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Chlorine in PDB 1w3m: Crystal Structure of Tsushimycin

Protein crystallography data

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

Other elements in 1w3m:

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

Calcium (Ca) 25 atoms

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Tsushimycin (pdb code 1w3m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Crystal Structure of Tsushimycin, PDB code: 1w3m:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 1w3m

Go back to Chlorine Binding Sites List in 1w3m
Chlorine binding site 1 out of 11 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Tsushimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3014

b:9.9
occ:0.61
 CA A:CA3013 2.5 6.5 1.0
O A:HOH2003 2.8 7.6 0.5
N A:VLL2 3.1 12.5 1.0
CL A:CL3015 3.1 8.9 0.6
O A:VLL2 3.3 9.2 1.0
O A:HOH2005 3.3 21.6 1.0
O A:GLY6 3.4 7.6 1.0
O A:VAL10 3.4 9.6 1.0
O A:GLY8 3.4 7.2 1.0
NG2 A:VLL2 3.4 11.9 1.0
N A:GLY8 3.5 6.4 1.0
CA A:ASP1 3.8 15.0 1.0
CB A:ASP1 3.9 18.9 1.0
C A:ASP1 3.9 15.6 1.0
CA A:VLL2 3.9 11.6 1.0
CA A:GLY8 4.0 7.4 1.0
CA A:PRO11 4.0 10.3 1.0
C A:VLL2 4.0 9.9 1.0
C A:PRO11 4.0 11.0 1.0
O A:HOH2002 4.1 5.4 0.5
C A:GLY8 4.1 6.5 1.0
CB A:VLL2 4.2 12.3 1.0
C A:ASP7 4.2 6.9 1.0
CA A:ASP7 4.4 7.6 1.0
O A:HOH2001 4.4 27.8 1.0
C A:VAL10 4.4 9.0 1.0
C A:GLY6 4.5 6.9 1.0
OD2 A:ASP1 4.5 22.8 1.0
CG A:ASP1 4.5 17.0 1.0
O11 A:LNG0 4.6 23.1 0.3
N A:PRO11 4.7 9.6 1.0
O K:HOH2014 4.8 9.3 1.0
OD2 A:ASP5 4.8 7.5 1.0
CG1 A:VLL2 4.8 16.1 1.0
N A:ASP7 4.9 7.2 1.0

Chlorine binding site 2 out of 11 in 1w3m

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Chlorine binding site 2 out of 11 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Tsushimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3015

b:8.9
occ:0.58
 O K:HOH2003 2.9 10.5 1.0
O A:HOH2013 2.9 10.8 1.0
CL A:CL3014 3.1 9.9 0.6
O A:HOH2005 3.1 21.6 1.0
CA A:GLY8 3.5 7.4 1.0
O A:HOH2003 3.7 7.6 0.5
CA A:PRO11 3.9 10.3 1.0
OD2 K:ASP1 3.9 7.6 1.0
CA K:GLY8 3.9 6.9 1.0
N A:GLY8 3.9 6.4 1.0
C A:GLY8 4.0 6.5 1.0
N K:GLY8 4.1 6.2 1.0
O A:GLY8 4.1 7.2 1.0
O K:HOH2014 4.2 9.3 1.0
O A:VAL10 4.4 9.6 1.0
O K:HOH2005 4.4 18.3 1.0
CB A:PRO11 4.4 14.2 1.0
N A:PRO11 4.4 9.6 1.0
O A:VDL9 4.5 8.3 1.0
CA K:CA3016 4.6 8.5 1.0
CG K:ASP1 4.7 7.2 1.0
C A:VAL10 4.7 9.0 1.0
NG2 A:VLL2 4.7 11.9 1.0
N A:VDL9 4.7 7.0 1.0
CA A:CA3013 4.7 6.5 1.0
OD1 K:ASP7 4.8 8.8 1.0
OD1 K:ASP1 4.8 6.9 1.0
O A:HOH2001 4.8 27.8 1.0
CG A:PRO11 4.8 17.3 1.0
C A:PRO11 4.8 11.0 1.0

