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Calcium in PDB 2wdb: A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose

Enzymatic activity of A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose

All present enzymatic activity of A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose:
3.2.1.35;

Protein crystallography data

The structure of A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose, PDB code: 2wdb was solved by E.Ficko-Blean, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.06 / 2.03
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.276, 91.276, 132.701, 90.00, 90.00, 120.00
R / Rfree (%) 19.411 / 25.958

Calcium Binding Sites:

The binding sites of Calcium atom in the A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose (pdb code 2wdb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose, PDB code: 2wdb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2wdb

Go back to Calcium Binding Sites List in 2wdb
Calcium binding site 1 out of 4 in the A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1948

b:31.3
occ:1.00
 OE1 A:GLU940 2.2 27.5 1.0
O A:ASN825 2.2 35.0 1.0
O A:SER939 2.3 29.8 1.0
O A:ASP830 2.3 38.2 1.0
O A:THR833 2.4 30.8 1.0
OG1 A:THR833 2.6 31.1 1.0
OD1 A:ASP828 2.6 38.0 1.0
C A:ASP830 3.4 38.2 1.0
C A:THR833 3.4 31.6 1.0
CD A:GLU940 3.4 28.4 1.0
C A:ASN825 3.5 34.7 1.0
C A:SER939 3.5 29.5 1.0
CG A:ASP828 3.7 37.7 1.0
CB A:THR833 3.8 32.1 1.0
N A:ASP830 4.0 38.5 1.0
OD2 A:ASP828 4.0 37.6 1.0
CA A:THR833 4.0 32.2 1.0
N A:THR833 4.1 33.2 1.0
CA A:ASP830 4.2 38.6 1.0
OE2 A:GLU940 4.2 27.5 1.0
CB A:GLU940 4.2 30.7 1.0
CA A:LEU826 4.3 34.3 1.0
N A:LEU826 4.3 34.6 1.0
CA A:SER939 4.4 28.7 1.0
N A:GLU940 4.4 30.2 1.0
CA A:GLU940 4.4 30.5 1.0
CG A:GLU940 4.4 29.5 1.0
N A:ASP831 4.4 37.1 1.0
CA A:ASN825 4.4 34.7 1.0
N A:GLY834 4.5 31.2 1.0
CB A:ASP830 4.5 39.0 1.0
CA A:ASP831 4.6 36.4 1.0
C A:LEU826 4.7 34.6 1.0
CB A:ASN825 4.7 34.6 1.0
C A:ASP831 4.7 35.7 1.0
CB A:SER939 4.7 28.6 1.0
N A:ASP828 4.8 37.2 1.0
CA A:GLY834 4.8 31.2 1.0
N A:GLY829 4.8 38.5 1.0
O A:ASP831 4.9 35.0 1.0
N A:LEU827 4.9 35.2 1.0
CB A:ASP828 5.0 37.8 1.0

Calcium binding site 2 out of 4 in 2wdb

Go back to Calcium Binding Sites List in 2wdb
Calcium binding site 2 out of 4 in the A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1952

b:20.1
occ:1.00
 O B:ASN825 2.2 21.1 1.0
O B:ASP830 2.3 22.1 1.0
OE1 B:GLU940 2.4 19.0 1.0
O B:THR833 2.4 18.7 1.0
OG1 B:THR833 2.4 19.0 1.0
O B:SER939 2.4 19.9 1.0
OD1 B:ASP828 2.5 19.3 1.0
C B:THR833 3.3 19.2 1.0
C B:ASP830 3.4 21.5 1.0
C B:ASN825 3.5 20.3 1.0
CG B:ASP828 3.5 20.7 1.0
CD B:GLU940 3.6 20.7 1.0
CB B:THR833 3.6 19.2 1.0
C B:SER939 3.7 19.8 1.0
OD2 B:ASP828 3.8 19.7 1.0
CA B:THR833 3.8 19.4 1.0
N B:THR833 3.9 20.0 1.0
N B:ASP830 4.0 21.6 1.0
CA B:ASP830 4.1 21.0 1.0
CB B:ASP830 4.3 20.5 1.0
CB B:GLU940 4.3 20.0 1.0
N B:LEU826 4.4 20.2 1.0
CA B:ASN825 4.4 20.0 1.0
CA B:LEU826 4.4 20.1 1.0
N B:ASP831 4.4 21.7 1.0
N B:GLY834 4.4 19.5 1.0
OE2 B:GLU940 4.5 24.7 1.0
CA B:SER939 4.5 19.9 1.0
CG B:GLU940 4.5 19.6 1.0
CA B:GLU940 4.6 20.0 1.0
CB B:ASN825 4.6 20.1 1.0
N B:GLU940 4.6 19.5 1.0
N B:ASP828 4.7 21.5 1.0
C B:LEU826 4.7 20.1 1.0
CA B:ASP831 4.7 21.7 1.0
C B:ASP831 4.7 21.5 1.0
CG2 B:THR833 4.7 17.4 1.0
CA B:GLY834 4.8 19.9 1.0
CB B:SER939 4.8 20.3 1.0
CB B:ASP828 4.8 21.0 1.0
N B:LEU827 4.9 20.7 1.0
N B:GLY829 4.9 22.1 1.0
N B:ASN832 5.0 21.8 1.0

