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

Go back to Calcium Binding Sites List in 5gqf
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: Sat Dec 12 05:26:55 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy