Calcium in PDB 1w3m: Crystal Structure of Tsushimycin

The structure of Crystal Structure of Tsushimycin, PDB code: 1w3m was solved by G.Bunkoczi, L.Vertesy, G.M.Sheldrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.00 / 1.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.488, 36.386, 37.511, 65.64, 68.35, 69.88
R / Rfree (%)	13.7 / 17.1

The structure of Crystal Structure of Tsushimycin also contains other interesting chemical elements:

Chlorine

(Cl)

11 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Tsushimycin (pdb code 1w3m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 25 binding sites of Calcium where determined in the Crystal Structure of Tsushimycin, PDB code: 1w3m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 25 in the Crystal Structure of Tsushimycin


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 Tsushimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3013 b:6.5 occ:0.96 OD2 A:ASP5 2.3 7.5 1.0 O A:VAL10 2.3 9.6 1.0 O A:GLY8 2.3 7.2 1.0 O A:VLL2 2.3 9.2 1.0 O A:GLY6 2.4 7.6 1.0 CL A:CL3014 2.5 9.9 0.6 CG A:ASP5 3.4 8.1 1.0 C A:VAL10 3.5 9.0 1.0 C A:GLY8 3.5 6.5 1.0 C A:VLL2 3.5 9.9 1.0 C A:GLY6 3.6 6.9 1.0 OD1 A:ASP5 3.9 12.0 1.0 N A:VAL10 4.0 7.9 1.0 N A:GLY8 4.0 6.4 1.0 N A:VLL2 4.0 12.5 1.0 N A:GLY6 4.1 8.2 1.0 C A:ASP7 4.2 6.9 1.0 C A:ASP5 4.3 7.4 1.0 CA A:GLY8 4.3 7.4 1.0 CA A:VAL10 4.3 9.1 1.0 C A:VDL9 4.3 7.3 1.0 CA A:VLL2 4.4 11.6 1.0 NG2 A:VLL2 4.4 11.9 1.0 C A:PRO11 4.4 11.0 1.0 N A:PRO11 4.4 9.6 1.0 CA A:GLY6 4.5 8.3 1.0 CA A:CPI3 4.5 9.9 1.0 CA A:PRO11 4.5 10.3 1.0 N A:CPI3 4.5 10.1 1.0 N A:ASP7 4.5 7.2 1.0 N A:VDL9 4.5 7.0 1.0 N A:ASP5 4.5 7.9 1.0 O A:ASP5 4.5 8.4 1.0 O A:ASP7 4.6 7.5 1.0 CA A:ASP7 4.6 7.6 1.0 CB A:ASP5 4.6 8.2 1.0 CA A:VDL9 4.7 7.3 1.0 CA A:ASP5 4.7 7.8 1.0 CL A:CL3015 4.7 8.9 0.6 O A:HOH2008 4.7 14.0 1.0 O A:HOH2003 4.8 7.6 0.5 CB A:ASP1 4.8 18.9 1.0 CB A:VAL10 4.8 10.7 1.0 O A:PRO11 4.8 12.7 1.0 O A:VDL9 4.9 8.3 1.0 C A:ASP1 5.0 15.6 1.0

Calcium binding site 2 out of 25 in the Crystal Structure of Tsushimycin


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 Tsushimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3015 b:5.2 occ:0.95 OD1 B:ASP5 2.3 7.4 1.0 O B:GLY8 2.4 6.7 1.0 O B:VAL10 2.4 6.3 1.0 OD1 B:ASP1 2.4 7.1 1.0 O B:VLL2 2.4 6.4 1.0 O B:HOH2005 2.5 8.8 1.0 O B:GLY6 2.5 7.8 1.0 CG B:ASP1 3.4 8.0 1.0 CG B:ASP5 3.5 7.2 1.0 C B:VAL10 3.6 5.9 1.0 C B:GLY8 3.6 6.8 1.0 C B:VLL2 3.7 6.1 1.0 C B:GLY6 3.7 7.8 1.0 N B:VAL10 4.0 5.8 1.0 OD2 B:ASP5 4.0 9.7 1.0 N B:VLL2 4.1 7.6 1.0 N B:GLY8 4.1 7.1 1.0 N B:GLY6 4.2 9.2 1.0 CB B:ASP1 4.2 9.1 1.0 OD2 B:ASP1 4.2 8.8 1.0 CA B:VAL10 4.3 6.1 1.0 N B:ASP5 4.4 7.3 1.0 C B:ASP5 4.4 8.0 1.0 CA B:GLY8 4.4 8.3 1.0 C B:VDL9 4.4 5.9 1.0 O B:HOH2002 4.4 10.7 1.0 C B:ASP7 4.4 7.7 1.0 CA B:CPI3 4.5 6.9 1.0 CA B:VLL2 4.5 6.8 1.0 CA B:GLY6 4.5 9.4 1.0 N B:CPI3 4.6 6.6 1.0 N B:PRO11 4.6 6.6 1.0 C B:PRO11 4.6 7.2 1.0 N B:VDL9 4.6 6.5 1.0 CA B:PRO11 4.6 6.7 1.0 CB B:ASP5 4.7 7.6 1.0 N B:ASP7 4.7 7.9 1.0 CA B:ASP5 4.7 7.3 1.0 CA B:VDL9 4.7 6.4 1.0 CB B:VAL10 4.8 7.3 1.0 CA B:ASP7 4.8 7.2 1.0 NG2 B:VLL2 4.8 7.8 1.0 N B:2AS4 4.8 8.1 1.0 O B:ASP5 4.9 12.5 1.0 C B:CPI3 4.9 7.1 1.0 O B:PRO11 4.9 7.7 1.0 O B:ASP7 4.9 10.1 1.0 O B:HOH2010 4.9 10.4 1.0 O B:VDL9 5.0 6.5 1.0

Calcium binding site 3 out of 25 in the Crystal Structure of Tsushimycin


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 Tsushimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3016 b:8.8 occ:0.87 OD2 B:ASP7 2.3 10.6 1.0 O11 B:LNG0 2.3 15.7 1.0 OD2 B:ASP1 2.3 8.8 1.0 O G:HOH2016 2.3 11.5 1.0 O B:HOH2009 2.4 13.3 1.0 CG B:ASP1 3.3 8.0 1.0 C1 B:LNG0 3.5 18.0 1.0 CG B:ASP7 3.5 8.3 1.0 CB B:ASP1 3.6 9.1 1.0 O G:VDL9 4.0 9.8 1.0 CA B:ASP1 4.1 11.1 1.0 CA B:ASP7 4.1 7.2 1.0 CB B:ASP7 4.2 8.4 1.0 N B:ASP1 4.2 14.9 1.0 NG2 G:VDL9 4.3 13.0 1.0 N B:GLY8 4.3 7.1 1.0 OD1 B:ASP7 4.4 11.9 1.0 OD1 B:ASP1 4.5 7.1 1.0 C2 B:LNG0 4.5 24.6 1.0 N G:VDL9 4.7 10.5 1.0 O G:HOH2001 4.7 15.3 1.0 C B:ASP7 4.8 7.7 1.0 CA G:GLY8 4.9 9.2 1.0

Calcium binding site 4 out of 25 in the Crystal Structure of Tsushimycin


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 Tsushimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3017 b:10.8 occ:0.56 O B:EOH3014 2.1 28.6 1.0 O B:ASP5 2.3 12.5 1.0 O B:HOH2007 2.4 22.7 1.0 O B:HOH2006 2.4 26.7 1.0 C1 B:EOH3014 3.1 26.8 1.0 C B:ASP5 3.5 8.0 1.0 CA B:GLY6 4.3 9.4 1.0 N B:GLY6 4.4 9.2 1.0 C2 B:EOH3013 4.4 31.1 1.0 CB B:ASP5 4.5 7.6 1.0 C2 B:EOH3014 4.5 20.0 1.0 CA B:ASP5 4.5 7.3 1.0 OD2 B:ASP5 4.5 9.7 1.0 CG B:ASP5 4.6 7.2 1.0 C B:GLY6 4.9 7.8 1.0 O G:HOH2013 4.9 22.2 1.0 O C:HOH2025 5.0 20.8 1.0

