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Calcium in PDB 5gqc: Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form

Enzymatic activity of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form

All present enzymatic activity of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form:
3.2.1.140;

Protein crystallography data

The structure of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form, PDB code: 5gqc 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) 143.39 / 2.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 128.317, 142.716, 157.008, 90.00, 114.04, 90.00
R / Rfree (%) 18.2 / 24

Other elements in 5gqc:

The structure of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form (pdb code 5gqc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form, PDB code: 5gqc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in 5gqc

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Calcium binding site 1 out of 14 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


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, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:57.6
occ:1.00
 O B:HOH883 2.1 46.3 1.0
O B:HOH911 2.3 30.4 1.0
O B:HOH900 2.3 36.2 1.0
O B:HOH854 2.3 54.4 1.0
O B:HOH833 2.4 49.0 1.0
O B:HOH888 2.6 43.8 1.0
OG1 B:THR192 3.8 47.9 1.0
N B:ASP196 4.1 42.3 1.0
OD1 B:ASP369 4.2 34.1 1.0
OE1 B:GLN368 4.2 31.9 1.0
OD1 B:ASP184 4.2 32.6 1.0
OG1 B:THR200 4.3 33.8 1.0
OD2 B:ASP184 4.3 37.2 1.0
OD2 B:ASP369 4.4 26.8 1.0
OD1 B:ASP196 4.4 40.8 1.0
NE1 B:TRP189 4.4 37.8 1.0
CG B:ASP184 4.7 33.4 1.0
O B:LYS190 4.7 40.5 1.0
CG B:ASP369 4.7 31.0 1.0
CA B:ASP196 4.7 47.5 1.0
CD1 B:TRP189 5.0 37.3 1.0

Calcium binding site 2 out of 14 in 5gqc

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Calcium binding site 2 out of 14 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


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, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:68.1
occ:1.00
 O B:VAL182 2.2 36.0 1.0
OD1 B:ASP178 2.4 50.3 1.0
OD2 B:ASP238 2.4 36.1 1.0
O B:ASP179 2.5 41.7 1.0
O B:HOH866 3.0 23.9 1.0
C B:VAL182 3.3 39.6 1.0
CG B:ASP178 3.4 43.2 1.0
C B:ASP179 3.5 41.1 1.0
CG B:ASP238 3.5 37.3 1.0
OD2 B:ASP178 3.7 44.9 1.0
N B:ASP179 3.9 34.5 1.0
OD1 B:ASP238 4.0 35.2 1.0
CA B:VAL182 4.1 41.8 1.0
CB B:VAL182 4.1 40.3 1.0
N B:VAL182 4.2 43.4 1.0
CA B:ASP179 4.3 36.5 1.0
N B:TYR183 4.3 36.6 1.0
N B:ALA180 4.4 45.3 1.0
CA B:ALA180 4.4 47.1 1.0
CA B:TYR183 4.5 36.6 1.0
CB B:ASP178 4.7 39.6 1.0
CB B:ASP238 4.8 34.9 1.0
OD1 B:ASP236 4.8 40.0 1.0
CB B:TYR183 4.8 36.2 1.0
CB B:ASP179 4.8 34.4 1.0
CA B:ASP178 4.8 37.1 1.0
C B:ALA180 4.8 47.8 1.0
C B:ASP178 4.9 36.4 1.0
CG1 B:VAL182 4.9 37.3 1.0

Calcium binding site 3 out of 14 in 5gqc

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Calcium binding site 3 out of 14 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


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, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:76.9
occ:1.00
 O C:HOH837 2.7 42.0 1.0
NE1 C:TRP189 3.5 32.5 1.0
OD2 C:ASP369 4.0 41.2 1.0
O C:LYS190 4.1 43.8 1.0
CE2 C:TRP189 4.1 32.2 1.0
OE1 C:GLN368 4.2 36.8 1.0
CD1 C:TRP189 4.3 33.5 1.0
OD2 C:ASP184 4.3 30.4 1.0
OD1 C:ASP369 4.3 40.8 1.0
OD1 C:ASP184 4.3 31.0 1.0
CZ2 C:TRP189 4.4 33.0 1.0
OG1 C:THR192 4.5 60.8 1.0
CG C:ASP369 4.6 38.5 1.0
CG C:ASP184 4.7 29.9 1.0
OG1 C:THR200 4.8 33.7 1.0
N C:ASP196 4.8 50.9 1.0
OD2 C:ASP198 4.9 88.1 1.0
OD1 C:ASP198 4.9 84.6 1.0
OD1 C:ASP196 5.0 49.1 1.0

Calcium binding site 4 out of 14 in 5gqc

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Calcium binding site 4 out of 14 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


