Calcium in PDB 3m0w: Structure of S100A4 with Pcp

The structure of Structure of S100A4 with Pcp, PDB code: 3m0w was solved by U.A.Ramagopal, N.G.Dulyaninova, 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)	24.98 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.577, 102.275, 117.370, 90.00, 92.60, 90.00
R / Rfree (%)	25.2 / 30.2

The structure of Structure of S100A4 with Pcp also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Calcium atom in the Structure of S100A4 with Pcp (pdb code 3m0w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 20 binding sites of Calcium where determined in the Structure of S100A4 with Pcp, PDB code: 3m0w:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 20 in the Structure of S100A4 with Pcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of S100A4 with Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:91.2 occ:1.00 O A:SER20 2.1 44.1 1.0 O A:ASP25 2.2 44.6 1.0 O A:GLU23 2.3 47.4 1.0 OE1 A:GLU33 2.5 28.0 1.0 O A:LYS28 2.6 41.0 1.0 OE2 A:GLU33 2.9 30.1 1.0 CD A:GLU33 3.0 32.4 1.0 C A:SER20 3.2 43.9 1.0 C A:ASP25 3.3 45.2 1.0 C A:GLU23 3.5 46.4 1.0 C A:LYS28 3.8 40.8 1.0 CA A:SER20 3.9 43.3 1.0 N A:ASP25 4.0 45.1 1.0 C A:GLY24 4.1 45.2 1.0 N A:GLU23 4.1 46.9 1.0 N A:LYS26 4.2 45.2 1.0 CA A:ASP25 4.2 45.1 1.0 CA A:LYS26 4.3 45.4 1.0 N A:GLY21 4.3 44.3 1.0 N A:LYS28 4.4 42.3 1.0 CA A:GLU23 4.4 46.6 1.0 N A:GLY24 4.4 46.0 1.0 O A:GLY24 4.4 45.5 1.0 C A:LYS26 4.4 45.2 1.0 CA A:GLY24 4.5 45.4 1.0 CG A:GLU33 4.5 36.7 1.0 CB A:SER20 4.6 42.6 1.0 N A:LYS22 4.6 45.3 1.0 CA A:GLY21 4.6 44.7 1.0 CA A:LYS28 4.6 41.7 1.0 O A:LYS26 4.7 45.6 1.0 O A:TYR19 4.8 42.8 1.0 N A:LEU29 4.8 40.4 1.0 CB A:ASP25 4.8 45.1 1.0 N A:ASN30 4.8 42.4 1.0 CA A:LEU29 4.8 40.6 1.0 C A:GLY21 4.8 45.3 1.0 ND2 A:ASN30 4.9 43.3 1.0 N A:PHE27 4.9 44.3 1.0

Calcium binding site 2 out of 20 in the Structure of S100A4 with Pcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of S100A4 with Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:89.9 occ:1.00 OD1 A:ASP67 2.1 47.3 1.0 OD1 A:ASN65 2.2 46.1 1.0 OD1 A:ASP63 2.4 44.4 1.0 OE1 A:GLU74 2.5 45.4 1.0 O A:GLU69 2.5 46.5 1.0 OE2 A:GLU74 2.9 38.9 1.0 CD A:GLU74 3.0 43.5 1.0 CG A:ASN65 3.1 44.4 1.0 CG A:ASP67 3.2 46.6 1.0 ND2 A:ASN65 3.6 44.1 1.0 CG A:ASP63 3.6 46.0 1.0 C A:GLU69 3.7 45.8 1.0 OD2 A:ASP67 3.8 48.1 1.0 OD2 A:ASP71 4.2 46.9 1.0 N A:ASP67 4.3 44.5 1.0 CG A:ASP71 4.3 44.2 1.0 OD1 A:ASP71 4.4 44.4 1.0 OD2 A:ASP63 4.4 45.0 1.0 N A:ASP71 4.4 42.9 1.0 CB A:ASP67 4.4 44.8 1.0 CB A:ASN65 4.4 44.9 1.0 CA A:ASP63 4.5 46.4 1.0 CA A:VAL70 4.5 43.7 1.0 N A:VAL70 4.5 44.8 1.0 CB A:ASP63 4.5 45.9 1.0 CG A:GLU74 4.5 41.6 1.0 N A:GLU69 4.5 46.5 1.0 N A:ASN65 4.6 45.2 1.0 CA A:GLU69 4.7 46.2 1.0 N A:ARG66 4.7 45.1 1.0 CA A:ASP67 4.8 44.8 1.0 C A:ASN65 4.8 45.1 1.0 C A:ASP63 4.8 46.4 1.0 CA A:ASN65 4.8 44.8 1.0 C A:VAL70 4.9 43.3 1.0 N A:SER64 5.0 46.1 1.0 CB A:ASP71 5.0 43.1 1.0

