Calcium in PDB 4cfr: Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia

The structure of Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia, PDB code: 4cfr was solved by A.Duelli, B.Kiss, I.Lundholm, A.Bodor, L.Radnai, M.Petoukhov, D.Svergun, L.Nyitray, G.Katona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.090 / 1.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	64.140, 64.140, 138.220, 90.00, 90.00, 90.00
R / Rfree (%)	16.05 / 17.52

The binding sites of Calcium atom in the Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia (pdb code 4cfr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia, PDB code: 4cfr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1096 b:13.2 occ:1.00 O A:SER20 2.3 14.2 1.0 O A:GLU23 2.4 15.7 1.0 O A:ASP25 2.4 13.4 1.0 O A:LYS28 2.4 12.4 1.0 O A:HOH2046 2.4 14.6 1.0 OE1 A:GLU33 2.4 14.0 1.0 OE2 A:GLU33 2.6 16.2 1.0 CD A:GLU33 2.9 13.9 1.0 C A:SER20 3.4 13.4 1.0 H A:GLU23 3.4 20.3 1.0 HA A:SER20 3.5 16.4 1.0 C A:ASP25 3.5 12.9 1.0 C A:GLU23 3.6 16.0 1.0 C A:LYS28 3.6 10.8 1.0 H A:ASN30 3.7 14.3 1.0 HA A:LEU29 3.8 13.9 1.0 H A:LYS28 3.8 13.7 1.0 HB3 A:ASP25 4.0 20.0 1.0 CA A:SER20 4.0 13.7 1.0 N A:ASP25 4.0 15.4 1.0 H A:ASP25 4.1 18.4 1.0 HB2 A:SER20 4.1 16.1 1.0 N A:GLU23 4.2 16.9 1.0 C A:GLY24 4.2 15.9 1.0 HA A:LYS26 4.2 17.8 1.0 HB2 A:GLU23 4.2 22.5 1.0 CA A:ASP25 4.3 13.9 1.0 N A:ASN30 4.4 12.0 1.0 CA A:GLU23 4.4 17.2 1.0 CG A:GLU33 4.4 14.1 1.0 HA2 A:GLY21 4.4 18.8 1.0 N A:LYS28 4.4 11.4 1.0 CA A:LEU29 4.5 11.6 1.0 N A:LEU29 4.5 11.2 1.0 HA3 A:GLY24 4.5 20.8 1.0 N A:GLY21 4.5 14.4 1.0 N A:LYS26 4.5 14.2 1.0 N A:GLY24 4.5 16.6 1.0 O A:GLY24 4.6 17.0 1.0 CA A:LYS28 4.6 12.3 1.0 CB A:SER20 4.6 13.4 1.0 H A:LYS22 4.6 20.3 1.0 CB A:ASP25 4.6 16.7 1.0 HB2 A:LYS28 4.6 16.6 1.0 CA A:GLY24 4.6 17.3 1.0 CA A:LYS26 4.7 14.8 1.0 HB3 A:ASN30 4.7 16.8 1.0 C A:LYS26 4.7 14.1 1.0 O A:TYR19 4.7 14.9 1.0 HG3 A:GLU33 4.8 16.9 1.0 C A:LEU29 4.8 11.3 1.0 HG2 A:GLU33 4.8 16.9 1.0 CA A:GLY21 4.8 15.7 1.0 CB A:GLU23 4.8 18.8 1.0 HB2 A:GLU33 4.9 14.2 1.0 N A:LYS22 4.9 17.0 1.0 O A:LYS26 5.0 15.2 1.0 OE1 A:GLU69 5.0 19.7 1.0

