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Calcium in PDB 2w1u: A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,3)Galnac

Enzymatic activity of A Family 32 Carbohydrate-Binding Module, From the Mu Toxin Produced By Clostridium Perfringens, in Complex with Beta- D-Glcnac-Beta(1,3)Galnac

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(1,3)Galnac:
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(1,3)Galnac, PDB code: 2w1u 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) 20.00 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.170, 91.170, 132.607, 90.00, 90.00, 120.00
R / Rfree (%) 16.915 / 21.33

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(1,3)Galnac (pdb code 2w1u). 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(1,3)Galnac, PDB code: 2w1u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2w1u

Go back to Calcium Binding Sites List in 2w1u
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(1,3)Galnac


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(1,3)Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1948

b:19.6
occ:1.00
 OE1 A:GLU940 2.2 16.9 1.0
O A:ASN825 2.2 22.0 1.0
O A:ASP830 2.3 23.4 1.0
O A:THR833 2.3 20.9 1.0
O A:SER939 2.3 17.7 1.0
OG1 A:THR833 2.6 21.0 1.0
OD1 A:ASP828 2.7 27.0 1.0
C A:THR833 3.3 22.0 1.0
C A:ASP830 3.4 25.0 1.0
CD A:GLU940 3.4 17.5 1.0
C A:ASN825 3.4 22.5 1.0
C A:SER939 3.5 17.9 1.0
CG A:ASP828 3.6 26.9 1.0
CB A:THR833 3.8 22.1 1.0
CA A:THR833 3.9 22.7 1.0
OD2 A:ASP828 3.9 24.4 1.0
N A:THR833 4.0 23.7 1.0
N A:ASP830 4.0 25.1 1.0
CA A:ASP830 4.2 25.3 1.0
CB A:GLU940 4.3 17.9 1.0
OE2 A:GLU940 4.3 21.3 1.0
CA A:ASN825 4.3 22.1 1.0
N A:LEU826 4.4 21.8 1.0
CG A:GLU940 4.4 17.1 1.0
CA A:LEU826 4.4 21.6 1.0
CA A:SER939 4.4 17.4 1.0
N A:GLY834 4.4 22.6 1.0
CB A:ASP830 4.4 25.1 1.0
CA A:GLU940 4.4 17.7 1.0
N A:ASP831 4.5 24.6 1.0
N A:GLU940 4.5 17.5 1.0
CB A:ASN825 4.6 21.7 1.0
CA A:ASP831 4.7 24.9 1.0
CB A:SER939 4.7 16.2 1.0
C A:LEU826 4.7 21.6 1.0
CA A:GLY834 4.8 22.4 1.0
C A:ASP831 4.8 25.0 1.0
N A:ASP828 4.9 25.3 1.0
N A:GLY829 5.0 27.5 1.0
CB A:ASP828 5.0 25.4 1.0
CG2 A:THR833 5.0 23.4 1.0

Calcium binding site 2 out of 4 in 2w1u

Go back to Calcium Binding Sites List in 2w1u
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(1,3)Galnac


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(1,3)Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1952

b:14.8
occ:1.00
 O B:ASN825 2.2 12.7 1.0
O B:ASP830 2.3 13.7 1.0
OE1 B:GLU940 2.4 15.7 1.0
O B:THR833 2.4 12.4 1.0
O B:SER939 2.5 14.2 1.0
OD1 B:ASP828 2.5 11.7 1.0
OG1 B:THR833 2.6 15.4 1.0
C B:THR833 3.3 13.3 1.0
C B:ASP830 3.4 14.3 1.0
C B:ASN825 3.5 12.9 1.0
CG B:ASP828 3.5 13.8 1.0
CD B:GLU940 3.6 14.7 1.0
C B:SER939 3.7 13.1 1.0
OD2 B:ASP828 3.8 13.7 1.0
CB B:THR833 3.8 13.7 1.0
CA B:THR833 3.9 14.2 1.0
N B:THR833 3.9 13.9 1.0
N B:ASP830 4.0 14.1 1.0
CA B:ASP830 4.1 13.9 1.0
CB B:ASP830 4.3 13.1 1.0
CA B:LEU826 4.3 13.4 1.0
N B:GLY834 4.3 13.6 1.0
N B:LEU826 4.4 12.4 1.0
CB B:GLU940 4.4 12.4 1.0
OE2 B:GLU940 4.4 19.2 1.0
CA B:ASN825 4.5 12.4 1.0
N B:ASP831 4.5 14.8 1.0
CA B:SER939 4.5 13.1 1.0
CA B:GLU940 4.5 13.7 1.0
CG B:GLU940 4.5 16.0 1.0
N B:GLU940 4.6 12.9 1.0
C B:LEU826 4.6 12.7 1.0
N B:ASP828 4.6 12.6 1.0
CB B:ASN825 4.7 11.6 1.0
CA B:GLY834 4.7 13.2 1.0
CA B:ASP831 4.8 15.0 1.0
C B:ASP831 4.8 14.7 1.0
N B:LEU827 4.8 12.1 1.0
CB B:SER939 4.8 13.8 1.0
CB B:ASP828 4.9 12.6 1.0
CG2 B:THR833 4.9 13.3 1.0
N B:GLY829 4.9 14.9 1.0
N B:ASN832 5.0 14.9 1.0