Calcium binding site 5 out of 25 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Tsushimycin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3014 b:5.2 occ:1.00 O C:VAL10 2.3 7.0 1.0 OD1 C:ASP5 2.3 5.7 1.0 O C:VLL2 2.3 7.2 1.0 O C:GLY8 2.3 5.8 1.0 O C:GLY6 2.4 6.7 1.0 CL C:CL3017 2.4 13.4 0.8 CG C:ASP5 3.4 5.5 1.0 C C:VAL10 3.5 6.5 1.0 C C:GLY8 3.5 5.4 1.0 C C:VLL2 3.6 6.5 1.0 C C:GLY6 3.6 7.0 1.0 CL C:CL3017 3.6 7.5 0.2 OD2 C:ASP5 3.9 6.9 1.0 N C:VAL10 4.0 5.9 1.0 N C:VLL2 4.0 8.7 1.0 N C:GLY8 4.0 6.4 1.0 N C:GLY6 4.2 6.7 1.0 C C:ASP7 4.2 6.5 1.0 C C:ASP5 4.2 5.8 1.0 CA C:VAL10 4.3 6.1 1.0 CA C:GLY8 4.3 7.4 1.0 C C:VDL9 4.4 5.7 1.0 CA C:VLL2 4.4 8.1 1.0 C C:PRO11 4.4 6.9 1.0 NG2 C:VLL2 4.4 8.1 1.0 N C:PRO11 4.4 6.6 1.0 CA C:PRO11 4.5 6.5 1.0 N C:CPI3 4.5 6.4 1.0 CA C:CPI3 4.5 6.3 1.0 CA C:GLY6 4.5 9.1 1.0 N C:ASP7 4.5 7.3 1.0 N C:ASP5 4.5 5.8 1.0 O C:HOH2022 4.5 15.4 1.0 N C:VDL9 4.6 5.9 1.0 O C:ASP5 4.6 8.1 1.0 CA C:ASP7 4.6 7.3 1.0 CL C:CL3018 4.6 9.0 0.6 CB C:ASP5 4.6 5.8 1.0 O C:ASP7 4.6 8.1 1.0 CB C:ASP1 4.7 16.4 1.0 CA C:ASP5 4.7 5.7 1.0 CA C:VDL9 4.7 6.3 1.0 CB C:VAL10 4.8 7.0 1.0 O C:HOH2013 4.8 20.9 0.6 O C:PRO11 4.8 7.7 1.0 O C:VDL9 5.0 6.8 1.0 C C:ASP1 5.0 12.2 1.0

Calcium binding site 6 out of 25 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Tsushimycin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3015 b:10.3 occ:0.99 O C:EOH3013 2.2 14.1 0.6 O C:HOH2015 2.2 7.8 0.4 O A:ASP5 2.3 8.4 1.0 O C:ASP5 2.3 8.1 1.0 O A:HOH2011 2.4 9.6 1.0 O A:HOH2008 2.4 14.0 1.0 C2 C:EOH3013 2.4 14.8 0.6 O C:HOH2013 2.4 20.9 0.6 C1 C:EOH3013 2.6 12.5 0.6 C C:ASP5 3.5 5.8 1.0 C A:ASP5 3.5 7.4 1.0 CB C:ASP5 4.1 5.8 1.0 CB A:ASP5 4.3 8.2 1.0 CA C:ASP5 4.3 5.7 1.0 CA A:ASP5 4.3 7.8 1.0 O C:HOH2007 4.4 30.0 1.0 OD2 C:ASP5 4.4 6.9 1.0 CG C:ASP5 4.4 5.5 1.0 O A:ASP7 4.4 7.5 1.0 CA A:GLY6 4.4 8.3 1.0 N A:GLY6 4.4 8.2 1.0 N C:GLY6 4.4 6.7 1.0 O A:HOH2006 4.5 27.4 1.0 CA C:GLY6 4.5 9.1 1.0 CG A:ASP5 4.5 8.1 1.0 O C:HOH2024 4.6 34.8 1.0 OD1 A:ASP5 4.6 12.0 1.0 C A:GLY6 4.6 6.9 1.0 O C:HOH2026 4.7 24.7 1.0 O C:ASP7 4.7 8.1 1.0 C C:GLY6 4.9 7.0 1.0 N A:ASP7 4.9 7.2 1.0