Calcium binding site 3 out of 20 in the Structure of S100A4 with Pcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of S100A4 with Pcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:54.4 occ:1.00 O B:HOH103 2.2 31.7 1.0 OE1 B:GLU33 2.3 22.8 1.0 O B:SER20 2.3 43.8 1.0 O B:GLU23 2.4 47.5 1.0 O B:ASP25 2.4 44.9 1.0 O B:LYS28 2.5 40.7 1.0 OE2 B:GLU33 2.8 26.2 1.0 CD B:GLU33 2.9 26.6 1.0 C B:SER20 3.4 43.9 1.0 C B:ASP25 3.5 45.3 1.0 C B:GLU23 3.6 46.6 1.0 C B:LYS28 3.7 40.5 1.0 CA B:SER20 4.0 43.1 1.0 N B:ASP25 4.1 44.6 1.0 N B:GLU23 4.2 46.7 1.0 C B:GLY24 4.2 44.5 1.0 CA B:ASP25 4.3 44.8 1.0 CG B:GLU33 4.4 24.6 1.0 N B:ASN30 4.5 41.8 1.0 N B:LYS28 4.5 42.1 1.0 N B:LYS26 4.5 45.9 1.0 ND2 B:ASN30 4.5 42.4 1.0 CA B:LEU29 4.5 40.3 1.0 N B:GLY24 4.5 45.8 1.0 N B:LEU29 4.5 40.6 1.0 CA B:GLU23 4.5 46.5 1.0 N B:GLY21 4.5 44.0 1.0 CA B:GLY24 4.5 44.9 1.0 CA B:LYS26 4.6 45.2 1.0 OE1 B:GLU69 4.6 54.5 1.0 CA B:LYS28 4.6 41.1 1.0 CB B:SER20 4.7 42.6 1.0 O B:GLY24 4.7 44.7 1.0 O B:TYR19 4.7 42.8 1.0 N B:LYS22 4.7 45.0 1.0 CB B:ASP25 4.8 45.1 1.0 C B:LYS26 4.8 44.7 1.0 C B:LEU29 4.9 40.8 1.0 CG B:ASN30 4.9 42.9 1.0 CA B:GLY21 4.9 44.3 1.0

Calcium binding site 4 out of 20 in the Structure of S100A4 with Pcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of S100A4 with Pcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:53.0 occ:1.00 OD1 B:ASP63 2.1 44.4 1.0 O B:GLU69 2.2 46.1 1.0 OE1 B:GLU74 2.2 37.5 1.0 OD1 B:ASP67 2.2 46.8 1.0 O B:HOH102 2.4 16.8 1.0 OD1 B:ASN65 2.4 46.3 1.0 OE2 B:GLU74 2.5 26.1 1.0 CD B:GLU74 2.7 37.3 1.0 CG B:ASP63 3.3 45.4 1.0 CG B:ASP67 3.3 46.8 1.0 CG B:ASN65 3.3 43.4 1.0 C B:GLU69 3.4 45.2 1.0 ND2 B:ASN65 3.7 43.3 1.0 OD2 B:ASP67 3.9 48.5 1.0 CA B:ASP63 4.0 46.0 1.0 CB B:ASP63 4.0 45.8 1.0 OD2 B:ASP63 4.1 43.9 1.0 N B:GLU69 4.2 46.8 1.0 CG B:GLU74 4.2 36.4 1.0 N B:VAL70 4.2 44.5 1.0 CA B:VAL70 4.2 43.5 1.0 N B:ASP67 4.2 44.4 1.0 N B:ASP71 4.3 42.7 1.0 CA B:GLU69 4.4 46.4 1.0 CB B:ASP67 4.5 44.5 1.0 C B:ASP63 4.5 46.4 1.0 N B:ASN65 4.6 45.3 1.0 CB B:ASN65 4.6 44.8 1.0 N B:ARG66 4.6 44.8 1.0 CA B:ASP67 4.7 44.6 1.0 C B:VAL70 4.7 43.4 1.0 N B:SER64 4.8 45.8 1.0 OD2 B:ASP71 4.8 40.0 1.0 CG B:ASP71 4.9 42.0 1.0 C B:ASN65 4.9 45.0 1.0 C B:ASP67 4.9 44.9 1.0 CA B:ASN65 4.9 44.9 1.0 N B:ASN68 4.9 45.4 1.0

