Calcium in PDB 2q91: Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor

The structure of Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor, PDB code: 2q91 was solved by V.N.Malashkevich, D.Knight, U.A.Ramagopal, S.C.Almo, A.R.Bresnick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.16 / 1.63
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.424, 52.424, 140.419, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 21.7

The binding sites of Calcium atom in the Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor (pdb code 2q91). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor, PDB code: 2q91:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:18.1 occ:1.00 O A:GLU23 2.3 21.9 1.0 O A:SER20 2.4 19.6 1.0 O A:HOH107 2.4 22.6 1.0 O A:ASP25 2.4 21.6 1.0 O A:LYS28 2.4 18.4 1.0 OE1 A:GLU33 2.5 19.1 1.0 OE2 A:GLU33 2.6 18.8 1.0 CD A:GLU33 2.9 17.2 1.0 C A:SER20 3.4 17.9 1.0 C A:ASP25 3.5 24.9 1.0 C A:GLU23 3.5 24.6 1.0 C A:LYS28 3.6 17.4 1.0 CA A:SER20 4.0 14.4 1.0 N A:ASP25 4.2 24.4 1.0 N A:GLU23 4.2 25.6 1.0 C A:GLY24 4.2 23.9 1.0 CA A:GLU23 4.3 25.2 1.0 CA A:LYS26 4.4 27.9 1.0 CG A:GLU33 4.4 16.9 1.0 N A:LYS28 4.4 19.9 1.0 OE1 A:GLU69 4.4 31.9 1.0 CA A:ASP25 4.4 25.1 1.0 N A:LYS26 4.4 26.1 1.0 N A:ASN30 4.4 16.8 1.0 O A:GLY24 4.5 25.1 1.0 CA A:LEU29 4.5 16.2 1.0 N A:LEU29 4.5 16.5 1.0 N A:GLY24 4.5 23.7 1.0 N A:GLY21 4.5 20.7 1.0 CA A:LYS28 4.6 18.1 1.0 CB A:SER20 4.6 15.8 1.0 CA A:GLY24 4.6 23.3 1.0 C A:LYS26 4.7 27.3 1.0 CB A:GLU23 4.8 25.9 1.0 O A:TYR19 4.8 18.2 1.0 N A:LYS22 4.8 22.1 1.0 CB A:ASP25 4.9 25.1 1.0 C A:LEU29 4.9 17.0 1.0 CA A:GLY21 4.9 22.6 1.0 ND2 A:ASN30 5.0 22.4 1.0

Calcium binding site 2 out of 4 in the Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:19.0 occ:1.00 OD1 A:ASN65 2.3 21.4 1.0 O A:HOH108 2.4 23.7 1.0 OD1 A:ASP63 2.4 20.4 1.0 OE1 A:GLU74 2.4 17.1 1.0 O A:GLU69 2.4 19.6 1.0 OD1 A:ASP67 2.5 22.2 1.0 OE2 A:GLU74 2.5 20.8 1.0 CD A:GLU74 2.8 18.1 1.0 CG A:ASP67 3.3 26.8 1.0 CG A:ASN65 3.4 30.9 1.0 CG A:ASP63 3.5 21.5 1.0 C A:GLU69 3.6 19.8 1.0 OD2 A:ASP67 3.6 24.3 1.0 ND2 A:ASN65 4.0 30.3 1.0 CA A:ASP63 4.1 20.6 1.0 CB A:ASP63 4.2 20.7 1.0 N A:ASP67 4.2 23.2 1.0 N A:GLU69 4.3 20.5 1.0 CG A:GLU74 4.3 14.5 1.0 OD2 A:ASP63 4.4 22.2 1.0 CA A:VAL70 4.4 17.1 1.0 N A:ASP71 4.4 16.1 1.0 N A:ASN65 4.4 23.7 1.0 N A:VAL70 4.4 17.3 1.0 C A:ASP63 4.4 22.4 1.0 CB A:ASP67 4.5 24.1 1.0 OD2 A:ASP71 4.5 25.6 1.0 CA A:GLU69 4.5 20.1 1.0 CB A:ASN65 4.6 25.0 1.0 N A:ARG66 4.6 24.5 1.0 CA A:ASP67 4.7 23.0 1.0 N A:SER64 4.7 21.7 1.0 CA A:ASN65 4.8 25.1 1.0 CG A:ASP71 4.8 21.9 1.0 C A:ASN65 4.8 26.3 1.0 C A:VAL70 4.9 15.9 1.0 N A:ASN68 4.9 22.3 1.0 C A:ASP67 4.9 22.9 1.0 O A:ASP63 4.9 21.9 1.0 O A:HOH115 4.9 33.0 1.0

