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Calcium in PDB 9vak: Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex

Enzymatic activity of Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex

All present enzymatic activity of Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex:
3.2.1.140;

Protein crystallography data

The structure of Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex, PDB code: 9vak was solved by X.Zhang, T.Kashima, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.54 / 2.00
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.489, 105.802, 122.102, 90, 90, 90
R / Rfree (%) 19.8 / 22.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex (pdb code 9vak). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex, PDB code: 9vak:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 9vak

Go back to Calcium Binding Sites List in 9vak
Calcium binding site 1 out of 4 in the Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:9.0
occ:1.00
 O A:ASN801 2.3 10.3 1.0
OE2 A:GLU931 2.3 10.8 1.0
O A:ASN806 2.4 11.1 1.0
O A:ALA930 2.4 8.4 1.0
O A:THR809 2.4 10.4 1.0
OD1 A:ASP804 2.4 10.8 1.0
OG1 A:THR809 2.5 10.8 1.0
C A:THR809 3.3 9.9 1.0
CD A:GLU931 3.4 12.2 1.0
CG A:ASP804 3.5 12.3 1.0
C A:ASN806 3.5 11.2 1.0
C A:ASN801 3.5 10.4 1.0
C A:ALA930 3.5 10.7 1.0
CB A:THR809 3.8 11.1 1.0
OD2 A:ASP804 3.8 11.5 1.0
CA A:THR809 3.9 11.1 1.0
N A:ASN806 4.0 11.3 1.0
N A:THR809 4.0 9.4 1.0
CG A:GLU931 4.1 12.7 1.0
CA A:ASN806 4.1 10.9 1.0
CA A:ALA930 4.2 9.8 1.0
N A:PHE810 4.3 8.2 1.0
CB A:ASN806 4.3 10.6 1.0
OE1 A:GLU931 4.4 14.1 1.0
CA A:ASN801 4.4 10.4 1.0
N A:ALA802 4.4 10.2 1.0
CA A:ALA802 4.4 10.8 1.0
N A:ALA807 4.5 11.4 1.0
N A:GLU931 4.6 9.6 1.0
N A:ASP804 4.6 11.2 1.0
CA A:PHE810 4.6 9.8 1.0
CB A:ALA930 4.6 11.1 1.0
CB A:ASN801 4.7 9.2 1.0
C A:ALA802 4.7 10.9 1.0
CA A:ALA807 4.8 12.5 1.0
CB A:ASP804 4.8 11.3 1.0
N A:LYS805 4.8 12.2 1.0
CA A:GLU931 4.8 9.9 1.0
CG2 A:THR809 4.9 11.3 1.0
C A:ALA807 4.9 11.3 1.0
N A:PHE803 5.0 10.4 1.0

Calcium binding site 2 out of 4 in 9vak

Go back to Calcium Binding Sites List in 9vak
Calcium binding site 2 out of 4 in the Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:8.9
occ:1.00
 O B:ASN801 2.2 9.1 1.0
O B:ASN806 2.3 10.9 1.0
OD1 B:ASP804 2.4 10.3 1.0
O B:THR809 2.4 8.8 1.0
OG1 B:THR809 2.5 9.8 1.0
O B:ALA930 2.5 9.6 1.0
OE2 B:GLU931 2.5 11.8 1.0
C B:THR809 3.3 9.4 1.0
C B:ASN806 3.4 10.3 1.0
CG B:ASP804 3.4 12.0 1.0
C B:ASN801 3.5 9.7 1.0
C B:ALA930 3.6 10.8 1.0
CD B:GLU931 3.6 12.6 1.0
CB B:THR809 3.6 11.0 1.0
OD2 B:ASP804 3.8 11.4 1.0
CA B:THR809 3.8 10.2 1.0
N B:ASN806 3.9 11.3 1.0
N B:THR809 4.0 11.8 1.0
CA B:ASN806 4.1 10.1 1.0
CG B:GLU931 4.2 12.7 1.0
CA B:ALA930 4.2 10.6 1.0
CB B:ASN806 4.2 10.2 1.0
N B:PHE810 4.3 9.0 1.0
CA B:ASN801 4.4 10.0 1.0
N B:ALA802 4.4 8.9 1.0
CA B:ALA802 4.4 10.2 1.0
N B:ALA807 4.5 10.4 1.0
N B:ASP804 4.6 11.1 1.0
OE1 B:GLU931 4.6 13.4 1.0
N B:GLU931 4.6 10.4 1.0
CA B:PHE810 4.6 9.7 1.0
CB B:ALA930 4.6 9.0 1.0
C B:ALA802 4.7 10.6 1.0
CB B:ASN801 4.7 8.6 1.0
CA B:ALA807 4.7 12.8 1.0
CB B:ASP804 4.8 11.2 1.0
CG2 B:THR809 4.8 13.1 1.0
N B:LYS805 4.8 11.3 1.0
C B:ALA807 4.9 13.2 1.0
N B:PHE803 4.9 10.0 1.0
CA B:GLU931 4.9 12.2 1.0
CG B:ASN806 5.0 11.0 1.0

