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Magnesium in PDB 3rdk: Protein Crystal Structure of Xylanase A1 of Paenibacillus Sp. Jdr-2

Enzymatic activity of Protein Crystal Structure of Xylanase A1 of Paenibacillus Sp. Jdr-2

All present enzymatic activity of Protein Crystal Structure of Xylanase A1 of Paenibacillus Sp. Jdr-2:
3.2.1.8;

Protein crystallography data

The structure of Protein Crystal Structure of Xylanase A1 of Paenibacillus Sp. Jdr-2, PDB code: 3rdk was solved by E.Pozharski, F.J.St John, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 117.04 / 1.49
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 165.113, 165.113, 66.355, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 18.4

Other elements in 3rdk:

The structure of Protein Crystal Structure of Xylanase A1 of Paenibacillus Sp. Jdr-2 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Protein Crystal Structure of Xylanase A1 of Paenibacillus Sp. Jdr-2 (pdb code 3rdk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Protein Crystal Structure of Xylanase A1 of Paenibacillus Sp. Jdr-2, PDB code: 3rdk:

Magnesium binding site 1 out of 1 in 3rdk

Go back to Magnesium Binding Sites List in 3rdk
Magnesium binding site 1 out of 1 in the Protein Crystal Structure of Xylanase A1 of Paenibacillus Sp. Jdr-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Protein Crystal Structure of Xylanase A1 of Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg354

b:29.8
occ:1.00
 O2 A:GOL347 2.7 25.4 0.5
O2 A:GOL347 2.8 25.2 0.5
O A:ILE21 2.8 21.0 1.0
N A:ASN45 2.9 20.8 1.0
N A:ALA46 3.0 20.5 1.0
C2 A:GOL347 3.2 19.5 0.5
N A:GLY44 3.3 19.1 1.0
O1 A:GOL347 3.4 26.7 0.5
CB A:ALA46 3.6 21.4 1.0
CE A:MET67 3.7 28.2 1.0
CA A:ASN45 3.7 19.7 1.0
O3 A:GOL347 3.8 37.7 0.5
C A:ASN45 3.8 22.1 1.0
C A:ALA43 3.8 19.2 1.0
CB A:ALA43 3.8 20.3 1.0
CA A:ALA46 3.9 21.2 1.0
CA A:SER22 3.9 22.0 1.0
C A:GLY44 3.9 19.3 1.0
CA A:GLY44 3.9 19.4 1.0
C A:ILE21 3.9 21.1 1.0
C2 A:GOL347 4.0 29.9 0.5
C3 A:GOL347 4.0 23.8 0.5
CA A:ALA43 4.0 18.9 1.0
CB A:ASN45 4.1 22.9 1.0
SD A:MET67 4.3 25.7 1.0
C1 A:GOL347 4.3 28.6 0.5
O3 A:GOL347 4.3 27.8 0.5
O A:HOH496 4.4 30.9 1.0
C3 A:GOL347 4.4 33.8 0.5
N A:SER22 4.4 21.3 1.0
C1 A:GOL347 4.4 21.1 0.5
CB A:SER22 4.6 24.7 1.0
O1 A:GOL347 4.6 23.5 0.5
O A:ALA43 4.7 20.8 1.0
C A:SER22 4.9 23.0 1.0
ND2 A:ASN45 4.9 23.7 1.0
O A:HOH466 5.0 40.9 1.0
CG A:ASN45 5.0 19.8 1.0

Reference:

F.J.St John, J.F.Preston, E.Pozharski. Novel Structural Features of Xylanase A1 From Paenibacillus Sp. Jdr-2. J.Struct.Biol. V. 180 303 2012.
ISSN: ISSN 1047-8477
PubMed: 23000703
DOI: 10.1016/J.JSB.2012.09.007
Page generated: Thu Aug 15 10:24:09 2024

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