Calcium binding site 3 out of 4 in the Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:17.5 occ:1.00 OD1 B:ASP63 2.3 17.9 1.0 O B:GLU69 2.3 19.2 1.0 OD1 B:ASN65 2.3 18.7 1.0 OD1 B:ASP67 2.4 19.4 1.0 OE1 B:GLU74 2.4 18.1 1.0 O B:HOH105 2.5 19.2 1.0 OE2 B:GLU74 2.5 19.1 1.0 CD B:GLU74 2.8 19.9 1.0 CG B:ASP67 3.3 21.3 1.0 CG B:ASP63 3.4 20.6 1.0 CG B:ASN65 3.4 21.4 1.0 C B:GLU69 3.5 18.6 1.0 OD2 B:ASP67 3.7 24.7 1.0 CA B:ASP63 4.0 18.5 1.0 CB B:ASP63 4.1 18.3 1.0 ND2 B:ASN65 4.1 26.1 1.0 N B:ASP67 4.2 21.2 1.0 N B:GLU69 4.2 20.6 1.0 CG B:GLU74 4.3 17.2 1.0 N B:ASN65 4.3 18.1 1.0 CA B:VAL70 4.4 17.9 1.0 N B:VAL70 4.4 16.9 1.0 OD2 B:ASP63 4.4 20.3 1.0 C B:ASP63 4.4 18.3 1.0 CB B:ASP67 4.4 22.4 1.0 N B:ASP71 4.5 16.4 1.0 CA B:GLU69 4.5 20.9 1.0 CB B:ASN65 4.5 21.8 1.0 N B:ARG66 4.5 21.0 1.0 OD2 B:ASP71 4.6 21.9 1.0 CA B:ASP67 4.7 22.9 1.0 N B:SER64 4.7 18.6 1.0 CA B:ASN65 4.7 21.1 1.0 C B:ASN65 4.8 22.9 1.0 N B:ASN68 4.8 22.8 1.0 C B:ASP67 4.9 22.5 1.0 CG B:ASP71 4.9 22.4 1.0 C B:VAL70 4.9 17.6 1.0 O B:ASP63 4.9 17.7 1.0 O B:HOH155 5.0 29.4 1.0

Calcium binding site 4 out of 4 in the Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:19.1 occ:1.00 O B:GLU23 2.4 20.7 1.0 O B:HOH153 2.4 25.9 1.0 O B:LYS28 2.4 18.1 1.0 O B:ASP25 2.4 19.3 1.0 OE1 B:GLU33 2.4 21.1 1.0 O B:SER20 2.4 21.3 1.0 OE2 B:GLU33 2.5 18.9 1.0 CD B:GLU33 2.8 22.4 1.0 C B:SER20 3.5 18.8 1.0 C B:ASP25 3.6 20.8 1.0 C B:GLU23 3.6 21.8 1.0 C B:LYS28 3.6 18.9 1.0 CA B:SER20 4.0 18.0 1.0 N B:GLU23 4.1 23.0 1.0 N B:ASP25 4.2 21.0 1.0 CG B:GLU33 4.3 18.1 1.0 C B:GLY24 4.3 21.1 1.0 CA B:GLU23 4.3 22.9 1.0 OE2 B:GLU69 4.4 35.5 1.0 N B:ASN30 4.4 18.6 1.0 CA B:ASP25 4.4 21.2 1.0 N B:LYS28 4.5 18.9 1.0 CA B:LYS26 4.5 20.8 1.0 N B:LYS26 4.5 18.8 1.0 CA B:LEU29 4.5 18.3 1.0 N B:LEU29 4.5 16.7 1.0 N B:GLY24 4.6 22.3 1.0 N B:GLY21 4.6 19.8 1.0 CA B:LYS28 4.6 20.1 1.0 CB B:SER20 4.6 16.9 1.0 O B:GLY24 4.6 21.4 1.0 O B:TYR19 4.7 19.1 1.0 C B:LYS26 4.7 18.9 1.0 CA B:GLY24 4.7 20.6 1.0 CB B:GLU23 4.7 22.8 1.0 N B:LYS22 4.8 20.5 1.0 CB B:ASP25 4.8 21.8 1.0 C B:LEU29 4.8 19.8 1.0 ND2 B:ASN30 4.9 24.4 1.0 CA B:GLY21 4.9 21.0 1.0 C B:GLY21 5.0 21.8 1.0 CG B:ASN30 5.0 26.4 1.0

V.N.Malashkevich, K.M.Varney, S.C.Garrett, P.T.Wilder, D.Knight, T.H.Charpentier, U.A.Ramagopal, S.C.Almo, D.J.Weber, A.R.Bresnick. Structure of Ca(2+)-Bound S100A4 and Its Interaction with Peptides Derived From Nonmuscle Myosin-Iia. Biochemistry V. 47 5111 2008.
ISSN: ISSN 0006-2960
PubMed: 18410126
DOI: 10.1021/BI702537S