0 CG D:ASP63 3.4 13.0 1.0 C D:GLU69 3.5 13.0 1.0 OD2 D:ASP67 3.7 16.9 1.0 ND2 D:ASN65 4.0 18.1 1.0 CA D:ASP63 4.1 13.5 1.0 CB D:ASP63 4.2 13.4 1.0 N D:ASP67 4.2 17.6 1.0 N D:GLU69 4.2 14.5 1.0 OD2 D:ASP63 4.4 13.1 1.0 N D:VAL70 4.4 12.0 1.0 N D:ASP71 4.4 10.4 1.0 N D:ASN65 4.4 16.3 1.0 CG D:GLU74 4.4 9.8 1.0 CA D:VAL70 4.4 11.2 1.0 CA D:GLU69 4.4 13.9 1.0 OD2 D:ASP71 4.4 12.2 1.0 C D:ASP63 4.5 14.3 1.0 CB D:ASP67 4.5 17.0 1.0 CB D:ASN65 4.5 17.2 1.0 N D:ARG66 4.6 18.1 1.0 N D:SER64 4.7 14.8 1.0 CA D:ASP67 4.7 17.0 1.0 CG D:ASP71 4.8 10.8 1.0 CA D:ASN65 4.8 17.1 1.0 N D:ASN68 4.8 16.1 1.0 C D:ASN65 4.9 17.7 1.0 C D:ASP67 4.9 16.7 1.0 C D:VAL70 4.9 10.7 1.0

Calcium binding site 8 out of 8 in the The 1.5 A Crystal Structure of CA2+-Bound S100A4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The 1.5 A Crystal Structure of CA2+-Bound S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca103 b:11.3 occ:1.00 O D:GLU23 2.3 18.1 1.0 O D:ASP25 2.4 19.5 1.0 O D:HOH107 2.4 15.1 1.0 O D:SER20 2.4 13.0 1.0 O D:LYS28 2.4 13.4 1.0 OE1 D:GLU33 2.4 10.2 1.0 OE2 D:GLU33 2.6 11.1 1.0 CD D:GLU33 2.9 10.7 1.0 C D:SER20 3.4 13.1 1.0 C D:ASP25 3.5 19.7 1.0 C D:GLU23 3.5 18.4 1.0 C D:LYS28 3.6 13.8 1.0 CA D:SER20 3.9 12.3 1.0 N D:ASP25 4.1 19.1 1.0 N D:GLU23 4.2 18.1 1.0 C D:GLY24 4.2 18.8 1.0 CA D:ASP25 4.3 19.4 1.0 CA D:GLU23 4.3 18.4 1.0 CG D:GLU33 4.4 10.8 1.0 N D:LYS26 4.4 20.1 1.0 OE1 D:GLU69 4.4 17.7 1.0 N D:ASN30 4.4 12.5 1.0 N D:LYS28 4.5 16.1 1.0 CA D:LYS26 4.5 20.3 0.5 CB D:SER20 4.5 12.0 1.0 N D:LEU29 4.5 12.7 1.0 CA D:LEU29 4.5 12.1 1.0 N D:GLY24 4.5 18.4 1.0 O D:GLY24 4.5 18.9 1.0 CA D:LYS26 4.6 20.3 0.5 CA D:LYS28 4.6 14.8 1.0 N D:GLY21 4.6 14.0 1.0 CA D:GLY24 4.7 18.6 1.0 ND2 D:ASN30 4.7 13.9 1.0 CB D:GLU23 4.8 18.4 1.0 O D:TYR19 4.8 11.3 1.0 CB D:ASP25 4.8 19.4 1.0 C D:LYS26 4.8 20.1 1.0 CG D:ASN30 4.9 13.1 1.0 C D:LEU29 4.9 12.2 1.0 N D:LYS22 4.9 16.8 1.0 O D:HOH187 5.0 28.4 1.0

A.R.Gingras, J.Basran, A.Prescott, M.Kriajevska, C.R.Bagshaw, I.L.Barsukov. Crystal Structure of the Ca(2+)-Form and Ca(2+)-Binding Kinetics of Metastasis-Associated Protein, S100A4 Febs Lett. V. 582 1651 2008.
ISSN: ISSN 0014-5793
PubMed: 18435928
DOI: 10.1016/J.FEBSLET.2008.04.017