Atomistry » Calcium » PDB 5cxl-5da8 » 5d9n
Atomistry »
  Calcium »
    PDB 5cxl-5da8 »
      5d9n »

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

Go back to Calcium Binding Sites List in 5d9n
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

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