Magnesium in PDB 5xxl: Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron

Protein crystallography data

The structure of Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron, PDB code: 5xxl was solved by M.Nakajima, R.Ishiguro, N.Tanaka, K.Abe, T.Maeda, A.Miyanaga, Y.Takahash, N.Sugimoto, H.Nakai, H.Taguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 81.940, 167.880, 224.090, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 22.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron (pdb code 5xxl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron, PDB code: 5xxl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5xxl

Go back to Magnesium Binding Sites List in 5xxl
Magnesium binding site 1 out of 2 in the Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:20.4
occ:1.00
O A:VAL701 2.1 19.8 1.0
O A:HOH935 2.1 21.5 1.0
O A:HOH1111 2.1 17.8 1.0
O A:HOH938 2.2 21.4 1.0
OD1 A:ASP699 2.2 16.4 1.0
O A:HOH995 2.2 21.0 1.0
CG A:ASP699 3.2 16.6 1.0
C A:VAL701 3.3 18.3 1.0
OD2 A:ASP699 3.5 17.6 1.0
N A:VAL701 3.9 18.6 1.0
CA A:VAL701 4.1 18.4 1.0
O A:PRO749 4.1 21.5 1.0
O A:HOH1369 4.2 36.6 1.0
O A:GLU748 4.2 19.8 1.0
N A:GLY702 4.3 18.1 1.0
O A:GLU751 4.3 21.9 1.0
O A:HOH1104 4.4 24.6 1.0
CA A:GLY702 4.4 18.6 1.0
CB A:VAL701 4.5 18.3 1.0
CA A:GLY750 4.5 21.6 1.0
OE1 A:GLU748 4.5 25.5 1.0
CB A:ASP699 4.5 16.8 1.0
CB A:GLU748 4.6 21.9 1.0
CZ A:PHE752 4.6 20.6 1.0
C A:PRO749 4.7 21.3 1.0
N A:LEU700 4.7 17.7 1.0
C A:ASP699 4.7 17.0 1.0
N A:GLU751 4.8 22.9 1.0
C A:GLY750 4.8 22.2 1.0
CA A:ASP699 4.8 16.9 1.0
N A:GLY750 4.9 21.2 1.0
C A:GLU748 4.9 21.4 1.0
CE1 A:PHE752 4.9 20.6 1.0
O A:HOH1209 5.0 24.1 1.0

Magnesium binding site 2 out of 2 in 5xxl

Go back to Magnesium Binding Sites List in 5xxl
Magnesium binding site 2 out of 2 in the Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:15.9
occ:1.00
O B:VAL701 2.1 16.4 1.0
O B:HOH999 2.1 16.4 1.0
O B:HOH1076 2.1 16.6 1.0
OD1 B:ASP699 2.1 14.8 1.0
O B:HOH988 2.1 17.1 1.0
O B:HOH1050 2.2 18.0 1.0
CG B:ASP699 3.1 13.9 1.0
C B:VAL701 3.3 15.7 1.0
OD2 B:ASP699 3.4 13.4 1.0
N B:VAL701 3.9 15.6 1.0
CA B:VAL701 4.1 15.4 1.0
O B:PRO749 4.2 20.7 1.0
N B:GLY702 4.2 14.9 1.0
O B:HOH1361 4.3 32.5 1.0
O B:GLU748 4.3 20.1 1.0
O B:GLU751 4.4 20.1 1.0
CA B:GLY702 4.4 15.6 1.0
CB B:ASP699 4.4 13.9 1.0
CB B:VAL701 4.5 15.5 1.0
O B:HOH1236 4.5 17.8 1.0
CA B:GLY750 4.5 21.1 1.0
OE1 B:GLU748 4.5 21.3 1.0
C B:ASP699 4.6 14.4 1.0
N B:LEU700 4.6 14.9 1.0
CZ B:PHE752 4.7 17.7 1.0
CB B:GLU748 4.7 21.3 1.0
C B:PRO749 4.8 21.1 1.0
C B:GLY750 4.8 21.5 1.0
N B:GLU751 4.8 21.9 1.0
CA B:ASP699 4.8 13.9 1.0
O B:HOH1187 4.8 16.7 1.0
N B:GLY750 4.9 21.3 1.0
C B:GLU748 5.0 21.4 1.0
CE1 B:PHE752 5.0 17.9 1.0

Reference:

R.Ishiguro, N.Tanaka, K.Abe, M.Nakajima, T.Maeda, A.Miyanaga, Y.Takahashi, N.Sugimoto, H.Nakai, H.Taguchi. Function and Structure Relationships of A Beta-1,2-Glucooligosaccharide-Degrading Beta-Glucosidase. Febs Lett. V. 591 3926 2017.
ISSN: ISSN 1873-3468
PubMed: 29131329
DOI: 10.1002/1873-3468.12911
Page generated: Mon Dec 14 22:11:59 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