Calcium binding site 2 out of 4 in the Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1097 b:12.2 occ:1.00 OD1 A:ASN65 2.3 13.7 1.0 O A:GLU69 2.3 12.7 1.0 OD1 A:ASP63 2.3 12.3 1.0 O A:HOH2105 2.4 14.7 1.0 OD1 A:ASP67 2.4 13.2 1.0 OE1 A:GLU74 2.4 12.9 1.0 OE2 A:GLU74 2.5 12.8 1.0 CD A:GLU74 2.8 11.3 1.0 HA A:ASP63 3.2 14.5 1.0 CG A:ASP67 3.3 14.1 1.0 H A:ASP67 3.3 18.1 1.0 CG A:ASN65 3.4 14.7 1.0 H A:GLU69 3.4 14.9 1.0 C A:GLU69 3.4 11.3 1.0 CG A:ASP63 3.5 12.8 1.0 H A:ASN65 3.5 17.8 1.0 HA A:VAL70 3.6 12.4 1.0 OD2 A:ASP67 3.7 16.0 1.0 H A:ASP71 3.7 13.4 1.0 HD22 A:ASN65 3.9 23.3 1.0 HB2 A:GLU69 3.9 18.3 1.0 CA A:ASP63 4.0 12.1 1.0 ND2 A:ASN65 4.1 19.5 1.0 H A:ARG66 4.1 18.4 1.0 N A:GLU69 4.1 12.4 1.0 N A:ASP67 4.2 15.1 1.0 CB A:ASP63 4.2 12.8 1.0 N A:ASN65 4.2 14.9 1.0 CA A:GLU69 4.3 12.9 1.0 C A:ASP63 4.3 12.9 1.0 N A:VAL70 4.3 10.8 1.0 CG A:GLU74 4.3 10.9 1.0 HB2 A:ASP63 4.3 15.3 1.0 CA A:VAL70 4.4 10.4 1.0 OD2 A:ASP63 4.4 14.2 1.0 N A:ASP71 4.4 11.2 1.0 CB A:ASN65 4.4 15.5 1.0 N A:ARG66 4.4 15.3 1.0 CB A:ASP67 4.4 14.9 1.0 OD2 A:ASP71 4.5 16.9 1.0 H A:SER64 4.5 15.9 1.0 HB3 A:ASN65 4.6 18.5 1.0 N A:SER64 4.6 13.3 1.0 CB A:GLU69 4.6 15.3 1.0 CA A:ASN65 4.6 14.9 1.0 HB3 A:ASP67 4.7 17.9 1.0 H A:ASN68 4.7 16.1 0.4 C A:ASN65 4.7 15.2 1.0 H A:ASN68 4.7 16.1 0.6 CA A:ASP67 4.7 14.5 1.0 HG3 A:GLU74 4.7 13.1 1.0 HB3 A:ASP71 4.7 15.8 1.0 HG2 A:GLU74 4.8 13.1 1.0 CG A:ASP71 4.8 14.0 1.0 O A:ASP63 4.8 14.0 1.0 HD3 A:LYS28 4.8 20.1 1.0 HB2 A:GLU74 4.9 12.0 1.0 N A:ASN68 4.9 13.4 1.0 HD21 A:ASN65 4.9 23.3 1.0 C A:VAL70 4.9 10.4 1.0 C A:ASP67 4.9 13.6 1.0 HZ1 A:LYS28 5.0 26.8 1.0

Calcium binding site 3 out of 4 in the Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1101 b:31.5 occ:1.00 O B:SER20 2.4 29.5 1.0 OE1 B:GLU33 2.4 30.8 1.0 O B:GLU23 2.4 33.9 1.0 O B:ASP25 2.4 31.7 1.0 O B:HOH2031 2.4 31.9 1.0 O B:LYS28 2.5 29.4 1.0 OE2 B:GLU33 2.6 31.9 1.0 CD B:GLU33 2.8 30.2 1.0 HA B:SER20 3.3 33.5 1.0 H B:GLU23 3.4 44.9 1.0 C B:SER20 3.4 29.6 1.0 C B:ASP25 3.5 32.5 1.0 C B:GLU23 3.6 36.3 1.0 H B:ASN30 3.6 32.9 1.0 HA B:LYS26 3.6 38.5 1.0 C B:LYS28 3.7 27.0 1.0 HA B:LEU29 3.8 30.6 1.0 H B:LYS28 3.8 32.9 1.0 CA B:SER20 3.9 28.0 1.0 HB2 B:SER20 4.0 32.7 1.0 N B:GLU23 4.1 37.5 1.0 HB3 B:ASP25 4.1 39.6 1.0 N B:ASP25 4.2 33.7 1.0 HB2 B:GLU23 4.2 49.0 1.0 H B:ASP25 4.2 40.4 1.0 CA B:LYS26 4.3 32.1 1.0 N B:ASN30 4.3 27.4 1.0 N B:LYS26 4.3 31.7 1.0 CG B:GLU33 4.3 28.8 1.0 H B:LYS22 4.4 40.5 1.0 CA B:GLU23 4.4 38.2 1.0 CA B:ASP25 4.4 33.1 1.0 C B:GLY24 4.4 35.6 1.0 CA B:LEU29 4.5 25.5 1.0 N B:LYS28 4.5 27.4 1.0 N B:LEU29 4.5 25.8 1.0 CB B:SER20 4.5 27.3 1.0 N B:GLY21 4.6 30.9 1.0 C B:LYS26 4.6 30.7 1.0 HD3 B:LYS26 4.6 46.0 1.0 O B:TYR19 4.6 27.4 1.0 N B:GLY24 4.6 36.0 1.0 HA3 B:GLY24 4.6 42.6 1.0 HA2 B:GLY21 4.6 38.9 1.0 HB3 B:ASN30 4.7 36.0 1.0 CA B:LYS28 4.7 27.4 1.0 HG3 B:GLU33 4.7 34.5 1.0 HG2 B:GLU33 4.7 34.5 1.0 ND2 B:ASN30 4.7 32.8 1.0 HB2 B:GLU33 4.8 34.6 1.0 HD21 B:ASN30 4.8 39.4 1.0 CB B:ASP25 4.8 33.0 1.0 N B:LYS22 4.8 33.8 1.0 CA B:GLY24 4.8 35.6 1.0 CB B:GLU23 4.8 40.9 1.0 C B:LEU29 4.8 26.1 1.0 OE1 B:GLU69 4.9 33.2 1.0 HB2 B:LYS28 4.9 33.9 1.0 CG B:ASN30 4.9 31.6 1.0 HD22 B:ASN30 4.9 39.4 1.0 O B:GLY24 4.9 36.4 1.0 N B:PHE27 5.0 30.5 1.0 O B:LYS26 5.0 31.8 1.0

