Atomistry » Calcium » PDB 5g39-5gth » 5gqf
Atomistry »
  Calcium »
    PDB 5g39-5gth »
      5gqf »

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: Sun Jul 14 19:40:07 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy