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

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

All present enzymatic activity of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Lacto-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, Lacto-N-Biose Complex, PDB code: 5gqf 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) 102.45 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.035, 143.625, 146.180, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Lacto-N-Biose Complex (pdb code 5gqf). 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, Lacto-N-Biose Complex, PDB code: 5gqf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5gqf

Go back to Calcium Binding Sites List in 5gqf
Calcium binding site 1 out of 4 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Lacto-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, Lacto-N-Biose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:37.6
occ:1.00
 OD1 A:ASP178 2.2 38.5 1.0
O A:VAL182 2.2 32.3 1.0
OD2 A:ASP238 2.3 30.8 1.0
O A:ASP179 2.5 34.6 1.0
O A:HOH878 2.5 31.3 1.0
O A:HOH1173 2.6 46.6 1.0
CG A:ASP178 3.3 41.2 1.0
CG A:ASP238 3.4 34.6 1.0
C A:VAL182 3.5 33.9 1.0
C A:ASP179 3.6 40.3 1.0
N A:ASP179 3.7 30.3 1.0
OD1 A:ASP238 3.8 30.9 1.0
OD2 A:ASP178 3.9 49.4 1.0
CA A:VAL182 4.3 34.2 1.0
CA A:ASP179 4.3 35.7 1.0
CB A:VAL182 4.3 35.2 1.0
N A:VAL182 4.3 32.6 1.0
OD1 A:ASP236 4.4 30.5 1.0
CB A:ASP178 4.4 35.6 1.0
N A:TYR183 4.4 28.5 1.0
CA A:ASP178 4.5 30.9 1.0
CA A:TYR183 4.5 29.5 1.0
N A:ALA180 4.5 36.3 1.0
C A:ASP178 4.6 36.9 1.0
CB A:ASP238 4.7 29.2 1.0
CA A:ALA180 4.7 42.5 1.0
O A:HOH1148 4.7 33.7 1.0
CG1 A:VAL182 4.8 34.0 1.0
CB A:ASP179 4.8 34.0 1.0
C A:ALA180 4.9 40.7 1.0
CB A:TYR183 5.0 29.9 1.0

Calcium binding site 2 out of 4 in 5gqf

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Calcium binding site 2 out of 4 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Lacto-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, Lacto-N-Biose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:38.2
occ:1.00
 O A:HOH913 2.1 28.9 1.0
O A:HOH896 2.1 30.1 1.0
O A:HOH965 2.2 27.0 1.0
O A:HOH870 2.2 29.5 1.0
O A:HOH921 2.3 27.9 1.0
O A:HOH810 2.4 30.2 1.0
NE1 A:TRP189 4.1 29.1 1.0
OD1 A:ASP184 4.1 31.1 1.0
O A:HOH802 4.1 39.8 1.0
OG1 A:THR200 4.2 31.5 1.0
OD1 A:ASP198 4.2 35.2 1.0
OD2 A:ASP184 4.2 29.4 1.0
OD2 A:ASP369 4.2 23.8 1.0
OD1 A:ASP369 4.2 25.5 1.0
OD1 A:ASP196 4.3 38.6 1.0
OE1 A:GLN368 4.3 38.8 1.0
OG1 A:THR192 4.3 39.9 1.0
N A:ASP196 4.4 41.0 1.0
OD2 A:ASP198 4.4 47.2 1.0
CG A:ASP184 4.5 29.6 1.0
O A:LYS190 4.5 34.3 1.0
CG A:ASP369 4.6 24.3 1.0
CD1 A:TRP189 4.7 28.4 1.0
CG A:ASP198 4.7 39.0 1.0
CA A:ASP196 4.8 39.5 1.0
CE2 A:TRP189 4.9 26.9 1.0

Calcium binding site 3 out of 4 in 5gqf

Go back to Calcium Binding Sites List in 5gqf
Calcium binding site 3 out of 4 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Lacto-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, Lacto-N-Biose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:33.5
occ:1.00
 O B:VAL182 2.2 26.1 1.0
OD1 B:ASP178 2.3 30.9 1.0
OD2 B:ASP238 2.4 23.5 1.0
O B:HOH1191 2.4 40.2 1.0
O B:ASP179 2.4 25.3 1.0
O B:HOH925 2.4 24.2 1.0
O B:HOH1073 2.8 51.3 1.0
CG B:ASP178 3.4 32.5 1.0
C B:VAL182 3.4 26.8 1.0
CG B:ASP238 3.4 25.7 1.0
C B:ASP179 3.5 26.0 1.0
OD1 B:ASP238 3.7 27.4 1.0
N B:ASP179 3.8 25.8 1.0
OD2 B:ASP178 3.9 43.5 1.0
CA B:ASP179 4.2 27.5 1.0
O B:HOH899 4.3 54.2 1.0
CA B:VAL182 4.3 27.2 1.0
N B:VAL182 4.3 27.2 1.0
CB B:VAL182 4.3 27.2 1.0
N B:TYR183 4.4 24.9 1.0
OD1 B:ASP236 4.4 26.9 1.0
N B:ALA180 4.4 28.9 1.0
CB B:ASP178 4.5 25.5 1.0
CA B:TYR183 4.5 27.2 1.0
O B:HOH1304 4.6 67.3 1.0
O B:HOH845 4.6 58.0 1.0
CA B:ASP178 4.6 25.1 1.0
C B:ASP178 4.7 26.9 1.0
CA B:ALA180 4.7 31.7 1.0
CB B:ASP238 4.7 25.6 1.0
CB B:ASP179 4.8 24.4 1.0
O B:HOH1090 4.8 28.0 1.0
CG1 B:VAL182 4.9 26.7 1.0
C B:ALA180 4.9 32.0 1.0
CB B:TYR183 4.9 30.0 1.0

Calcium binding site 4 out of 4 in 5gqf

Go back to Calcium Binding Sites List in 5gqf
Calcium binding site 4 out of 4 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Lacto-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, Lacto-N-Biose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:35.5
occ:1.00
 O B:HOH1140 2.0 26.5 1.0
O B:HOH951 2.2 28.0 1.0
O B:HOH959 2.2 27.5 1.0
O B:HOH861 2.2 27.2 1.0
O B:HOH890 2.2 25.1 1.0
O B:HOH963 2.3 26.8 1.0
NE1 B:TRP189 4.0 31.9 1.0
OD1 B:ASP184 4.1 26.1 1.0
OG1 B:THR200 4.1 31.1 1.0
OD2 B:ASP184 4.1 25.9 1.0
O B:HOH829 4.2 36.7 1.0
OD1 B:ASP369 4.2 26.2 1.0
OG1 B:THR192 4.2 36.8 1.0
OD2 B:ASP369 4.2 26.2 1.0
OD1 B:ASP198 4.3 37.4 1.0
OD1 B:ASP196 4.3 29.6 1.0
OE1 B:GLN368 4.4 35.1 1.0
CG B:ASP184 4.4 25.7 1.0
N B:ASP196 4.5 35.0 1.0
O B:LYS190 4.5 33.1 1.0
OD2 B:ASP198 4.6 51.4 1.0
CD1 B:TRP189 4.6 26.9 1.0
CG B:ASP369 4.7 31.2 1.0
CG B:ASP198 4.9 42.5 1.0
CE2 B:TRP189 4.9 28.1 1.0
CA B:ASP196 4.9 36.9 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 06:13:41 2025

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