Calcium binding site 5 out of 20 in the Structure of S100A4 with Pcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of S100A4 with Pcp within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:0.4 occ:1.00 O C:SER20 1.9 44.1 1.0 O C:GLU23 1.9 47.6 1.0 OE1 C:GLU33 2.2 36.1 1.0 OE2 C:GLU33 2.7 41.7 1.0 N C:GLU23 2.8 46.9 1.0 CD C:GLU33 2.8 38.6 1.0 C C:SER20 2.9 43.7 1.0 C C:GLU23 2.9 46.5 1.0 O C:ASP25 3.0 44.7 1.0 N C:LYS22 3.3 45.6 1.0 CA C:GLU23 3.4 46.7 1.0 C C:GLY21 3.7 45.5 1.0 N C:GLY21 3.7 44.2 1.0 CA C:GLY21 3.8 44.7 1.0 C C:LYS22 3.8 46.8 1.0 O C:LYS28 3.8 40.8 1.0 CA C:SER20 3.9 43.2 1.0 C C:ASP25 3.9 45.1 1.0 CA C:LYS22 4.0 46.3 1.0 N C:GLY24 4.1 46.0 1.0 O C:TYR19 4.2 43.0 1.0 C C:GLY24 4.3 45.2 1.0 CA C:LYS26 4.3 45.5 1.0 CB C:GLU23 4.3 46.4 1.0 O C:GLY24 4.3 45.3 1.0 CG C:GLU33 4.4 39.5 1.0 O C:GLY21 4.4 45.8 1.0 N C:LYS26 4.5 45.1 1.0 CA C:GLY24 4.6 45.4 1.0 N C:ASP25 4.6 45.1 1.0 CB C:LYS22 4.7 45.9 1.0 C C:LYS26 4.7 45.2 1.0 O C:LYS26 4.8 45.2 1.0 O C:LYS22 4.8 47.5 1.0 N C:SER20 4.9 43.2 1.0 CB C:SER20 4.9 43.0 1.0 C C:TYR19 4.9 42.9 1.0 CG C:GLU23 4.9 47.5 1.0 CA C:ASP25 4.9 45.1 1.0

Calcium binding site 6 out of 20 in the Structure of S100A4 with Pcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of S100A4 with Pcp within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:0.3 occ:1.00 OD1 C:ASP63 1.9 44.1 1.0 O C:GLU69 2.3 46.7 1.0 OD1 C:ASP67 2.3 47.4 1.0 OD1 C:ASN65 2.4 46.2 1.0 OE2 C:GLU74 2.5 43.5 1.0 OE1 C:GLU74 2.7 45.9 1.0 CD C:GLU74 2.9 44.6 1.0 CG C:ASP63 3.2 46.0 1.0 CG C:ASN65 3.5 44.2 1.0 C C:GLU69 3.5 45.9 1.0 CG C:ASP67 3.5 46.6 1.0 CA C:ASP63 4.0 46.4 1.0 OD2 C:ASP63 4.0 44.9 1.0 CB C:ASP63 4.0 46.1 1.0 ND2 C:ASN65 4.1 44.0 1.0 OD2 C:ASP67 4.1 48.2 1.0 N C:ASP67 4.3 44.8 1.0 CA C:VAL70 4.3 43.6 1.0 N C:VAL70 4.3 44.8 1.0 N C:GLU69 4.3 46.5 1.0 N C:ASP71 4.3 42.8 1.0 CG C:GLU74 4.4 41.2 1.0 C C:ASP63 4.4 46.5 1.0 CA C:GLU69 4.5 46.5 1.0 N C:ASN65 4.5 45.3 1.0 N C:ARG66 4.6 45.1 1.0 CB C:ASN65 4.6 44.7 1.0 CB C:ASP67 4.6 44.8 1.0 N C:SER64 4.7 46.1 1.0 C C:VAL70 4.8 43.4 1.0 CA C:ASP67 4.8 45.0 1.0 C C:ASN65 4.8 45.2 1.0 CA C:ASN65 4.8 44.9 1.0 N C:ASN68 5.0 45.3 1.0