Chlorine binding site 3 out of 11 in 1w3m

Go back to Chlorine Binding Sites List in 1w3m
Chlorine binding site 3 out of 11 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Tsushimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl3018

b:9.3
occ:0.81
 O B:HOH2001 3.0 31.3 1.0
O B:HOH2005 3.2 8.8 1.0
N B:2AS4 3.2 8.1 1.0
C B:VLL2 3.3 6.1 1.0
CA B:VLL2 3.5 6.8 1.0
N B:CPI3 3.5 6.6 1.0
N B:VLL2 3.6 7.6 1.0
O B:VLL2 3.6 6.4 1.0
CA B:2AS4 3.7 8.8 1.0
CE B:CPI3 3.7 7.4 1.0
C B:ASP1 3.8 8.9 1.0
O B:ASP1 3.9 10.2 1.0
C B:CPI3 4.3 7.1 1.0
CB B:ASP1 4.3 9.1 1.0
CA B:CPI3 4.4 6.9 1.0
C4 B:2AS4 4.5 12.8 1.0
O B:HOH2010 4.6 10.4 1.0
CA B:ASP1 4.6 11.1 1.0
CB B:2AS4 4.7 10.1 1.0
C B:2AS4 4.8 9.3 1.0
N B:ASP5 4.9 7.3 1.0
CB B:VLL2 5.0 7.5 1.0

Chlorine binding site 4 out of 11 in 1w3m

Go back to Chlorine Binding Sites List in 1w3m
Chlorine binding site 4 out of 11 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Tsushimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl3017

b:13.4
occ:0.75
 CL C:CL3017 0.0 13.4 0.8
CL C:CL3017 1.3 7.5 0.2
CA C:CA3014 2.4 5.2 1.0
O C:HOH2022 2.6 15.4 1.0
N C:VLL2 3.0 8.7 1.0
CL C:CL3018 3.1 9.0 0.6
O C:VLL2 3.2 7.2 1.0
O C:HOH2006 3.3 24.3 1.0
O C:GLY6 3.3 6.7 1.0
O C:VAL10 3.4 7.0 1.0
O C:GLY8 3.4 5.8 1.0
N C:GLY8 3.5 6.4 1.0
NG2 C:VLL2 3.6 8.1 1.0
CA C:ASP1 3.7 12.1 1.0
C C:ASP1 3.8 12.2 1.0
CB C:ASP1 3.8 16.4 1.0
CA C:VLL2 3.9 8.1 1.0
C C:VLL2 4.0 6.5 1.0
CA C:PRO11 4.1 6.5 1.0
CA C:GLY8 4.1 7.4 1.0
C C:GLY8 4.1 5.4 1.0
C C:PRO11 4.1 6.9 1.0
CA C:CA3016 4.2 7.8 0.4
C C:ASP7 4.2 6.5 1.0
CB C:VLL2 4.3 8.6 1.0
CA C:ASP7 4.4 7.3 1.0
OD2 C:ASP1 4.4 16.4 1.0
C C:VAL10 4.4 6.5 1.0
O C:HOH2001 4.4 25.4 1.0
C C:GLY6 4.4 7.0 1.0
CG C:ASP1 4.5 19.2 1.0
OD1 C:ASP5 4.7 5.7 1.0
N C:PRO11 4.7 6.6 1.0
O E:HOH2015 4.8 12.0 1.0
N C:ASP7 4.9 7.3 1.0
O11 C:LNG0 4.9 18.4 0.6
CG1 C:VLL2 5.0 10.9 1.0
N C:ASP1 5.0 16.5 1.0
O C:ASP1 5.0 15.5 1.0

Chlorine binding site 5 out of 11 in 1w3m

Go back to Chlorine Binding Sites List in 1w3m
Chlorine binding site 5 out of 11 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Tsushimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl3017