Calcium binding site 7 out of 25 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Tsushimycin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3016 b:7.8 occ:0.37 O C:HOH2022 1.9 15.4 1.0 OD2 C:ASP1 2.2 16.4 1.0 OD2 C:ASP7 2.4 11.0 0.5 O11 C:LNG0 2.4 18.4 0.6 O E:HOH2015 2.5 12.0 1.0 OD1 C:ASP7 3.3 22.4 0.6 CG C:ASP1 3.3 19.2 1.0 C1 C:LNG0 3.4 20.6 0.6 O C:HOH2001 3.5 25.4 1.0 CG C:ASP7 3.6 9.5 0.5 CA C:ASP1 3.6 12.1 1.0 CL C:CL3017 3.7 7.5 0.2 O E:VDL9 3.8 10.2 1.0 CG C:ASP7 3.8 9.8 0.6 N C:ASP1 3.9 16.5 1.0 CB C:ASP1 3.9 16.4 1.0 O11 C:LNG0 3.9 20.6 0.4 C1 C:LNG0 4.1 20.6 0.4 NG2 E:VDL9 4.1 11.7 1.0 CL C:CL3017 4.2 13.4 0.8 CA C:ASP7 4.2 7.3 1.0 OD2 C:ASP7 4.2 12.6 0.6 CB C:ASP7 4.3 10.8 0.5 OD1 C:ASP1 4.4 24.4 1.0 N C:GLY8 4.5 6.4 1.0 N E:VDL9 4.5 9.5 1.0 OD1 C:ASP7 4.5 12.1 0.5 CB C:ASP7 4.5 10.9 0.6 C2 C:LNG0 4.7 25.1 0.6 CA E:GLY8 4.7 8.8 1.0 C E:VDL9 4.8 8.9 1.0 C E:GLY8 4.8 9.3 1.0 O C:HOH2006 4.9 24.3 1.0 C C:ASP7 4.9 6.5 1.0 C C:ASP1 5.0 12.2 1.0

Calcium binding site 8 out of 25 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Tsushimycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca3013 b:6.2 occ:0.98 OD1 D:ASP5 2.3 7.1 1.0 OD2 D:ASP1 2.3 8.2 1.0 O D:GLY8 2.4 7.5 1.0 O D:VLL2 2.4 6.2 1.0 O D:VAL10 2.4 6.6 1.0 O D:HOH2007 2.5 9.0 1.0 O D:GLY6 2.5 9.7 1.0 CG D:ASP1 3.4 9.0 1.0 CG D:ASP5 3.5 7.9 1.0 C D:GLY8 3.5 7.6 1.0 C D:VAL10 3.6 6.0 1.0 C D:VLL2 3.6 6.4 1.0 C D:GLY6 3.8 11.4 1.0 N D:VAL10 4.0 6.2 1.0 OD2 D:ASP5 4.0 9.8 1.0 N D:VLL2 4.1 7.2 1.0 CB D:ASP1 4.2 10.1 1.0 N D:GLY8 4.2 7.8 1.0 N D:GLY6 4.2 11.6 1.0 OD1 D:ASP1 4.3 10.0 1.0 O D:HOH2003 4.3 13.7 1.0 CA D:VAL10 4.3 5.9 1.0 N D:ASP5 4.3 7.6 1.0 C D:VDL9 4.3 6.6 1.0 C D:ASP5 4.4 9.3 1.0 CA D:GLY8 4.4 8.7 1.0 CA D:CPI3 4.5 6.5 1.0 C D:ASP7 4.5 8.8 1.0 CA D:VLL2 4.5 6.3 1.0 N D:CPI3 4.5 6.0 1.0 N D:VDL9 4.5 8.6 1.0 C D:PRO11 4.6 6.8 1.0 CA D:VDL9 4.6 7.6 1.0 N D:PRO11 4.6 6.5 1.0 CB D:ASP5 4.6 8.5 1.0 CA D:GLY6 4.6 13.5 1.0 CA D:ASP5 4.7 8.2 1.0 CA D:PRO11 4.7 7.1 1.0 NG2 D:VLL2 4.7 7.1 1.0 CB D:VAL10 4.8 6.4 1.0 N D:ASP7 4.8 10.1 1.0 O D:ASP5 4.8 16.1 1.0 N D:2AS4 4.8 6.8 1.0 C D:CPI3 4.8 6.5 1.0 CA D:ASP7 4.8 9.5 1.0 O D:PRO11 4.9 7.0 1.0 O D:HOH2009 4.9 24.1 1.0 O D:VDL9 5.0 7.8 1.0 O D:ASP7 5.0 10.4 1.0

Calcium binding site 9 out of 25 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Tsushimycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca3014 b:10.3 occ:0.85 OD1 G:2AS4 2.2 17.0 1.0 O11 D:LNG0 2.3 14.7 1.0 OD1 D:ASP7 2.3 12.3 1.0 O L:HOH2010 2.3 13.4 1.0 OD1 D:ASP1 2.3 10.0 1.0 O D:HOH2001 2.3 18.6 1.0 CG G:2AS4 3.3 16.4 1.0 CG D:ASP1 3.3 9.0 1.0 C1 D:LNG0 3.5 17.9 1.0 CG D:ASP7 3.5 11.3 1.0 CB D:ASP1 3.6 10.1 1.0 OD2 G:2AS4 4.0 18.1 1.0 CA D:ASP1 4.1 10.0 1.0 CA D:ASP7 4.1 9.5 1.0 CB D:ASP7 4.2 11.5 1.0 N D:ASP1 4.2 14.4 1.0 O L:VDL9 4.2 11.2 1.0 NG2 L:VDL9 4.2 13.9 1.0 N D:GLY8 4.3 7.8 1.0 CB G:2AS4 4.4 13.4 1.0 C2 D:LNG0 4.5 25.6 1.0 OD2 D:ASP7 4.5 14.9 1.0 O D:HOH2004 4.5 17.3 1.0 OD2 D:ASP1 4.5 8.2 1.0 C3 D:LNG0 4.5 36.2 1.0 C D:ASP7 4.8 8.8 1.0 C4 G:2AS4 4.8 17.4 1.0 O D:HOH2002 4.9 48.8 1.0 N L:VDL9 5.0 12.3 1.0

Calcium binding site 10 out of 25 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Tsushimycin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca3013 b:8.3 occ:1.00 OD1 E:ASP5 2.3 10.3 1.0 O E:GLY8 2.3 9.1 1.0 OD2 E:ASP1 2.4 10.8 1.0 O E:VAL10 2.4 10.1 1.0 O E:VLL2 2.4 12.4 1.0 O E:HOH2004 2.5 13.8 1.0 O E:GLY6 2.5 10.8 1.0 CG E:ASP1 3.4 11.3 1.0 CG E:ASP5 3.5 10.6 1.0 C E:GLY8 3.5 9.3 1.0 C E:VAL10 3.6 9.9 1.0 C E:VLL2 3.6 13.0 1.0 C E:GLY6 3.7 12.6 1.0 N E:VAL10 4.0 9.4 1.0 OD2 E:ASP5 4.0 11.4 1.0 O E:HOH2001 4.0 22.1 1.0 N E:VLL2 4.1 14.5 1.0 N E:GLY8 4.1 7.1 1.0 CB E:ASP1 4.2 15.9 1.0 N E:GLY6 4.2 14.5 1.0 OD1 E:ASP1 4.2 11.5 1.0 C E:ASP5 4.3 13.4 1.0 C E:VDL9 4.3 8.9 1.0 N E:ASP5 4.4 11.3 1.0 CA E:VAL10 4.4 10.2 1.0 CA E:CPI3 4.4 11.4 1.0 C E:ASP7 4.4 7.5 1.0 CA E:GLY8 4.4 8.8 1.0 N E:CPI3 4.5 11.7 1.0 N E:VDL9 4.5 9.5 1.0 CA E:VLL2 4.5 14.8 1.0 CA E:GLY6 4.6 18.1 1.0 N E:PRO11 4.6 12.0 1.0 O E:ASP5 4.6 19.1 1.0 CB E:ASP5 4.6 11.7 1.0 CA E:VDL9 4.6 9.1 1.0 CA E:ASP5 4.6 11.3 1.0 C E:PRO11 4.6 13.0 1.0 CA E:PRO11 4.7 13.1 1.0 N E:ASP7 4.7 11.3 1.0 NG2 E:VLL2 4.8 17.1 1.0 CA E:ASP7 4.8 8.2 1.0 C E:CPI3 4.8 10.6 1.0 N E:2AS4 4.8 11.1 1.0 CB E:VAL10 4.8 10.5 1.0 O E:HOH2008 4.9 31.4 1.0 O E:VDL9 4.9 10.2 1.0 O E:ASP7 4.9 11.0 1.0 O E:HOH2011 5.0 36.2 1.0

G.Bunkoczi, L.Vertesy, G.M.Sheldrick. Structure of the Lipopeptide Antibiotic Tsushimycin. Acta Crystallogr. D Biol. V. 61 1160 2005CRYSTALLOGR..
ISSN: ISSN 0907-4449
PubMed: 16041082
DOI: 10.1107/S0907444905017270