Calcium binding site 3 out of 4 in 9vak

Go back to Calcium Binding Sites List in 9vak
Calcium binding site 3 out of 4 in the Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1001

b:12.0
occ:1.00
 O C:ASN801 2.3 10.5 1.0
OE2 C:GLU931 2.3 9.8 1.0
O C:ASN806 2.3 10.4 1.0
OD1 C:ASP804 2.5 11.2 1.0
O C:ALA930 2.5 11.4 1.0
O C:THR809 2.5 9.2 1.0
OG1 C:THR809 2.6 10.8 1.0
C C:THR809 3.4 9.4 1.0
C C:ASN806 3.4 11.5 1.0
CD C:GLU931 3.5 10.6 1.0
CG C:ASP804 3.5 12.4 1.0
C C:ASN801 3.5 8.6 1.0
C C:ALA930 3.6 9.6 1.0
CB C:THR809 3.8 10.4 1.0
OD2 C:ASP804 3.8 11.1 1.0
CA C:THR809 3.9 10.3 1.0
N C:ASN806 4.0 10.8 1.0
N C:THR809 4.0 12.0 1.0
CA C:ASN806 4.1 10.1 1.0
CG C:GLU931 4.2 10.0 1.0
CA C:ALA930 4.2 9.7 1.0
CB C:ASN806 4.2 10.3 1.0
N C:PHE810 4.3 7.8 1.0
CA C:ASN801 4.3 9.1 1.0
OE1 C:GLU931 4.4 12.5 1.0
N C:ALA802 4.5 9.6 1.0
N C:ALA807 4.5 10.8 1.0
CA C:ALA802 4.5 11.5 1.0
CB C:ASN801 4.6 8.6 1.0
CB C:ALA930 4.6 8.7 1.0
N C:GLU931 4.6 9.2 1.0
CA C:PHE810 4.6 8.7 1.0
N C:ASP804 4.7 11.4 1.0
C C:ALA802 4.7 10.9 1.0
CA C:ALA807 4.7 12.9 1.0
N C:LYS805 4.8 11.2 1.0
CB C:ASP804 4.8 11.7 1.0
CG2 C:THR809 4.9 9.8 1.0
C C:ALA807 4.9 13.7 1.0
CA C:GLU931 4.9 10.5 1.0
N C:PHE803 5.0 10.7 1.0

Calcium binding site 4 out of 4 in 9vak

Go back to Calcium Binding Sites List in 9vak
Calcium binding site 4 out of 4 in the Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Carbohydrate-Binding Module 32 of Lnbb From Bifidobacterium Bifidum, Lnb Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1001

b:11.3
occ:1.00
 O D:ASN806 2.3 10.6 1.0
O D:ASN801 2.4 11.4 1.0
O D:THR809 2.4 12.9 1.0
OD1 D:ASP804 2.4 11.2 1.0
OE2 D:GLU931 2.4 14.8 1.0
O D:ALA930 2.4 12.3 1.0
OG1 D:THR809 2.4 11.5 1.0
C D:THR809 3.3 11.8 1.0
CG D:ASP804 3.4 13.8 1.0
C D:ASN806 3.4 13.3 1.0
CD D:GLU931 3.5 15.0 1.0
C D:ALA930 3.5 12.0 1.0
C D:ASN801 3.6 11.8 1.0
CB D:THR809 3.7 12.9 1.0
OD2 D:ASP804 3.7 13.8 1.0
CA D:THR809 3.8 12.0 1.0
N D:THR809 4.0 11.3 1.0
N D:ASN806 4.0 13.4 1.0
CG D:GLU931 4.1 14.3 1.0
CA D:ASN806 4.1 10.9 1.0
CA D:ALA930 4.2 12.7 1.0
CB D:ASN806 4.2 12.2 1.0
N D:PHE810 4.2 11.6 1.0
CA D:ASN801 4.4 11.8 1.0
OE1 D:GLU931 4.5 15.2 1.0
N D:ALA807 4.5 12.8 1.0
N D:ALA802 4.5 10.1 1.0
CA D:ALA802 4.5 11.9 1.0
CB D:ALA930 4.5 14.9 1.0
N D:GLU931 4.6 12.1 1.0
N D:ASP804 4.6 13.1 1.0
CA D:PHE810 4.6 12.4 1.0
CB D:ASN801 4.7 10.8 1.0
C D:ALA802 4.7 12.8 1.0
CA D:ALA807 4.7 14.3 1.0
CB D:ASP804 4.8 13.2 1.0
CG2 D:THR809 4.8 11.7 1.0
CA D:GLU931 4.8 13.9 1.0
N D:PHE803 4.9 11.4 1.0
N D:LYS805 4.9 12.7 1.0
C D:ALA807 5.0 13.5 1.0

Reference:

X.Zhang, N.Sunagawa, T.Kashima, K.Igarashi, A.Miyanaga, S.Fushinobu. Structural Insights Into Lacto-N-Biose I Recognition By A Family 32 Carbohydrate-Binding Module From Bifidobacterium Bifidum To Be Published.
Page generated: Fri Aug 22 22:42:31 2025

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