b:7.5
occ:0.25
 CL C:CL3017 0.0 7.5 0.2
CL C:CL3017 1.3 13.4 0.8
O C:HOH2022 2.1 15.4 1.0
CL C:CL3018 2.2 9.0 0.6
O C:HOH2006 2.4 24.3 1.0
O C:HOH2001 3.5 25.4 1.0
CA C:CA3014 3.6 5.2 1.0
N C:GLY8 3.6 6.4 1.0
N C:VLL2 3.6 8.7 1.0
O E:HOH2015 3.7 12.0 1.0
CA C:CA3016 3.7 7.8 0.4
NG2 C:VLL2 3.8 8.1 1.0
CA C:ASP1 4.0 12.1 1.0
O C:GLY8 4.0 5.8 1.0
CA C:GLY8 4.0 7.4 1.0
O E:HOH2001 4.1 22.1 1.0
CA C:PRO11 4.1 6.5 1.0
O C:VAL10 4.1 7.0 1.0
C C:ASP1 4.3 12.2 1.0
O C:VLL2 4.4 7.2 1.0
C C:GLY8 4.4 5.4 1.0
O C:GLY6 4.4 6.7 1.0
C C:PRO11 4.4 6.9 1.0
CB C:ASP1 4.4 16.4 1.0
O11 C:LNG0 4.5 18.4 0.6
OD2 C:ASP1 4.5 16.4 1.0
C C:ASP7 4.6 6.5 1.0
CA C:VLL2 4.6 8.1 1.0
CB C:VLL2 4.7 8.6 1.0
CA E:GLY8 4.7 8.8 1.0
OD2 C:ASP7 4.7 11.0 0.5
CA C:ASP7 4.8 7.3 1.0
O C:HOH2023 4.8 14.4 1.0
O11 C:LNG0 4.8 20.6 0.4
C C:VAL10 4.9 6.5 1.0
C C:VLL2 4.9 6.5 1.0
CG C:ASP1 5.0 19.2 1.0
N C:PRO11 5.0 6.6 1.0

Chlorine binding site 6 out of 11 in 1w3m

Go back to Chlorine Binding Sites List in 1w3m
Chlorine binding site 6 out of 11 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Tsushimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl3018

b:9.0
occ:0.59
 CL C:CL3017 2.2 7.5 0.2
O C:HOH2023 2.8 14.4 1.0
O E:HOH2001 2.9 22.1 1.0
CL C:CL3017 3.1 13.4 0.8
O C:HOH2006 3.1 24.3 1.0
O C:HOH2022 3.5 15.4 1.0
CA C:GLY8 3.5 7.4 1.0
CA C:PRO11 3.8 6.5 1.0
OD1 E:ASP1 3.9 11.5 1.0
N C:GLY8 3.9 6.4 1.0
C C:GLY8 3.9 5.4 1.0
CA E:GLY8 4.0 8.8 1.0
O C:GLY8 4.0 5.8 1.0
N E:GLY8 4.1 7.1 1.0
O E:HOH2015 4.1 12.0 1.0
O C:VAL10 4.3 7.0 1.0
CB C:PRO11 4.4 8.7 1.0
N C:PRO11 4.4 6.6 1.0
O E:HOH2005 4.5 23.5 1.0
CA E:CA3014 4.5 11.6 1.0
O C:VDL9 4.5 6.8 1.0
CA C:CA3014 4.6 5.2 1.0
C C:VAL10 4.6 6.5 1.0
NG2 C:VLL2 4.6 8.1 1.0
OD1 E:ASP7 4.7 9.5 1.0
O C:HOH2001 4.7 25.4 1.0
CG E:ASP1 4.7 11.3 1.0
N C:VDL9 4.7 5.9 1.0
OD2 E:ASP1 4.7 10.8 1.0
C C:PRO11 4.8 6.9 1.0
CG C:PRO11 5.0 15.8 1.0

Chlorine binding site 7 out of 11 in 1w3m

Go back to Chlorine Binding Sites List in 1w3m
Chlorine binding site 7 out of 11 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Tsushimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3015

b:9.2
occ:0.83
 O D:HOH2007 3.1 9.0 1.0
N D:2AS4 3.2 6.8 1.0
C D:VLL2 3.3 6.4 1.0
CA D:VLL2 3.5 6.3 1.0
N D:CPI3 3.6 6.0 1.0
N D:VLL2 3.6 7.2 1.0
C D:ASP1 3.7 8.7 1.0
CA D:2AS4 3.7 7.2 1.0
O D:VLL2 3.7 6.2 1.0
O D:ASP1 3.7 9.7 1.0
CE D:CPI3 3.7 6.8 1.0
CB D:ASP1 4.2 10.1 1.0
C D:CPI3 4.2 6.5 1.0
C4 D:2AS4 4.5 10.6 1.0
CA D:CPI3 4.5 6.5 1.0
CA D:ASP1 4.5 10.0 1.0
O D:HOH2009 4.5 24.1 1.0
CB D:2AS4 4.7 8.6 1.0
C D:2AS4 4.8 7.8 1.0
N D:ASP5 4.8 7.6 1.0
OD2 D:2AS4 4.9 14.0 1.0
N D:ASP1 5.0 14.4 1.0