Calcium binding site 7 out of 20 in the Structure of S100A4 with Pcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of S100A4 with Pcp within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:0.5 occ:1.00 O D:GLU23 1.9 47.5 1.0 OE2 D:GLU33 2.4 39.2 1.0 O D:SER20 2.5 44.1 1.0 O D:ASP25 2.5 44.7 1.0 OE1 D:GLU33 2.5 38.7 1.0 CD D:GLU33 2.7 39.5 1.0 O D:LYS28 2.9 40.7 1.0 C D:GLU23 3.1 46.5 1.0 C D:ASP25 3.6 45.2 1.0 C D:SER20 3.6 43.7 1.0 N D:GLU23 3.8 46.9 1.0 N D:ASP25 3.9 45.3 1.0 C D:GLY24 4.0 45.3 1.0 CA D:GLU23 4.0 46.7 1.0 N D:GLY24 4.1 46.0 1.0 C D:LYS28 4.1 40.8 1.0 CG D:GLU33 4.2 39.5 1.0 CA D:GLY24 4.2 45.5 1.0 CA D:SER20 4.3 43.1 1.0 CA D:ASP25 4.3 45.1 1.0 ND2 D:ASN30 4.3 43.5 1.0 O D:GLY24 4.4 45.6 1.0 N D:LYS26 4.5 45.4 1.0 N D:LYS22 4.6 45.5 1.0 CA D:LYS26 4.7 45.5 1.0 N D:GLY21 4.7 44.4 1.0 N D:ASN30 4.7 42.3 1.0 CB D:GLU23 4.8 46.5 1.0 CA D:GLY21 4.9 44.9 1.0 O D:TYR19 4.9 43.1 1.0 CG D:ASN30 4.9 43.6 1.0 N D:LYS28 4.9 42.3 1.0 CB D:ASP25 4.9 45.2 1.0 OE1 D:GLU69 4.9 54.5 1.0 C D:GLY21 5.0 45.5 1.0 C D:LYS26 5.0 45.1 1.0 CA D:LEU29 5.0 40.6 1.0 C D:LYS22 5.0 46.9 1.0

Calcium binding site 8 out of 20 in the Structure of S100A4 with Pcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of S100A4 with Pcp within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:0.2 occ:1.00 OD1 D:ASN65 2.2 46.0 1.0 OD1 D:ASP67 2.2 47.0 1.0 OD1 D:ASP63 2.4 44.2 1.0 O D:GLU69 2.6 46.8 1.0 OE1 D:GLU74 2.7 39.8 1.0 OE2 D:GLU74 2.9 40.4 1.0 CD D:GLU74 3.0 40.0 1.0 CG D:ASN65 3.1 44.2 1.0 CG D:ASP67 3.3 46.4 1.0 ND2 D:ASN65 3.6 44.0 1.0 CG D:ASP63 3.6 46.0 1.0 C D:GLU69 3.8 45.9 1.0 OD2 D:ASP67 3.8 48.0 1.0 OD1 D:ASP71 4.1 45.3 1.0 CG D:GLU74 4.2 40.0 1.0 N D:ASP71 4.3 42.9 1.0 CB D:ASN65 4.3 44.7 1.0 N D:ASP67 4.4 44.7 1.0 CG D:ASP71 4.4 44.3 1.0 CA D:ASP63 4.4 46.5 1.0 OD2 D:ASP63 4.5 45.0 1.0 N D:ASN65 4.5 45.3 1.0 CA D:VAL70 4.5 43.6 1.0 CB D:ASP67 4.5 44.7 1.0 CB D:ASP63 4.6 46.1 1.0 N D:VAL70 4.6 44.9 1.0 N D:GLU69 4.6 46.5 1.0 N D:ARG66 4.7 45.1 1.0 CA D:GLU69 4.7 46.4 1.0 CA D:ASN65 4.7 45.0 1.0 CB D:ASP71 4.8 43.2 1.0 C D:ASP63 4.8 46.5 1.0 C D:ASN65 4.8 45.2 1.0 C D:VAL70 4.9 43.4 1.0 CA D:ASP67 4.9 44.9 1.0 N D:SER64 4.9 46.2 1.0 OD2 D:ASP71 5.0 46.0 1.0