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, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:61.5
occ:1.00
 OD2 C:ASP238 2.3 31.2 1.0
O C:VAL182 2.3 32.0 1.0
O C:HOH877 2.4 32.5 1.0
OD1 C:ASP178 2.6 43.5 1.0
O C:ASP179 2.6 36.4 1.0
CG C:ASP238 3.3 31.4 1.0
CG C:ASP178 3.4 41.3 1.0
C C:VAL182 3.4 33.1 1.0
C C:ASP179 3.6 37.4 1.0
OD1 C:ASP238 3.7 30.4 1.0
OD2 C:ASP178 3.7 46.4 1.0
N C:ASP179 3.8 37.5 1.0
CA C:VAL182 4.2 35.2 1.0
CB C:VAL182 4.2 36.8 1.0
N C:VAL182 4.3 38.4 1.0
CA C:ASP179 4.3 38.1 1.0
N C:TYR183 4.4 32.0 1.0
CB C:ASP178 4.4 37.6 1.0
CA C:TYR183 4.6 32.2 1.0
CA C:ASP178 4.6 34.6 1.0
N C:ALA180 4.6 39.7 1.0
OD1 C:ASP236 4.6 29.8 1.0
C C:ASP178 4.6 36.1 1.0
CB C:ASP238 4.6 30.3 1.0
CG1 C:VAL182 4.8 33.8 1.0
CB C:ASP179 4.8 41.5 1.0
CA C:ALA180 4.8 39.3 1.0
CB C:ASP236 4.9 32.0 1.0
C C:ALA180 5.0 40.3 1.0

Calcium binding site 5 out of 14 in 5gqc

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Calcium binding site 5 out of 14 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:78.2
occ:1.00
 O D:HOH939 2.3 49.6 1.0
O D:HOH869 2.4 31.9 1.0
O D:HOH815 2.6 42.1 1.0
O D:HOH861 2.7 35.8 1.0
OD2 D:ASP184 3.7 41.4 1.0
OD1 D:ASP184 3.8 36.0 1.0
OG1 D:THR200 4.0 36.9 1.0
CG D:ASP184 4.1 36.1 1.0
OD1 D:ASP369 4.1 34.0 1.0
OD1 D:ASP196 4.2 63.7 1.0
N D:ASP196 4.2 55.8 1.0
NE1 D:TRP189 4.3 35.3 1.0
OD2 D:ASP369 4.4 37.1 1.0
OE1 D:GLN368 4.6 47.7 1.0
CA D:ASP196 4.6 56.8 1.0
CD1 D:LEU202 4.7 43.8 1.0
CG D:ASP369 4.7 37.3 1.0
CB D:THR200 4.7 37.8 1.0
CD1 D:TRP189 4.8 34.5 1.0
OG1 D:THR192 4.9 57.5 1.0

Calcium binding site 6 out of 14 in 5gqc

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Calcium binding site 6 out of 14 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:56.8
occ:1.00
 O D:VAL182 2.2 34.1 1.0
OD1 D:ASP178 2.5 37.7 1.0
OD2 D:ASP238 2.5 29.9 1.0
O D:ASP179 2.6 41.3 1.0
CG D:ASP178 3.3 34.0 1.0
C D:VAL182 3.4 38.0 1.0
CG D:ASP238 3.4 33.6 1.0
C D:ASP179 3.5 38.7 1.0
OD2 D:ASP178 3.6 37.0 1.0
OD1 D:ASP238 3.8 32.5 1.0
N D:ASP179 3.8 36.8 1.0
CA D:VAL182 4.2 39.0 1.0
CA D:ASP179 4.2 39.0 1.0
N D:VAL182 4.2 43.7 1.0
CB D:VAL182 4.2 38.1 1.0
OD1 D:ASP236 4.4 30.4 1.0
N D:ALA180 4.4 36.2 1.0
N D:TYR183 4.4 35.2 1.0
CB D:ASP178 4.5 34.8 1.0
O D:HOH864 4.6 41.8 1.0
CA D:ASP178 4.6 34.3 1.0
C D:ASP178 4.6 34.9 1.0
CA D:TYR183 4.7 39.6 1.0
CA D:ALA180 4.7 38.1 1.0
CB D:ASP179 4.7 41.9 1.0
CB D:ASP238 4.8 33.3 1.0
C D:ALA180 4.8 40.7 1.0
CG1 D:VAL182 4.9 37.1 1.0
CB D:ASP236 5.0 31.2 1.0

Calcium binding site 7 out of 14 in 5gqc

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Calcium binding site 7 out of 14 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca701

b:79.0
occ:1.00
 O E:HOH914 2.0 37.6 1.0
O E:HOH928 2.2 59.4 1.0
O E:HOH920 2.4 46.4 1.0
O E:HOH870 2.5 39.0 1.0
O E:HOH852 2.6 44.0 1.0
O E:HOH813 2.9 54.7 1.0
NE1 E:TRP189 4.0 38.2 1.0
OD1 E:ASP184 4.1 36.4 1.0
NE2 E:GLN368 4.1 44.4 1.0
OD1 E:ASP369 4.2 41.6 1.0
OG1 E:THR192 4.2 58.1 1.0
OD2 E:ASP369 4.3 45.1 1.0
OG1 E:THR200 4.3 43.6 1.0
OD2 E:ASP184 4.4 37.0 1.0
O E:LYS190 4.4 46.3 1.0
OD1 E:ASP196 4.5 56.4 1.0
CD1 E:TRP189 4.5 36.2 1.0
CG E:ASP184 4.6 37.1 1.0
N E:ASP196 4.6 55.6 1.0
CG E:ASP369 4.7 39.0 1.0
OD1 E:ASP198 4.7 82.3 1.0
CE2 E:TRP189 4.8 39.2 1.0
OD2 E:ASP198 4.9 80.2 1.0