Calcium binding site 4 out of 4 in the Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ca-Bound S100A4 C3S, C81S, C86S and F45W Mutant Complexed with Non-Muscle Myosin Iia within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1102 b:26.2 occ:1.00 OD1 B:ASP63 2.3 27.9 1.0 O B:GLU69 2.3 26.4 1.0 OD1 B:ASN65 2.3 29.3 1.0 OD1 B:ASP67 2.4 30.4 1.0 O B:HOH2036 2.4 28.4 1.0 OE1 B:GLU74 2.4 22.6 1.0 OE2 B:GLU74 2.6 25.4 1.0 CD B:GLU74 2.9 22.7 1.0 HA B:ASP63 3.3 29.8 1.0 CG B:ASP67 3.3 31.5 1.0 CG B:ASN65 3.4 33.2 1.0 H B:ASP67 3.4 42.0 1.0 CG B:ASP63 3.4 27.7 1.0 H B:GLU69 3.5 33.8 1.0 C B:GLU69 3.5 26.3 1.0 H B:ASN65 3.5 38.6 1.0 HD22 B:ASN65 3.6 43.5 1.0 HA B:VAL70 3.6 27.3 1.0 OD2 B:ASP67 3.6 32.0 1.0 H B:ASP71 3.7 24.8 1.0 HB2 B:GLU69 3.9 36.0 1.0 ND2 B:ASN65 3.9 36.3 1.0 CA B:ASP63 4.0 24.9 1.0 CB B:ASP63 4.1 25.3 1.0 N B:GLU69 4.2 28.2 1.0 H B:ARG66 4.2 42.0 1.0 HB2 B:ASP63 4.2 30.4 1.0 N B:ASP67 4.2 35.0 1.0 OD2 B:ASP63 4.3 29.8 1.0 CA B:GLU69 4.3 27.4 1.0 N B:ASN65 4.3 32.2 1.0 C B:ASP63 4.3 26.6 1.0 N B:VAL70 4.4 24.6 1.0 CA B:VAL70 4.4 22.7 1.0 CG B:GLU74 4.4 20.0 1.0 N B:ASP71 4.4 20.7 1.0 OD2 B:ASP71 4.5 26.3 1.0 CB B:ASP67 4.5 32.2 1.0 N B:ARG66 4.5 35.1 1.0 H B:SER64 4.5 33.3 1.0 CB B:GLU69 4.6 30.1 1.0 CB B:ASN65 4.6 33.2 1.0 N B:SER64 4.6 27.7 1.0 HD21 B:ASN65 4.7 43.5 1.0 HZ1 B:LYS28 4.7 44.8 1.0 C B:ASN65 4.7 33.6 1.0 HB3 B:ASP71 4.7 25.4 1.0 HB3 B:ASP67 4.7 38.6 1.0 CA B:ASN65 4.7 32.4 1.0 HG3 B:GLU74 4.7 23.9 1.0 CA B:ASP67 4.8 33.4 1.0 CG B:ASP71 4.8 23.1 1.0 HG2 B:GLU74 4.8 23.9 1.0 H B:ASN68 4.8 39.4 1.0 HD3 B:LYS28 4.8 39.1 1.0 O B:ASP63 4.8 27.4 1.0 O B:HOH2059 4.8 34.9 1.0 C B:VAL70 4.9 21.8 1.0 HB2 B:GLU74 4.9 21.3 1.0 HB3 B:ASN65 5.0 39.9 1.0 N B:ASN68 5.0 32.8 1.0 C B:ASP67 5.0 33.5 1.0

A.Duelli, B.Kiss, I.Lundholm, A.Bodor, L.Radnai, M.Petoukhov, D.Svergun, L.Nyitray, G.Katona. The C-Terminal Random Coil Region Tunes the CA2+-Binding Affinity of S100A4 Through Conformational Activation. Plos One V. 9 97654 2014.
ISSN: ISSN 1932-6203
PubMed: 24830809
DOI: 10.1371/JOURNAL.PONE.0097654