Chlorine binding site 8 out of 11 in 1w3m

Go back to Chlorine Binding Sites List in 1w3m
Chlorine binding site 8 out of 11 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Tsushimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl3015

b:11.9
occ:0.83
 N F:2AS4 3.2 7.7 1.0
O F:HOH2006 3.2 12.1 1.0
O F:HOH2002 3.2 27.1 1.0
C F:VLL2 3.3 7.1 1.0
CA F:VLL2 3.4 8.0 1.0
N F:CPI3 3.5 6.6 1.0
O F:HOH2015 3.6 39.0 1.0
N F:VLL2 3.6 8.5 1.0
CE F:CPI3 3.7 7.5 1.0
O F:VLL2 3.7 7.8 1.0
CA F:2AS4 3.7 8.4 1.0
C F:ASP1 3.8 12.3 1.0
O F:ASP1 3.9 13.9 1.0
C F:CPI3 4.2 7.0 1.0
CA F:CPI3 4.4 6.7 1.0
CB F:ASP1 4.5 14.1 1.0
C4 F:2AS4 4.6 10.1 1.0
O F:HOH2019 4.7 27.6 1.0
CA F:ASP1 4.8 15.7 1.0
C F:2AS4 4.8 9.2 1.0
CB F:2AS4 4.8 8.7 1.0
N F:ASP5 4.8 8.0 1.0
CB F:VLL2 4.9 8.7 1.0

Chlorine binding site 9 out of 11 in 1w3m

Go back to Chlorine Binding Sites List in 1w3m
Chlorine binding site 9 out of 11 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Tsushimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl3016

b:10.8
occ:0.80
 O J:HOH2003 3.1 10.2 1.0
N J:2AS4 3.2 8.6 1.0
C J:VLL2 3.3 8.9 1.0
CA J:VLL2 3.5 9.9 1.0
N J:CPI3 3.5 9.5 1.0
N J:VLL2 3.6 10.5 1.0
CE J:CPI3 3.7 11.8 1.0
CA J:2AS4 3.7 8.6 1.0
O J:VLL2 3.7 9.2 1.0
C J:ASP1 3.8 11.3 1.0
O J:ASP1 3.9 13.0 1.0
C J:CPI3 4.2 8.7 1.0
CB J:ASP1 4.3 10.2 1.0
C4 J:2AS4 4.4 12.4 1.0
CA J:CPI3 4.4 8.7 1.0
CA J:ASP1 4.6 10.9 1.0
O J:HOH2009 4.6 19.6 1.0
CB J:2AS4 4.7 10.6 1.0
C J:2AS4 4.8 8.8 1.0
N J:ASP5 4.9 8.8 1.0
CB J:VLL2 5.0 10.7 1.0
OD2 J:2AS4 5.0 14.4 1.0

Chlorine binding site 10 out of 11 in 1w3m

Go back to Chlorine Binding Sites List in 1w3m
Chlorine binding site 10 out of 11 in the Crystal Structure of Tsushimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Tsushimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl3017

b:8.7
occ:0.82
 O K:HOH2006 3.1 8.5 1.0
N K:2AS4 3.2 7.0 1.0
O K:HOH2004 3.2 42.8 1.0
C K:VLL2 3.3 5.5 1.0
CA K:VLL2 3.5 6.0 1.0
N K:CPI3 3.6 6.1 1.0
N K:VLL2 3.6 6.1 1.0
CA K:2AS4 3.7 7.3 1.0
C K:ASP1 3.7 6.8 1.0
O K:VLL2 3.7 5.7 1.0
CE K:CPI3 3.8 6.8 1.0
O K:ASP1 3.8 9.5 1.0
C K:CPI3 4.2 7.1 1.0
CB K:ASP1 4.2 7.9 1.0
CA K:CPI3 4.5 6.5 1.0
C4 K:2AS4 4.5 9.4 1.0
O K:HOH2011 4.5 26.0 1.0
CA K:ASP1 4.5 7.7 1.0
CB K:2AS4 4.7 8.4 1.0
C K:2AS4 4.7 7.2 1.0
N K:ASP5 4.8 7.8 1.0
OD2 K:2AS4 4.9 12.9 1.0
CB K:VLL2 5.0 6.6 1.0

Reference:

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
Page generated: Sat Jul 20 03:32:26 2024

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