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Calcium in PDB 5d9n: Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg

Protein crystallography data

The structure of Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg, PDB code: 5d9n was solved by M.Morar, P.J.Stogios, X.Xu, H.Cui, R.Di Leo, V.Yim, A.Savchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.87 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.560, 84.116, 138.630, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 16.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg (pdb code 5d9n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg, PDB code: 5d9n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5d9n

Go back to Calcium Binding Sites List in 5d9n
Calcium binding site 1 out of 5 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg


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 PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:22.9
occ:1.00
 O A:HOH698 2.4 22.4 1.0
O A:HOH815 2.4 29.0 1.0
O A:HOH538 2.4 16.8 1.0
O A:HOH656 2.4 25.8 1.0
O A:HOH880 2.4 26.2 1.0
O A:HOH956 2.4 21.3 1.0
O A:HOH679 2.4 20.2 1.0
O A:HOH941 2.4 28.8 1.0
O A:HOH1016 4.0 55.6 1.0
O A:HOH793 4.1 18.4 1.0
O A:HOH552 4.2 21.9 1.0
O4 A:BGC407 4.3 33.3 1.0
OE1 A:GLU280 4.3 15.7 1.0
O A:HOH823 4.4 23.6 1.0
OH A:TYR240 4.5 15.1 1.0
OE1 A:GLU162 4.5 19.2 1.0
O A:HOH705 4.7 17.5 1.0
C6 A:BGC407 4.7 28.0 1.0
OE2 A:GLU162 4.8 19.9 1.0
OD1 A:ASP288 4.9 45.6 1.0
CZ A:TYR240 4.9 17.2 1.0
O5 A:XYS408 4.9 30.2 1.0

Calcium binding site 2 out of 5 in 5d9n

Go back to Calcium Binding Sites List in 5d9n
Calcium binding site 2 out of 5 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg


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 PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:17.4
occ:1.00
 OD2 A:ASP56 2.3 16.2 1.0
O A:HOH561 2.4 17.7 1.0
O A:HOH1029 2.4 16.9 1.0
O A:HOH830 2.4 20.3 1.0
O A:HOH937 2.4 17.2 1.0
O A:HOH804 2.4 18.6 1.0
CG A:ASP56 3.4 16.1 1.0
OD1 A:ASP56 3.8 17.9 1.0
O A:HOH858 4.3 19.6 1.0
O A:HOH814 4.4 21.4 1.0
O A:HOH639 4.7 21.8 1.0
CB A:ASP56 4.7 15.0 1.0

Calcium binding site 3 out of 5 in 5d9n

Go back to Calcium Binding Sites List in 5d9n
Calcium binding site 3 out of 5 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg


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 PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:20.8
occ:1.00
 O A:HOH578 2.4 22.0 1.0
O A:HOH1009 2.4 24.9 1.0
O A:HOH865 2.4 20.0 1.0
O A:HOH944 2.4 23.5 1.0
O A:HOH1051 2.4 25.0 1.0
O A:HOH896 2.4 21.8 1.0
O A:HOH666 2.4 18.4 1.0
ND1 A:HIS318 4.1 19.2 1.0
O A:HOH1030 4.4 35.0 1.0
O A:HOH541 4.4 35.1 1.0
OD1 A:ASP18 4.5 16.6 1.0
O A:HOH1023 4.5 17.7 1.0
O A:HOH932 4.5 24.6 1.0
O A:HOH670 4.6 16.2 1.0
CE1 A:HIS318 4.6 17.2 1.0
CG A:ASP18 4.6 16.6 1.0
O A:HOH594 4.7 17.8 1.0
O A:HOH1076 4.7 31.8 1.0
O A:HOH886 4.7 49.1 1.0
O A:LYS315 4.7 17.1 1.0
O A:HOH957 4.8 20.8 1.0
OD2 A:ASP18 4.8 17.9 1.0
O A:HOH894 4.8 29.0 1.0
CE A:LYS315 4.9 29.7 1.0
CG A:LYS315 5.0 25.1 1.0

Calcium binding site 4 out of 5 in 5d9n

Go back to Calcium Binding Sites List in 5d9n
Calcium binding site 4 out of 5 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg


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 PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:23.9
occ:1.00
 O B:HOH551 2.4 21.4 1.0
O B:HOH812 2.4 23.0 1.0
O B:HOH783 2.4 28.6 1.0
O B:HOH653 2.4 25.3 1.0
O B:HOH645 2.4 24.8 1.0
O B:HOH752 2.4 27.8 1.0
O B:HOH822 2.4 25.8 1.0
O B:HOH618 2.5 22.2 1.0
OE1 B:GLU280 4.3 18.6 1.0
O B:HOH570 4.3 24.0 1.0
O B:HOH689 4.3 20.1 1.0
O4 B:BGC406 4.4 31.6 1.0
OE1 B:GLU162 4.4 22.7 1.0
O B:HOH741 4.4 25.4 1.0
OH B:TYR240 4.5 17.1 1.0
O B:HOH605 4.7 22.9 1.0
C6 B:BGC406 4.7 29.7 1.0
OE2 B:GLU162 4.8 25.6 1.0
CZ B:TYR240 4.8 18.7 1.0
O5 B:XYS407 4.9 32.1 1.0
O B:HOH785 4.9 32.6 1.0
CD B:GLU162 5.0 23.7 1.0

Calcium binding site 5 out of 5 in 5d9n

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Calcium binding site 5 out of 5 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg


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 PBGH5A, A Glycoside Hydrolase Family 5 Member From Prevotella Bryantii B14, in Complex with the Xyloglucan Heptasaccharide Xxxg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:38.6
occ:1.00
 O B:HOH720 2.4 50.8 1.0
O B:THR272 2.4 40.4 1.0
O B:HOH592 2.4 35.4 1.0
O B:HOH654 2.4 43.5 1.0
O B:HOH630 2.4 40.1 1.0
O B:HOH841 2.4 43.7 1.0
O B:HOH609 2.4 33.9 1.0
C B:THR272 3.5 41.5 1.0
CA B:THR272 4.2 41.2 1.0
O B:HOH624 4.5 27.7 1.0
N B:THR273 4.5 40.6 1.0
O B:HOH819 4.7 48.4 1.0
O B:HIS317 4.7 28.7 1.0
O B:HOH798 4.7 39.1 1.0
CA B:THR273 4.7 39.9 1.0
N B:THR272 4.7 42.8 1.0
O B:ILE274 4.8 34.1 1.0
OG B:SER268 4.8 33.9 1.0
O B:SER268 4.9 37.3 1.0
OE1 B:GLN14 4.9 31.6 1.0

Reference:

N.Mcgregor, M.Morar, T.H.Fenger, P.Stogios, N.Lenfant, V.Yin, X.Xu, E.Evdokimova, H.Cui, B.Henrissat, A.Savchenko, H.Brumer. Structure-Function Analysis of A Mixed-Linkage Beta-Glucanase/Xyloglucanase From Key Ruminal Bacteroidetes Prevotella Bryantii B14. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
PubMed: 26507654
DOI: 10.1074/JBC.M115.691659
Page generated: Sun Jul 14 17:50:57 2024

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