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Magnesium in PDB 8vzf: Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp

Enzymatic activity of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp

All present enzymatic activity of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp:
4.1.1.8;

Protein crystallography data

The structure of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp, PDB code: 8vzf was solved by P.Gade, Y.Kim, M.Endres, S.Lee, Y.Yoshikuni, R.Gonzalez, K.Michalska, A.Joachimiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.35 / 2.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.8, 178.131, 196.482, 90, 90, 90
R / Rfree (%) 20.7 / 24.7

Other elements in 8vzf:

The structure of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp (pdb code 8vzf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp, PDB code: 8vzf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8vzf

Go back to Magnesium Binding Sites List in 8vzf
Magnesium binding site 1 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp


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 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:32.3
occ:1.00
 O1A A:TPP602 2.0 35.7 1.0
OD1 A:ASP445 2.0 39.2 1.0
OD1 A:ASN472 2.1 35.5 1.0
O A:GLY474 2.1 33.4 1.0
O A:HOH701 2.1 24.5 1.0
O2B A:TPP602 2.1 34.7 1.0
CG A:ASN472 3.1 38.1 1.0
CG A:ASP445 3.1 34.8 1.0
PA A:TPP602 3.2 31.4 1.0
PB A:TPP602 3.3 29.6 1.0
C A:GLY474 3.3 35.2 1.0
O3A A:TPP602 3.5 34.0 1.0
ND2 A:ASN472 3.5 37.2 1.0
OD2 A:ASP445 3.5 35.8 1.0
O7 A:TPP602 3.8 30.2 1.0
N A:GLY474 3.9 34.9 1.0
N A:ASP445 4.0 31.8 1.0
N A:GLY476 4.0 40.7 1.0
O3B A:TPP602 4.0 34.8 1.0
N A:SER446 4.2 29.1 1.0
N A:ASN472 4.3 36.1 1.0
CA A:GLY474 4.3 34.4 1.0
N A:ILE475 4.3 37.1 1.0
CB A:ASP445 4.4 30.7 1.0
CA A:ILE475 4.4 36.1 1.0
CB A:ASN472 4.4 38.2 1.0
O2A A:TPP602 4.4 30.2 1.0
O A:LEU470 4.5 33.7 1.0
O1B A:TPP602 4.5 35.1 1.0
C A:ILE475 4.6 37.2 1.0
CA A:ASP445 4.6 31.9 1.0
N A:GLY473 4.6 36.6 1.0
CB A:SER446 4.7 32.0 1.0
CA A:ASN472 4.7 38.6 1.0
C A:GLY444 4.8 32.6 1.0
CA A:GLY444 4.8 30.7 1.0
CA A:GLY476 4.8 36.5 1.0
N A:MET477 4.9 44.9 1.0
C A:ASN472 4.9 38.0 1.0
C A:ASP445 4.9 30.4 1.0

Magnesium binding site 2 out of 4 in 8vzf

Go back to Magnesium Binding Sites List in 8vzf
Magnesium binding site 2 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp


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 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:26.3
occ:1.00
 OD1 B:ASP445 2.0 32.0 1.0
OD1 B:ASN472 2.1 36.3 1.0
O1A B:TPP602 2.1 28.7 1.0
O2B B:TPP602 2.2 29.8 1.0
O B:HOH722 2.2 28.5 1.0
O B:GLY474 2.3 34.0 1.0
CG B:ASN472 3.0 36.7 1.0
CG B:ASP445 3.1 31.4 1.0
PA B:TPP602 3.3 31.1 1.0
PB B:TPP602 3.3 29.6 1.0
ND2 B:ASN472 3.3 35.9 1.0
C B:GLY474 3.5 34.8 1.0
OD2 B:ASP445 3.6 38.5 1.0
O3A B:TPP602 3.7 31.0 1.0
O7 B:TPP602 3.8 30.8 1.0
O3B B:TPP602 3.8 32.2 1.0
N B:ASP445 4.0 29.7 1.0
N B:GLY474 4.0 34.9 1.0
N B:GLY476 4.2 39.5 1.0
N B:ASN472 4.2 33.8 1.0
N B:SER446 4.3 29.8 1.0
CB B:ASN472 4.3 35.9 1.0
CA B:GLY474 4.4 35.4 1.0
CB B:ASP445 4.4 30.3 1.0
N B:ILE475 4.5 37.5 1.0
O B:LEU470 4.5 35.3 1.0
N B:GLY473 4.5 34.6 1.0
O2A B:TPP602 4.6 28.4 1.0
O1B B:TPP602 4.6 25.3 1.0
CA B:ILE475 4.6 36.7 1.0
CA B:ASP445 4.6 29.4 1.0
CA B:ASN472 4.7 35.2 1.0
CA B:GLY444 4.8 29.7 1.0
C B:ASN472 4.8 35.5 1.0
C B:ILE475 4.8 36.6 1.0
C B:GLY444 4.8 29.1 1.0
N B:MET477 4.9 40.9 1.0
CB B:SER446 4.9 30.9 1.0
CA B:GLY476 5.0 36.9 1.0
C B:ASP445 5.0 29.2 1.0