Calcium binding site 3 out of 4 in 2w1u

Go back to Calcium Binding Sites List in 2w1u
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(1,3)Galnac


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(1,3)Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1950

b:14.4
occ:1.00
 O C:ASN825 2.2 12.6 1.0
O C:ASP830 2.3 15.9 1.0
O C:SER939 2.4 13.1 1.0
O C:THR833 2.4 12.5 1.0
OE1 C:GLU940 2.4 15.9 1.0
OG1 C:THR833 2.5 14.4 1.0
OD1 C:ASP828 2.6 14.3 1.0
C C:THR833 3.4 13.9 1.0
C C:ASP830 3.4 16.7 1.0
C C:ASN825 3.4 13.3 1.0
CG C:ASP828 3.6 16.1 1.0
C C:SER939 3.6 13.0 1.0
CD C:GLU940 3.7 16.4 1.0
CB C:THR833 3.7 14.8 1.0
OD2 C:ASP828 3.9 13.7 1.0
CA C:THR833 3.9 14.4 1.0
N C:ASP830 4.0 16.6 1.0
N C:THR833 4.0 15.9 1.0
CA C:ASP830 4.1 17.2 1.0
CB C:GLU940 4.3 14.1 1.0
CA C:ASN825 4.3 13.9 1.0
N C:LEU826 4.4 12.8 1.0
CB C:ASP830 4.4 17.1 1.0
CA C:LEU826 4.4 13.7 1.0
N C:ASP831 4.4 16.3 1.0
CA C:GLU940 4.5 14.3 1.0
CA C:SER939 4.5 12.1 1.0
N C:GLY834 4.5 12.7 1.0
OE2 C:GLU940 4.5 17.0 1.0
N C:GLU940 4.5 13.2 1.0
CG C:GLU940 4.5 15.5 1.0
CB C:ASN825 4.6 13.4 1.0
CA C:ASP831 4.6 16.2 1.0
N C:ASP828 4.6 17.0 1.0
C C:ASP831 4.6 16.2 1.0
C C:LEU826 4.6 14.5 1.0
N C:LEU827 4.8 15.4 1.0
CG2 C:THR833 4.9 15.3 1.0
O C:ASP831 4.9 15.5 1.0
CA C:GLY834 4.9 13.1 1.0
CB C:ASP828 4.9 17.0 1.0
CB C:SER939 4.9 12.5 1.0
N C:GLY829 4.9 17.8 1.0
N C:ASN832 5.0 16.9 1.0

Calcium binding site 4 out of 4 in 2w1u

Go back to Calcium Binding Sites List in 2w1u
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(1,3)Galnac


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(1,3)Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1950

b:17.2
occ:1.00
 O D:ASN825 2.1 15.8 1.0
O D:ASP830 2.3 19.4 1.0
O D:SER939 2.4 14.9 1.0
OE1 D:GLU940 2.4 18.4 1.0
OD1 D:ASP828 2.5 20.1 1.0
O D:THR833 2.5 17.0 1.0
OG1 D:THR833 2.6 15.8 1.0
C D:ASN825 3.3 15.1 1.0
C D:ASP830 3.4 20.0 1.0
C D:THR833 3.4 16.7 1.0
CG D:ASP828 3.5 20.9 1.0
C D:SER939 3.6 14.6 1.0
CD D:GLU940 3.6 19.8 1.0
CB D:THR833 3.8 16.1 1.0
OD2 D:ASP828 3.9 23.1 1.0
N D:ASP830 4.0 21.3 1.0
CA D:THR833 4.0 16.7 1.0
CA D:ASP830 4.0 20.2 1.0
N D:THR833 4.1 17.7 1.0
CB D:ASP830 4.2 20.6 1.0
CA D:ASN825 4.2 16.1 1.0
N D:LEU826 4.3 14.9 1.0
CB D:GLU940 4.3 15.3 1.0
CA D:LEU826 4.3 15.6 1.0
CA D:GLU940 4.4 14.5 1.0
OE2 D:GLU940 4.4 19.8 1.0
CA D:SER939 4.5 14.0 1.0
CB D:ASN825 4.5 15.0 1.0
N D:GLY834 4.5 16.8 1.0
N D:GLU940 4.5 15.2 1.0
N D:ASP831 4.5 19.7 1.0
CG D:GLU940 4.6 16.0 1.0
N D:ASP828 4.6 19.3 1.0
C D:LEU826 4.7 16.0 1.0
CB D:ASP828 4.8 20.4 1.0
CA D:ASP831 4.8 19.9 1.0
CA D:GLY834 4.8 16.1 1.0
CB D:SER939 4.8 12.6 1.0
CG2 D:THR833 4.9 16.8 1.0
C D:ASP831 4.9 20.3 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: Sat Dec 12 03:54:53 2020

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