Calcium binding site 9 out of 20 in the Structure of S100A4 with Pcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of S100A4 with Pcp within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:96.8 occ:1.00 O E:LYS28 2.6 40.7 1.0 N E:ASN30 2.9 42.5 1.0 CB E:GLU33 3.2 40.1 1.0 CA E:LEU29 3.4 40.5 1.0 O E:SER20 3.5 44.4 1.0 C E:LEU29 3.6 41.7 1.0 C E:LYS28 3.6 40.9 1.0 CG E:ASN30 3.7 43.4 1.0 ND2 E:ASN30 3.7 43.4 1.0 O E:GLU23 3.7 47.7 1.0 N E:LEU29 4.0 40.5 1.0 CA E:SER20 4.0 43.2 1.0 OD1 E:ASN30 4.0 45.5 1.0 CB E:ASN30 4.0 42.4 1.0 CA E:ASN30 4.0 42.4 1.0 O E:TYR19 4.0 42.7 1.0 C E:SER20 4.1 43.8 1.0 O E:ASP25 4.2 44.7 1.0 CB E:LEU29 4.6 40.3 1.0 CD2 E:LEU29 4.6 38.3 1.0 CA E:GLU33 4.6 40.6 1.0 C E:GLU23 4.7 46.6 1.0 N E:GLU23 4.8 46.9 1.0 O E:ASN30 4.8 42.5 1.0 OE1 E:GLU69 4.8 54.5 1.0 O E:LEU29 4.8 42.4 1.0 C E:TYR19 4.9 43.0 1.0 N E:SER20 4.9 43.3 1.0 C E:ASN30 4.9 42.5 1.0 CB E:SER20 4.9 43.0 1.0 N E:GLU33 5.0 41.8 1.0

Calcium binding site 10 out of 20 in the Structure of S100A4 with Pcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of S100A4 with Pcp within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca202 b:97.4 occ:1.00 OD1 E:ASP63 2.1 44.1 1.0 OD1 E:ASN65 2.7 46.0 1.0 CA E:ASP63 2.9 46.4 1.0 CG E:ASP63 3.0 46.1 1.0 C E:ASP63 3.1 46.5 1.0 N E:SER64 3.1 46.2 1.0 O E:GLU69 3.3 46.8 1.0 N E:ASN65 3.5 45.1 1.0 CB E:ASP63 3.5 46.1 1.0 OD1 E:ASP67 3.6 47.5 1.0 CG E:ASN65 3.7 44.1 1.0 O E:LEU62 3.8 47.5 1.0 O E:ASP63 3.9 47.2 1.0 N E:ASP63 4.0 46.8 1.0 OD2 E:ASP63 4.1 45.1 1.0 N E:ARG66 4.2 45.0 1.0 CA E:SER64 4.2 46.0 1.0 CA E:ASN65 4.3 44.9 1.0 CB E:GLU74 4.3 40.0 1.0 C E:SER64 4.3 45.7 1.0 CB E:ASN65 4.3 44.6 1.0 C E:LEU62 4.4 47.4 1.0 C E:GLU69 4.4 45.8 1.0 OG E:SER64 4.5 46.9 1.0 OD2 E:ASP71 4.5 45.1 1.0 C E:ASN65 4.6 45.2 1.0 ND2 E:ASN65 4.6 44.1 1.0 CA E:VAL70 4.8 43.6 1.0 N E:ASP67 4.8 44.4 1.0 CG E:ASP67 4.8 46.7 1.0 N E:ASP71 4.9 43.0 1.0

U.A.Ramagopal, N.G.Dulyaninova, S.C.Almo, A.R.Bresnick. Structure of S100A4 with Pcp To Be Published.