Magnesium in PDB 5tma: Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3

Enzymatic activity of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3

All present enzymatic activity of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3:
4.1.1.1;

Protein crystallography data

The structure of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3, PDB code: 5tma was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 101.18 / 1.67
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 124.440, 124.440, 173.825, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3 (pdb code 5tma). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3, PDB code: 5tma:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5tma

Go back to Magnesium Binding Sites List in 5tma
Magnesium binding site 1 out of 2 in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:20.7
occ:1.00
O1A A:TPP601 2.0 22.0 0.9
O2B A:TPP601 2.0 21.9 0.9
O A:GLY469 2.1 24.3 1.0
OD1 A:ASP440 2.1 22.1 1.0
O A:HOH961 2.2 24.2 1.0
OD1 A:ASN467 2.2 25.4 1.0
PA A:TPP601 3.1 22.6 0.9
CG A:ASN467 3.2 28.9 1.0
PB A:TPP601 3.2 27.8 0.9
C A:GLY469 3.3 29.0 1.0
CG A:ASP440 3.4 23.3 1.0
O3A A:TPP601 3.5 23.7 0.9
ND2 A:ASN467 3.5 24.7 1.0
OD2 A:ASP440 3.9 28.1 1.0
O7 A:TPP601 4.0 23.3 0.9
N A:ASP440 4.0 16.6 1.0
N A:GLY469 4.1 27.2 1.0
N A:GLY441 4.1 18.4 1.0
O3B A:TPP601 4.1 27.0 0.9
N A:THR471 4.1 28.3 1.0
CA A:GLY469 4.2 26.3 1.0
N A:TYR470 4.3 24.4 1.0
O A:HOH719 4.3 38.0 1.0
CA A:TYR470 4.4 26.0 1.0
O1B A:TPP601 4.4 34.8 0.9
O2A A:TPP601 4.4 21.5 0.9
O A:ILE465 4.4 18.7 1.0
CB A:ASN467 4.5 25.9 1.0
CB A:ASP440 4.6 19.5 1.0
CA A:GLY439 4.6 15.4 1.0
OG1 A:THR471 4.6 36.2 1.0
N A:ASN467 4.7 21.7 1.0
O A:HOH784 4.7 26.3 1.0
C A:GLY439 4.7 15.3 1.0
C A:ASN467 4.7 29.3 1.0
CA A:ASP440 4.7 18.4 1.0
CB A:THR471 4.8 32.6 1.0
C A:TYR470 4.8 26.1 1.0
CA A:ASN467 4.8 26.6 1.0
CA A:GLY441 4.9 17.8 1.0
O A:ASN467 4.9 27.7 1.0
N A:TYR468 4.9 27.9 1.0
C A:ASP440 4.9 18.2 1.0

Magnesium binding site 2 out of 2 in 5tma

Go back to Magnesium Binding Sites List in 5tma
Magnesium binding site 2 out of 2 in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:24.7
occ:1.00
O2A B:TPP601 2.0 17.9 0.8
O1B B:TPP601 2.1 21.1 0.8
OD1 B:ASP440 2.2 24.5 1.0
OD1 B:ASN467 2.2 23.3 1.0
O B:HOH962 2.2 23.9 1.0
O B:GLY469 2.2 26.3 1.0
CG B:ASN467 3.1 26.6 1.0
PA B:TPP601 3.1 21.5 0.8
PB B:TPP601 3.3 24.1 0.8
CG B:ASP440 3.4 24.1 1.0
C B:GLY469 3.4 29.6 1.0
O3A B:TPP601 3.4 23.8 0.8
ND2 B:ASN467 3.4 28.9 1.0
N B:ASP440 4.0 19.2 1.0
OD2 B:ASP440 4.0 31.8 1.0
O7 B:TPP601 4.0 22.2 0.8
N B:GLY441 4.1 20.2 1.0
N B:GLY469 4.1 26.8 1.0
O2B B:TPP601 4.2 26.7 0.8
N B:THR471 4.2 28.2 1.0
O B:ILE465 4.3 21.6 1.0
N B:TYR470 4.3 27.6 1.0
CA B:GLY469 4.3 27.1 1.0
O1A B:TPP601 4.3 23.0 0.8
CA B:TYR470 4.4 29.6 1.0
O3B B:TPP601 4.4 28.9 0.8
CB B:ASN467 4.5 23.7 1.0
CA B:GLY439 4.5 17.7 1.0
N B:ASN467 4.5 23.0 1.0
CB B:ASP440 4.6 21.9 1.0
C B:GLY439 4.6 19.5 1.0
CA B:ASP440 4.6 19.5 1.0
O B:HOH1021 4.7 29.0 1.0
C B:ASN467 4.7 25.9 1.0
CA B:ASN467 4.8 21.5 1.0
OG1 B:THR471 4.8 33.4 1.0
C B:TYR470 4.8 30.7 1.0
C B:ASP440 4.9 20.9 1.0
O B:HOH777 4.9 40.0 1.0
CA B:GLY441 4.9 20.0 1.0
N B:TYR468 4.9 28.4 1.0

Reference:

D.W.Sammond, N.Kastelowitz, B.S.Donohoe, M.Alahuhta, V.V.Lunin, D.Chung, N.S.Sarai, H.Yin, A.Mittal, M.E.Himmel, A.M.Guss, Y.J.Bomble. An Iterative Computational Design Approach to Increase the Thermal Endurance of A Mesophilic Enzyme. Biotechnol Biofuels V. 11 189 2018.
ISSN: ESSN 1754-6834
PubMed: 30002729
DOI: 10.1186/S13068-018-1178-9
Page generated: Mon Dec 14 21:12:42 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