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Calcium in PDB 5j72: CWP6 From Clostridium Difficile

Enzymatic activity of CWP6 From Clostridium Difficile

All present enzymatic activity of CWP6 From Clostridium Difficile:
3.5.1.28;

Protein crystallography data

The structure of CWP6 From Clostridium Difficile, PDB code: 5j72 was solved by M.Renko, A.Usenik, D.Turk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.85 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.357, 212.916, 84.931, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.1

Other elements in 5j72:

The structure of CWP6 From Clostridium Difficile also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the CWP6 From Clostridium Difficile (pdb code 5j72). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the CWP6 From Clostridium Difficile, PDB code: 5j72:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5j72

Go back to Calcium Binding Sites List in 5j72
Calcium binding site 1 out of 6 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of CWP6 From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:45.6
occ:0.70
 CA A:CA701 0.0 45.6 0.7
CA A:CA701 1.7 57.1 0.3
O A:HOH979 2.1 48.8 1.0
O A:HOH1181 2.3 38.6 1.0
O A:HOH1204 2.3 34.7 1.0
O A:HOH1007 2.4 26.2 1.0
OD1 A:ASN15 2.6 32.6 1.0
CG A:ASN15 3.5 33.8 1.0
O A:HOH1155 3.6 50.1 1.0
OD2 A:ASP190 3.9 48.0 1.0
NZ A:LYS395 4.0 36.7 1.0
OD2 A:ASP163 4.0 29.2 1.0
O A:HOH1361 4.2 71.7 1.0
O A:HOH1173 4.2 24.4 1.0
CB A:ASN15 4.2 21.4 1.0
OD1 A:ASP163 4.3 31.8 1.0
ND2 A:ASN15 4.3 38.1 1.0
O A:GLY160 4.4 18.4 1.0
CD1 A:TRP161 4.4 17.4 1.0
CA A:ASN15 4.4 17.1 1.0
CG A:ASP163 4.6 28.0 1.0
CG A:ASP190 4.6 43.5 1.0
NE1 A:TRP161 4.8 18.8 1.0
OD1 A:ASP190 4.8 39.8 1.0
O A:GLY164 4.8 18.4 1.0

Calcium binding site 2 out of 6 in 5j72

Go back to Calcium Binding Sites List in 5j72
Calcium binding site 2 out of 6 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of CWP6 From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:57.1
occ:0.30
 CA A:CA701 0.0 57.1 0.3
CA A:CA701 1.7 45.6 0.7
O A:HOH1155 2.3 50.1 1.0
O A:HOH979 2.5 48.8 1.0
O A:HOH1181 2.8 38.6 1.0
O A:HOH1361 2.8 71.7 1.0
OD2 A:ASP190 2.9 48.0 1.0
O A:HOH1007 3.0 26.2 1.0
OD1 A:ASN15 3.5 32.6 1.0
CG A:ASP190 3.7 43.5 1.0
CG A:ASN15 3.9 33.8 1.0
O A:HOH1204 4.0 34.7 1.0
OD1 A:ASP190 4.2 39.8 1.0
ND2 A:ASN15 4.2 38.1 1.0
O A:HOH1082 4.3 29.7 1.0
O A:ASP190 4.4 24.1 1.0
CD1 A:TRP161 4.4 17.4 1.0
NE1 A:TRP161 4.6 18.8 1.0
CB A:ASP190 4.6 34.5 1.0
CB A:ASN15 4.6 21.4 1.0
NZ A:LYS395 4.9 36.7 1.0
O A:GLY164 4.9 18.4 1.0

Calcium binding site 3 out of 6 in 5j72

Go back to Calcium Binding Sites List in 5j72
Calcium binding site 3 out of 6 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of CWP6 From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:60.1
occ:1.00
 O A:HOH997 2.2 31.7 1.0
O A:SER338 2.4 27.4 1.0
O A:ALA341 2.5 26.3 1.0
C A:ALA341 3.5 28.2 1.0
C A:SER338 3.6 26.3 1.0
O A:HOH969 3.8 27.9 1.0
O A:LYS339 3.9 31.0 1.0
C A:LYS339 3.9 31.5 1.0
N A:ALA341 4.0 30.1 1.0
CA A:LYS339 4.1 27.3 1.0
CA A:LYS342 4.2 26.6 1.0
O A:LYS342 4.2 27.9 1.0
N A:LYS342 4.3 26.0 1.0
N A:LYS339 4.3 25.8 1.0
N A:ILE340 4.4 29.5 1.0
C A:LYS342 4.4 31.0 1.0
CA A:ALA341 4.4 27.6 1.0
C A:ILE340 4.7 33.8 1.0
CA A:SER338 4.8 27.6 1.0
OG A:SER338 4.8 35.3 1.0
CA A:ILE340 4.9 31.7 1.0