Calcium binding site 8 out of 14 in 5gqc

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Calcium binding site 8 out of 14 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca702

b:58.9
occ:1.00
 O E:VAL182 2.3 32.3 1.0
OD1 E:ASP178 2.3 37.6 1.0
OD2 E:ASP238 2.5 33.1 1.0
O E:HOH835 2.6 32.8 1.0
O E:ASP179 2.7 35.9 1.0
CG E:ASP178 3.3 36.6 1.0
C E:VAL182 3.4 38.9 1.0
CG E:ASP238 3.5 30.9 1.0
C E:ASP179 3.7 39.4 1.0
OD2 E:ASP178 3.7 41.6 1.0
OD1 E:ASP238 3.8 33.5 1.0
N E:ASP179 3.9 35.5 1.0
OD1 E:ASP236 4.2 40.2 1.0
CA E:VAL182 4.2 39.8 1.0
CB E:VAL182 4.4 41.3 1.0
N E:VAL182 4.4 42.7 1.0
CA E:ASP179 4.4 35.9 1.0
N E:TYR183 4.4 38.1 1.0
O E:HOH911 4.5 27.0 1.0
CB E:ASP178 4.6 36.9 1.0
CA E:TYR183 4.6 35.3 1.0
N E:ALA180 4.6 44.8 1.0
CA E:ASP178 4.7 34.9 1.0
CB E:ASP238 4.8 30.1 1.0
C E:ASP178 4.8 36.6 1.0
CA E:ALA180 4.8 47.5 1.0
CB E:ASP179 4.9 35.1 1.0

Calcium binding site 9 out of 14 in 5gqc

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Calcium binding site 9 out of 14 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca701

b:65.7
occ:1.00
 O F:HOH904 2.3 45.1 1.0
O F:HOH902 2.3 48.4 1.0
O F:HOH824 2.4 47.6 1.0
O F:HOH833 2.5 44.7 1.0
O F:HOH937 2.5 54.5 1.0
O F:HOH936 2.6 41.1 1.0
OD1 F:ASP184 3.8 37.7 1.0
OG1 F:THR200 4.0 42.4 1.0
OD2 F:ASP184 4.2 45.2 1.0
NE1 F:TRP189 4.2 36.4 1.0
CG F:ASP184 4.3 39.8 1.0
OD1 F:ASP198 4.4 74.1 1.0
OE1 F:GLN368 4.4 40.5 1.0
N F:ASP196 4.5 58.0 1.0
O F:LYS190 4.5 49.2 1.0
OD1 F:ASP369 4.5 42.6 1.0
OD2 F:ASP369 4.6 37.8 1.0
CD1 F:TRP189 4.6 34.5 1.0
OG1 F:THR192 4.7 56.2 1.0
CB F:THR200 4.8 39.4 1.0
CA F:ASP196 4.9 56.7 1.0
OD1 F:ASP196 4.9 64.6 1.0
CE2 F:TRP189 5.0 32.8 1.0

Calcium binding site 10 out of 14 in 5gqc

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Calcium binding site 10 out of 14 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca702

b:61.7
occ:1.00
 O F:VAL182 2.2 32.6 1.0
O F:ASP179 2.3 43.9 1.0
OD2 F:ASP238 2.3 37.6 1.0
OD1 F:ASP178 2.4 35.3 1.0
C F:ASP179 3.3 41.6 1.0
CG F:ASP238 3.3 37.8 1.0
C F:VAL182 3.4 34.3 1.0
CG F:ASP178 3.4 37.8 1.0
N F:ASP179 3.6 33.3 1.0
OD1 F:ASP238 3.7 36.7 1.0
OD2 F:ASP178 3.9 46.9 1.0
CA F:ASP179 4.0 37.8 1.0
CB F:VAL182 4.0 40.1 1.0
CA F:VAL182 4.1 36.4 1.0
N F:VAL182 4.1 39.4 1.0
N F:ALA180 4.2 40.6 1.0
N F:TYR183 4.4 34.7 1.0
CA F:ALA180 4.4 42.0 1.0
CB F:ASP178 4.5 32.9 1.0
CB F:ASP179 4.6 39.7 1.0
C F:ASP178 4.6 32.1 1.0
CB F:ASP238 4.6 35.9 1.0
CG1 F:VAL182 4.6 39.5 1.0
CA F:ASP178 4.6 32.8 1.0
CA F:TYR183 4.7 34.1 1.0
C F:ALA180 4.8 43.0 1.0
O F:HOH885 4.8 33.3 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 19:40:04 2024

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