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Magnesium in PDB 4wdq: Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26

Enzymatic activity of Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26

All present enzymatic activity of Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26:
3.8.1.5;

Protein crystallography data

The structure of Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26, PDB code: 4wdq was solved by O.Degtjarik, P.Rezacova, R.Chaloupkova, J.Damborsky, I.Kuta-Smatanova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.49 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.729, 68.490, 81.055, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20.6

Other elements in 4wdq:

The structure of Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26 (pdb code 4wdq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26, PDB code: 4wdq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4wdq

Go back to Magnesium Binding Sites List in 4wdq
Magnesium binding site 1 out of 3 in the Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26


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 Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:7.3
occ:1.00
 O A:HOH528 2.1 8.1 1.0
O A:HOH497 2.1 7.1 1.0
O A:HOH820 2.1 6.4 1.0
O A:HOH456 2.1 7.6 1.0
O A:HOH992 2.1 10.4 1.0
O A:HOH577 4.1 10.7 1.0
OD1 A:ASP68 4.2 9.1 1.0
OE1 A:GLU192 4.3 12.5 1.0
O A:HOH564 4.3 11.2 1.0
OE2 A:GLU192 4.3 9.6 1.0
O A:HOH885 4.3 22.7 1.0
O A:HOH484 4.3 6.9 1.0
O A:GLY67 4.4 5.3 1.0
O A:HOH987 4.4 19.8 1.0
CD A:GLU192 4.7 11.3 1.0
CA A:ASP68 4.8 6.3 1.0
O A:HOH849 5.0 52.5 1.0

Magnesium binding site 2 out of 3 in 4wdq

Go back to Magnesium Binding Sites List in 4wdq
Magnesium binding site 2 out of 3 in the Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26


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 Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:11.3
occ:1.00
 O A:HOH944 2.0 11.3 1.0
O A:HOH523 2.1 8.1 1.0
O A:HOH536 2.1 10.2 1.0
O A:HOH424 2.2 10.3 1.0
OD2 A:ASP70 4.1 6.2 1.0
O A:HOH515 4.1 6.8 1.0
O A:HOH510 4.1 6.4 1.0
O A:HOH622 4.2 18.2 1.0
O A:HOH1030 4.2 36.8 1.0
OE2 A:GLU15 4.2 12.5 1.0
NE A:ARG20 4.2 16.2 1.0
O A:HOH864 4.3 24.5 1.0
OE1 A:GLU15 4.3 8.1 1.0
O A:GLY18 4.3 6.7 1.0
CG A:ARG20 4.4 12.6 1.0
O A:HOH838 4.5 26.5 1.0
CD A:GLU15 4.7 8.7 1.0
CD A:ARG20 4.9 15.4 1.0
NH2 A:ARG20 5.0 16.4 1.0

Magnesium binding site 3 out of 3 in 4wdq

Go back to Magnesium Binding Sites List in 4wdq
Magnesium binding site 3 out of 3 in the Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Haloalkane Dehalogenase LINB32 Mutant (L177W) From Sphingobium Japonicum UT26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:12.1
occ:1.00
 O A:HOH671 2.0 12.4 1.0
O A:HOH551 2.0 9.6 1.0
O A:HOH496 2.1 11.2 1.0
O A:HOH822 2.1 14.0 1.0
O A:HOH438 2.2 12.8 1.0
OE2 A:GLU145 4.0 24.5 1.0
OG1 A:THR250 4.0 8.0 1.0
OE1 A:GLU145 4.1 25.3 1.0
O A:ASP142 4.2 10.1 1.0
O A:HOH537 4.2 13.3 1.0
O A:HOH917 4.3 25.7 1.0
O A:HOH474 4.4 12.4 1.0
O A:ALA141 4.4 10.6 1.0
CD A:GLU145 4.5 23.8 1.0
C A:ASP142 4.6 9.8 1.0
O A:PHE143 4.6 13.2 1.0
CA A:ASP142 4.8 9.9 1.0
CA A:GLY251 4.8 8.8 1.0
N A:GLY251 4.9 7.8 1.0
CB A:THR250 5.0 7.1 1.0

Reference:

O.Degtjarik, P.Rezacova, R.Chaloupkova, J.Damborsky, I.Kuta-Smatanova. Crystal Structure of Haloalkane Dehalogenase Linb Mutant (L177W) From Sphingobium Japonicum UT26 Acs Catalysis 2016.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.6B02081
Page generated: Tue Aug 20 13:10:57 2024

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