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Calcium in PDB 5gqg: Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex

Enzymatic activity of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex

All present enzymatic activity of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex:
3.2.1.140;

Protein crystallography data

The structure of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex, PDB code: 5gqg was solved by C.Yamada, T.Arakawa, T.Katayama, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 102.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.103, 144.061, 144.445, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 25.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex (pdb code 5gqg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex, PDB code: 5gqg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5gqg

Go back to Calcium Binding Sites List in 5gqg
Calcium binding site 1 out of 4 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:74.0
occ:1.00
 O A:HOH841 2.3 60.6 1.0
O A:HOH834 2.3 44.1 1.0
O A:HOH811 2.4 49.6 1.0
O A:HOH849 2.4 38.2 1.0
O A:HOH826 2.4 45.0 1.0
O A:HOH806 2.8 42.1 1.0
OD1 A:ASP369 4.0 34.9 1.0
OD2 A:ASP184 4.0 43.8 1.0
NE1 A:TRP189 4.1 36.1 1.0
OE1 A:GLN368 4.1 45.7 1.0
N A:ASP196 4.3 53.2 1.0
OG1 A:THR192 4.3 49.6 1.0
OD1 A:ASP196 4.3 47.0 1.0
OD2 A:ASP369 4.3 35.3 1.0
OG1 A:THR200 4.4 45.7 1.0
OD2 A:ASP198 4.5 81.1 1.0
OD1 A:ASP198 4.6 84.7 1.0
OD1 A:ASP184 4.6 42.8 1.0
CG A:ASP369 4.6 34.6 1.0
CG A:ASP184 4.6 43.0 1.0
CD1 A:TRP189 4.7 36.5 1.0
O A:LYS190 4.8 38.9 1.0
CA A:ASP196 4.9 54.0 1.0
CE2 A:TRP189 4.9 35.8 1.0

Calcium binding site 2 out of 4 in 5gqg

Go back to Calcium Binding Sites List in 5gqg
Calcium binding site 2 out of 4 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:62.9
occ:1.00
 O A:VAL182 2.3 43.9 1.0
OD1 A:ASP178 2.3 56.9 1.0
O A:ASP179 2.4 48.3 1.0
OD2 A:ASP238 2.7 41.2 1.0
CG A:ASP178 3.3 46.5 1.0
C A:VAL182 3.5 45.1 1.0
C A:ASP179 3.6 46.0 1.0
OD2 A:ASP178 3.6 47.3 1.0
CG A:ASP238 3.6 38.7 1.0
OD1 A:ASP238 3.8 37.4 1.0
N A:ASP179 4.1 44.7 1.0
OD1 A:ASP236 4.2 35.0 1.0
CA A:TYR183 4.3 46.3 1.0
N A:TYR183 4.3 44.4 1.0
CA A:ASP179 4.4 47.1 1.0
CA A:VAL182 4.4 47.4 1.0
CB A:ASP178 4.5 44.2 1.0
N A:ALA180 4.5 43.7 1.0
CB A:VAL182 4.5 46.3 1.0
N A:VAL182 4.6 49.6 1.0
CA A:ALA180 4.7 44.2 1.0
CA A:ASP178 4.7 42.2 1.0
C A:ASP178 4.8 44.1 1.0
CG1 A:VAL182 4.8 43.5 1.0
CB A:TYR183 4.8 49.5 1.0
CB A:ASP179 4.9 47.3 1.0
CB A:ASP236 4.9 36.4 1.0
C A:ALA180 4.9 46.8 1.0
CG A:ASP236 5.0 35.2 1.0
CB A:ASP238 5.0 38.6 1.0

Calcium binding site 3 out of 4 in 5gqg

Go back to Calcium Binding Sites List in 5gqg
Calcium binding site 3 out of 4 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:66.8
occ:1.00
 O B:HOH806 2.2 40.2 1.0
O B:HOH807 2.2 48.1 1.0
O B:HOH821 2.2 43.9 1.0
O B:HOH814 2.4 37.4 1.0
O B:HOH837 2.7 42.1 1.0
O B:HOH802 2.7 42.8 1.0
OD2 B:ASP184 4.0 37.1 1.0
NE1 B:TRP189 4.1 36.4 1.0
OE1 B:GLN368 4.2 50.5 1.0
N B:ASP196 4.2 50.7 1.0
OD1 B:ASP369 4.2 35.2 1.0
OD1 B:ASP184 4.2 32.5 1.0
OG1 B:THR200 4.3 53.3 1.0
OG1 B:THR192 4.3 46.0 1.0
OD2 B:ASP369 4.4 36.5 1.0
CG B:ASP184 4.4 36.5 1.0
OD1 B:ASP196 4.6 57.5 1.0
CA B:ASP196 4.7 54.3 1.0
CG B:ASP369 4.7 35.5 1.0
O B:LYS190 4.7 42.2 1.0
CD1 B:TRP189 4.8 35.8 1.0
CE2 B:TRP189 4.8 36.1 1.0
OD1 B:ASP198 4.9 84.9 1.0

Calcium binding site 4 out of 4 in 5gqg

Go back to Calcium Binding Sites List in 5gqg
Calcium binding site 4 out of 4 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Galacto-N-Biose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:78.7
occ:1.00
 OD2 B:ASP238 2.5 42.2 1.0
OD1 B:ASP178 2.5 51.0 1.0
O B:VAL182 2.5 46.7 1.0
OD1 B:ASP238 3.2 38.3 1.0
CG B:ASP238 3.2 38.0 1.0
O B:ASP179 3.4 51.7 1.0
OD2 B:ASP236 3.6 37.8 1.0
C B:VAL182 3.6 45.2 1.0
CG B:ASP178 3.7 49.4 1.0
CA B:TYR183 4.2 43.0 1.0
N B:TYR183 4.3 43.0 1.0
OD2 B:ASP178 4.4 57.0 1.0
N B:ASP179 4.4 43.9 1.0
CB B:VAL182 4.4 48.1 1.0
CG B:ASP236 4.4 37.5 1.0
CG1 B:VAL182 4.5 46.0 1.0
CB B:ASP236 4.5 39.1 1.0
C B:ASP179 4.5 48.9 1.0
CA B:VAL182 4.5 47.5 1.0
CB B:ASP178 4.6 49.3 1.0
CB B:ASP238 4.7 37.1 1.0
CA B:ASP178 4.8 48.6 1.0
CD1 B:TYR183 4.9 46.0 1.0
CB B:TYR183 4.9 45.1 1.0
N B:VAL182 5.0 48.6 1.0

Reference:

C.Yamada, A.Gotoh, M.Sakanaka, M.Hattie, K.A.Stubbs, A.Katayama-Ikegami, J.Hirose, S.Kurihara, T.Arakawa, M.Kitaoka, S.Okuda, T.Katayama, S.Fushinobu. Molecular Insight Into Evolution of Symbiosis Between Breast-Fed Infants and A Member of the Human Gut Microbiome Bifidobacterium Longum Cell Chem Biol V. 24 515 2017.
ISSN: ESSN 2451-9456
PubMed: 28392148
DOI: 10.1016/J.CHEMBIOL.2017.03.012
Page generated: Wed Jul 9 06:13:43 2025

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