Calcium binding site 4 out of 6 in 5j72

Go back to Calcium Binding Sites List in 5j72
Calcium binding site 4 out of 6 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of CWP6 From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:39.4
occ:1.00
 O B:HOH886 2.3 31.8 1.0
O B:HOH1088 2.3 25.5 1.0
O B:HOH997 2.4 23.8 1.0
O B:HOH909 2.4 24.9 1.0
O B:HOH1273 2.4 21.3 1.0
OD1 B:ASN15 2.5 21.7 1.0
CG B:ASN15 3.3 25.5 1.0
OD2 B:ASP163 3.9 23.7 1.0
O B:HOH896 4.0 32.5 1.0
CB B:ASN15 4.0 22.5 1.0
NZ B:LYS395 4.1 23.8 1.0
ND2 B:ASN15 4.1 24.9 1.0
O B:HOH1137 4.1 24.9 1.0
CA B:ASN15 4.1 22.7 1.0
O B:GLY160 4.2 20.6 1.0
OD1 B:ASP163 4.2 27.9 1.0
O B:HOH1145 4.3 49.2 1.0
O B:HOH1021 4.3 22.3 1.0
OD2 B:ASP190 4.5 46.0 1.0
CG B:ASP163 4.5 24.9 1.0
CD1 B:TRP161 4.6 21.3 1.0
OD1 B:ASP190 4.6 42.9 1.0
CG B:ASP190 4.8 42.6 1.0
O B:ILE14 4.9 22.6 1.0
CE B:LYS395 4.9 24.7 1.0
NE1 B:TRP161 5.0 22.0 1.0

Calcium binding site 5 out of 6 in 5j72

Go back to Calcium Binding Sites List in 5j72
Calcium binding site 5 out of 6 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of CWP6 From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:61.4
occ:1.00
 OD1 B:ASN109 2.1 50.8 1.0
OD1 B:ASP112 2.4 26.8 1.0
O B:HOH891 2.4 42.2 1.0
O B:HOH1349 2.5 42.9 1.0
O B:HOH1201 2.6 40.6 1.0
O B:HOH1061 2.8 31.4 1.0
CG B:ASN109 3.1 47.1 1.0
CG B:ASP112 3.3 28.1 1.0
CB B:ASN109 3.5 31.4 1.0
OD2 B:ASP112 3.6 25.7 1.0
O B:HOH853 3.6 25.4 1.0
ND2 B:ASN109 4.3 50.8 1.0
O B:HOH1040 4.5 33.0 1.0
N B:ASN109 4.6 27.4 1.0
CA B:ASP163 4.6 25.3 1.0
O B:HOH1245 4.7 40.6 1.0
CA B:ASN109 4.7 28.5 1.0
O B:LYS162 4.7 24.4 1.0
CB B:ASP112 4.7 22.4 1.0
O B:HOH1103 4.7 38.2 1.0
O B:HOH1214 4.7 38.3 1.0
O B:ASP163 4.8 27.4 1.0
C B:ASP163 4.9 28.6 1.0

Calcium binding site 6 out of 6 in 5j72

Go back to Calcium Binding Sites List in 5j72
Calcium binding site 6 out of 6 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of CWP6 From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:33.4
occ:0.50
 OG1 B:THR590 2.5 16.7 1.0
O B:THR590 2.5 17.7 1.0
O B:LEU591 2.5 16.8 1.0
C B:THR590 3.0 15.0 1.0
C B:LEU591 3.2 18.9 1.0
CB B:THR590 3.4 15.6 1.0
CA B:THR590 3.7 17.0 1.0
N B:LEU591 3.7 17.8 1.0
N B:ASP592 4.0 19.6 1.0
CA B:LEU591 4.0 18.6 1.0
O B:HOH874 4.0 38.5 1.0
N B:THR590 4.2 19.0 1.0
CA B:ASP592 4.2 20.9 1.0
CG2 B:THR590 4.7 18.6 1.0
C B:ASP592 4.8 24.3 1.0
N B:GLY594 4.9 19.5 1.0
OD2 B:ASP592 5.0 37.9 1.0

Reference:

A.Usenik, M.Renko, M.Mihelic, N.Lindic, J.Borisek, A.Perdih, G.Pretnar, U.Muller, D.Turk. The CWB2 Cell Wall-Anchoring Module Is Revealed By the Crystal Structures of the Clostridium Difficile Cell Wall Proteins CWP8 and CWP6. Structure V. 25 514 2017.
ISSN: ISSN 1878-4186
PubMed: 28132783
DOI: 10.1016/J.STR.2016.12.018
Page generated: Sun Jul 14 20:53:21 2024

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