Calcium binding site 3 out of 4 in 2wdb

Go back to Calcium Binding Sites List in 2wdb
Calcium binding site 3 out of 4 in the A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1950

b:19.3
occ:1.00
 O C:ASN825 2.1 22.3 1.0
O C:ASP830 2.2 25.4 1.0
OE1 C:GLU940 2.4 23.2 1.0
O C:THR833 2.4 20.1 1.0
O C:SER939 2.4 19.4 1.0
OG1 C:THR833 2.5 20.6 1.0
OD1 C:ASP828 2.6 28.4 1.0
C C:ASN825 3.3 22.7 1.0
C C:THR833 3.4 21.0 1.0
C C:ASP830 3.4 24.9 1.0
CG C:ASP828 3.6 26.8 1.0
CB C:THR833 3.6 21.8 1.0
CD C:GLU940 3.7 22.4 1.0
C C:SER939 3.7 19.6 1.0
CA C:THR833 3.8 21.3 1.0
N C:THR833 3.9 22.3 1.0
OD2 C:ASP828 4.0 27.9 1.0
N C:ASP830 4.0 25.5 1.0
CA C:ASP830 4.1 25.2 1.0
CA C:ASN825 4.2 22.7 1.0
N C:LEU826 4.2 23.0 1.0
CB C:GLU940 4.3 20.8 1.0
CA C:LEU826 4.3 23.3 1.0
CB C:ASP830 4.3 25.1 1.0
N C:ASP831 4.4 24.2 1.0
OE2 C:GLU940 4.5 22.5 1.0
N C:GLY834 4.5 20.4 1.0
CA C:GLU940 4.5 20.7 1.0
CB C:ASN825 4.5 22.4 1.0
CA C:SER939 4.5 19.1 1.0
N C:GLU940 4.5 20.1 1.0
CG C:GLU940 4.6 21.3 1.0
C C:LEU826 4.6 24.4 1.0
CA C:ASP831 4.6 23.9 1.0
C C:ASP831 4.6 23.6 1.0
N C:ASP828 4.7 26.0 1.0
CG2 C:THR833 4.8 21.7 1.0
CA C:GLY834 4.8 20.2 1.0
N C:ASN832 4.9 23.7 1.0
CB C:ASP828 4.9 26.1 1.0
CB C:SER939 4.9 19.2 1.0
O C:ASP831 4.9 23.2 1.0
N C:LEU827 5.0 25.1 1.0
O C:LEU826 5.0 25.3 1.0

Calcium binding site 4 out of 4 in 2wdb

Go back to Calcium Binding Sites List in 2wdb
Calcium binding site 4 out of 4 in the A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,2)Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1950

b:26.9
occ:1.00
 O D:ASN825 2.1 27.6 1.0
OE1 D:GLU940 2.2 28.9 1.0
O D:ASP830 2.3 31.9 1.0
OD1 D:ASP828 2.4 33.2 1.0
O D:SER939 2.4 25.9 1.0
OG1 D:THR833 2.4 28.2 1.0
O D:THR833 2.6 27.1 1.0
C D:ASN825 3.4 27.8 1.0
C D:THR833 3.4 26.9 1.0
C D:ASP830 3.4 32.0 1.0
CG D:ASP828 3.4 33.6 1.0
CD D:GLU940 3.5 29.5 1.0
C D:SER939 3.6 25.4 1.0
CB D:THR833 3.7 28.1 1.0
OD2 D:ASP828 3.7 34.5 1.0
CA D:THR833 3.9 27.9 1.0
N D:THR833 4.0 28.5 1.0
N D:ASP830 4.0 32.9 1.0
CA D:ASP830 4.2 32.5 1.0
OE2 D:GLU940 4.2 31.9 1.0
CA D:ASN825 4.2 28.0 1.0
N D:LEU826 4.3 27.8 1.0
CB D:GLU940 4.3 27.3 1.0
CA D:LEU826 4.4 27.8 1.0
CB D:ASP830 4.4 32.7 1.0
N D:GLY834 4.4 26.0 1.0
CG D:GLU940 4.4 27.8 1.0
CB D:ASN825 4.4 28.1 1.0
N D:ASP831 4.4 31.1 1.0
CA D:GLU940 4.5 27.0 1.0
CA D:SER939 4.5 24.3 1.0
N D:GLU940 4.5 26.6 1.0
CG2 D:THR833 4.6 29.0 1.0
CA D:ASP831 4.7 30.5 1.0
N D:ASP828 4.7 31.7 1.0
C D:ASP831 4.7 30.3 1.0
C D:LEU826 4.8 28.2 1.0
CA D:GLY834 4.8 25.2 1.0
CB D:ASP828 4.8 32.7 1.0
N D:GLY829 4.9 33.4 1.0
CB D:SER939 4.9 24.2 1.0
O D:ASP831 5.0 30.6 1.0

Reference:

E.Ficko-Blean, A.B.Boraston. N-Acetylglucosamine Recognition By A Family 32 Carbohydrate-Binding Module From Clostridium Perfringens Nagh. J.Mol.Biol. V. 390 208 2009.
ISSN: ISSN 0022-2836
PubMed: 19422833
DOI: 10.1016/J.JMB.2009.04.066
Page generated: Fri Jul 12 18:36:30 2024

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