Magnesium binding site 3 out of 4 in 8vzf

Go back to Magnesium Binding Sites List in 8vzf
Magnesium binding site 3 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp


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 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:30.2
occ:1.00
 OD1 C:ASP445 2.0 36.0 1.0
O1A C:TPP602 2.0 38.7 1.0
OD1 C:ASN472 2.1 40.5 1.0
O C:GLY474 2.1 36.9 1.0
O2B C:TPP602 2.1 38.3 1.0
O C:HOH701 2.2 36.2 1.0
CG C:ASP445 3.0 36.6 1.0
CG C:ASN472 3.1 37.7 1.0
PA C:TPP602 3.2 40.0 1.0
OD2 C:ASP445 3.3 38.9 1.0
C C:GLY474 3.4 40.7 1.0
PB C:TPP602 3.4 35.5 1.0
ND2 C:ASN472 3.5 37.5 1.0
O3A C:TPP602 3.6 36.0 1.0
O7 C:TPP602 3.8 36.4 1.0
N C:GLY474 3.9 39.0 1.0
N C:ASP445 4.0 34.7 1.0
O3B C:TPP602 4.1 34.0 1.0
N C:GLY476 4.1 41.1 1.0
N C:SER446 4.2 35.0 1.0
CA C:GLY474 4.3 38.9 1.0
N C:ASN472 4.3 38.0 1.0
CB C:ASP445 4.3 36.4 1.0
N C:ILE475 4.3 40.3 1.0
CB C:ASN472 4.4 38.5 1.0
CA C:ILE475 4.4 38.5 1.0
O2A C:TPP602 4.5 37.9 1.0
O C:LEU470 4.5 43.8 1.0
O1B C:TPP602 4.5 32.0 1.0
CA C:ASP445 4.6 35.4 1.0
N C:GLY473 4.6 39.5 1.0
C C:ILE475 4.7 39.8 1.0
CA C:ASN472 4.7 39.6 1.0
CB C:SER446 4.8 39.0 1.0
C C:GLY444 4.8 37.5 1.0
CA C:GLY444 4.8 36.6 1.0
C C:ASN472 4.9 39.8 1.0
C C:ASP445 4.9 37.4 1.0
N C:MET477 4.9 41.7 1.0
CA C:GLY476 5.0 36.0 1.0

Magnesium binding site 4 out of 4 in 8vzf

Go back to Magnesium Binding Sites List in 8vzf
Magnesium binding site 4 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, Coenzyme A, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:28.3
occ:1.00
 O2B D:TPP602 2.0 31.4 1.0
O D:GLY474 2.0 31.7 1.0
OD1 D:ASN472 2.1 36.8 1.0
OD1 D:ASP445 2.2 33.8 1.0
O1A D:TPP602 2.2 30.9 1.0
O D:HOH715 2.3 35.0 1.0
CG D:ASN472 2.9 35.0 1.0
ND2 D:ASN472 3.2 31.3 1.0
C D:GLY474 3.2 36.8 1.0
PB D:TPP602 3.3 32.0 1.0
CG D:ASP445 3.3 36.3 1.0
PA D:TPP602 3.4 38.1 1.0
O3A D:TPP602 3.7 38.2 1.0
OD2 D:ASP445 3.7 36.3 1.0
O3B D:TPP602 3.8 35.6 1.0
N D:GLY476 3.8 40.2 1.0
O7 D:TPP602 3.9 38.4 1.0
N D:GLY474 3.9 36.7 1.0
N D:ILE475 4.2 39.7 1.0
CA D:GLY474 4.2 34.0 1.0
N D:ASP445 4.2 32.9 1.0
CA D:ILE475 4.3 37.3 1.0
CB D:ASN472 4.4 34.9 1.0
N D:ASN472 4.4 35.1 1.0
N D:SER446 4.4 32.1 1.0
O1B D:TPP602 4.5 28.8 1.0
C D:ILE475 4.5 37.4 1.0
N D:MET477 4.5 50.8 1.0
CB D:ASP445 4.6 35.2 1.0
N D:GLY473 4.6 36.5 1.0
CA D:GLY476 4.6 35.6 1.0
O2A D:TPP602 4.7 31.0 1.0
O D:LEU470 4.7 35.1 1.0
CA D:ASN472 4.8 35.2 1.0
C D:GLY476 4.8 42.4 1.0
CA D:ASP445 4.9 30.7 1.0
CB D:SER446 4.9 32.1 1.0
C D:ASN472 4.9 38.2 1.0
CA D:GLY444 5.0 30.3 1.0

Reference:

Y.Kim, S.H.Lee, P.Gade, M.Nattermann, N.Maltseva, M.Endres, J.Chen, P.Wichmann, Y.Hu, D.G.Marchal, Y.Yoshikuni, T.J.Erb, R.Gonzalez, K.Michalska, A.Joachimiak. Revealing Reaction Intermediates in One-Carbon Elongation By Thiamine Diphosphate/Coa-Dependent Enzyme Family. Commun Chem V. 7 160 2024.
ISSN: ESSN 2399-3669
PubMed: 39034323
DOI: 10.1038/S42004-024-01242-Y
Page generated: Fri Aug 15 18:07:04 2025

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