Atomistry » Magnesium » PDB 3jwq-3k8t » 3k1u
Atomistry »
  Magnesium »
    PDB 3jwq-3k8t »
      3k1u »

Magnesium in PDB 3k1u: Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum

Protein crystallography data

The structure of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum, PDB code: 3k1u was solved by J.Osipiuk, R.Wu, R.Jedrzejczak, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.20 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.450, 59.658, 112.391, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 16.1

Other elements in 3k1u:

The structure of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum (pdb code 3k1u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum, PDB code: 3k1u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3k1u

Go back to Magnesium Binding Sites List in 3k1u
Magnesium binding site 1 out of 3 in the Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:9.6
occ:1.00
O A:HOH512 2.1 5.0 1.0
OE2 A:GLU75 2.1 5.6 1.0
O A:HOH560 2.1 3.4 1.0
O A:HOH424 2.1 5.6 1.0
O A:HOH369 2.1 6.1 1.0
NE2 A:HIS260 2.3 7.1 1.0
CD A:GLU75 3.1 7.4 1.0
CD2 A:HIS260 3.2 7.8 1.0
CE1 A:HIS260 3.3 8.9 1.0
CG A:GLU75 3.6 5.9 1.0
O A:PRO198 3.9 4.8 1.0
O A:HOH352 3.9 6.9 1.0
O A:HOH427 4.0 10.5 1.0
O A:HOH372 4.1 8.9 1.0
OE1 A:GLU75 4.2 7.1 1.0
O A:ASP135 4.4 5.3 1.0
CG A:HIS260 4.4 6.2 1.0
ND1 A:HIS260 4.4 7.1 1.0
O A:HOH358 4.5 6.7 1.0
O A:ASN261 4.6 5.8 1.0
O A:ALA136 4.7 4.7 1.0
C A:ASP135 4.8 3.0 1.0
O A:ALA73 4.9 5.5 1.0
CA A:GLY197 4.9 4.5 1.0
C A:GLY197 4.9 5.1 1.0
CB A:THR137 4.9 4.5 1.0
CB A:ASP135 5.0 4.9 1.0
CA A:ASP135 5.0 4.3 1.0

Magnesium binding site 2 out of 3 in 3k1u

Go back to Magnesium Binding Sites List in 3k1u
Magnesium binding site 2 out of 3 in the Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:29.4
occ:1.00
O A:HOH504 1.9 22.4 1.0
O A:HOH576 2.0 27.7 1.0
O A:HOH441 2.1 17.8 1.0
O A:HOH470 2.1 20.4 1.0
O A:HOH665 2.2 27.3 1.0
O A:HOH450 2.2 16.7 1.0
OD2 A:ASP98 3.8 15.0 1.0
O A:HOH591 4.0 28.6 1.0
OD1 A:ASP98 4.1 11.0 1.0
CG A:ASP98 4.2 11.7 1.0
OD1 A:ASP97 4.3 12.1 1.0
CA A:ASP97 4.4 8.1 1.0
O A:HOH627 4.5 28.8 1.0
O A:HOH642 4.5 34.0 1.0
O A:ASP97 4.6 9.5 1.0
C A:ASP97 4.6 8.3 1.0
CB A:ASP97 4.7 7.6 1.0
CG A:ASP97 5.0 8.7 1.0

Magnesium binding site 3 out of 3 in 3k1u

Go back to Magnesium Binding Sites List in 3k1u
Magnesium binding site 3 out of 3 in the Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg411

b:25.2
occ:0.70
O A:HOH650 2.0 28.3 1.0
O A:HOH648 2.0 30.2 1.0
O A:HOH646 2.0 27.1 1.0
O A:HOH561 2.1 23.3 1.0
O A:HOH604 2.1 27.1 1.0
O A:HOH649 2.1 27.0 1.0
O A:HOH647 4.0 36.5 1.0
O A:HOH595 4.1 28.2 1.0
OH A:TYR20 4.1 15.3 1.0
OD1 A:ASN23 4.4 13.2 0.5
O A:PHE78 4.4 8.9 1.0
O A:HOH536 4.5 17.3 1.0
CE1 A:TYR20 4.7 17.8 1.0
CZ A:TYR20 4.9 15.1 1.0

Reference:

J.Osipiuk, R.Wu, R.Jedrzejczak, A.Joachimiak. X-Ray Crystal Structure of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum at 1.55 A Resolution To Be Published.
Page generated: Mon Dec 14 08:21:16 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy