Magnesium in PDB 8vza: Crystal Structure of 2-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, and Adp

Enzymatic activity of Crystal Structure of 2-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, and Adp

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

Protein crystallography data

The structure of Crystal Structure of 2-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, and Adp, PDB code: 8vza 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) 49.52 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.409, 102.679, 104.344, 114.1, 96.74, 105.23
R / Rfree (%) 20.7 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, and Adp (pdb code 8vza). 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-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, and Adp, PDB code: 8vza:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8vza

Go back to Magnesium Binding Sites List in 8vza
Magnesium binding site 1 out of 4 in the Crystal Structure of 2-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, 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-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:21.5
occ:1.00
 OD1 A:ASP445 2.0 21.2 1.0
O2B A:8FL601 2.1 24.1 1.0
O1A A:8FL601 2.1 24.1 1.0
O A:GLY474 2.1 23.5 1.0
OD1 A:ASN472 2.2 26.3 1.0
O A:HOH703 2.5 20.4 1.0
CG A:ASP445 3.0 24.4 1.0
CG A:ASN472 3.1 25.7 1.0
PA A:8FL601 3.2 23.4 1.0
PB A:8FL601 3.3 21.1 1.0
C A:GLY474 3.3 25.4 1.0
OD2 A:ASP445 3.4 22.9 1.0
ND2 A:ASN472 3.4 24.6 1.0
O3A A:8FL601 3.5 22.6 1.0
O7 A:8FL601 3.7 20.9 1.0
N A:GLY474 3.9 25.5 1.0
N A:ASP445 3.9 19.2 1.0
O3B A:8FL601 4.0 24.0 1.0
N A:GLY476 4.2 24.1 1.0
CA A:GLY474 4.2 25.6 1.0
N A:SER446 4.3 19.3 1.0
N A:ILE475 4.3 23.7 1.0
CB A:ASP445 4.3 23.4 1.0
N A:ASN472 4.4 24.8 1.0
CA A:ILE475 4.4 24.3 1.0
O A:LEU470 4.4 21.2 1.0
O1B A:8FL601 4.5 20.8 1.0
CB A:ASN472 4.5 25.7 1.0
O2A A:8FL601 4.5 21.6 1.0
CA A:ASP445 4.6 20.7 1.0
N A:GLY473 4.7 26.5 1.0
CA A:GLY444 4.7 18.3 1.0
C A:ILE475 4.7 27.1 1.0
C A:GLY444 4.8 18.4 1.0
CB A:SER446 4.8 21.2 1.0
CA A:ASN472 4.8 26.3 1.0
C A:ASN472 5.0 27.2 1.0
C A:ASP445 5.0 20.5 1.0

Magnesium binding site 2 out of 4 in 8vza

Go back to Magnesium Binding Sites List in 8vza
Magnesium binding site 2 out of 4 in the Crystal Structure of 2-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, 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-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg606

b:16.1
occ:1.00
 OD1 B:ASP445 2.0 19.3 1.0
O1A B:8FL602 2.0 17.5 1.0
O B:GLY474 2.1 19.8 1.0
OD1 B:ASN472 2.2 22.3 1.0
O B:HOH715 2.2 18.2 1.0
O3B B:8FL602 2.3 19.0 1.0
CG B:ASP445 3.1 21.1 1.0
CG B:ASN472 3.1 21.7 1.0
PA B:8FL602 3.2 20.1 1.0
C B:GLY474 3.3 22.5 1.0
PB B:8FL602 3.4 22.6 1.0
ND2 B:ASN472 3.4 20.6 1.0
O3A B:8FL602 3.6 19.7 1.0
OD2 B:ASP445 3.6 19.6 1.0
O7 B:8FL602 3.7 20.9 1.0
O1B B:8FL602 3.9 17.5 1.0
N B:GLY474 3.9 22.7 1.0
N B:ASP445 3.9 18.0 1.0
N B:SER446 4.2 21.2 1.0
CA B:GLY474 4.2 21.1 1.0
N B:GLY476 4.2 22.4 1.0
N B:ASN472 4.3 19.7 1.0
CB B:ASP445 4.3 18.9 1.0
N B:ILE475 4.3 19.8 1.0
O B:LEU470 4.4 21.9 1.0
CB B:ASN472 4.4 19.9 1.0
O2A B:8FL602 4.5 21.0 1.0
CA B:ILE475 4.5 21.0 1.0
CA B:ASP445 4.6 22.5 1.0
N B:GLY473 4.6 22.9 1.0
O2B B:8FL602 4.7 18.8 1.0
C B:GLY444 4.8 17.7 1.0
CA B:ASN472 4.8 20.1 1.0
CA B:GLY444 4.8 17.5 1.0
C B:ILE475 4.8 21.9 1.0
CB B:SER446 4.8 21.3 1.0
C B:ASP445 4.9 19.8 1.0
C B:ASN472 4.9 20.6 1.0

Magnesium binding site 3 out of 4 in 8vza

Go back to Magnesium Binding Sites List in 8vza
Magnesium binding site 3 out of 4 in the Crystal Structure of 2-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, 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-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg606

b:19.1
occ:1.00
 OD1 C:ASN472 2.0 23.1 1.0
O2B C:8FL601 2.1 18.8 1.0
OD1 C:ASP445 2.1 20.1 1.0
O C:GLY474 2.1 21.3 1.0
O1A C:8FL601 2.3 20.9 1.0
O C:HOH707 2.4 24.3 1.0
CG C:ASN472 2.9 24.4 1.0
CG C:ASP445 3.2 25.0 1.0
PB C:8FL601 3.2 22.4 1.0
ND2 C:ASN472 3.3 21.1 1.0
C C:GLY474 3.3 23.3 1.0
PA C:8FL601 3.4 22.5 1.0
O3A C:8FL601 3.5 20.7 1.0
O3B C:8FL601 3.7 23.7 1.0
OD2 C:ASP445 3.7 25.5 1.0
O7 C:8FL601 3.7 20.4 1.0
N C:GLY474 3.8 23.8 1.0
N C:ASP445 4.1 19.6 1.0
N C:GLY476 4.1 21.5 1.0
CA C:GLY474 4.2 24.6 1.0
N C:ASN472 4.2 20.8 1.0
N C:ILE475 4.3 22.6 1.0
CB C:ASN472 4.3 21.6 1.0
N C:SER446 4.4 20.6 1.0
O C:LEU470 4.4 20.7 1.0
CB C:ASP445 4.5 23.5 1.0
CA C:ILE475 4.5 24.3 1.0
O1B C:8FL601 4.5 18.3 1.0
N C:GLY473 4.6 25.1 1.0
CA C:ASN472 4.7 23.5 1.0
O2A C:8FL601 4.7 23.9 1.0
C C:ILE475 4.7 24.3 1.0
CA C:ASP445 4.7 20.8 1.0
N C:MET477 4.8 26.8 1.0
C C:ASN472 4.8 26.2 1.0
CA C:GLY444 4.9 21.9 1.0
OH C:TYR371 4.9 24.5 1.0
C C:GLY444 4.9 20.6 1.0
CA C:GLY476 4.9 23.6 1.0

Magnesium binding site 4 out of 4 in 8vza

Go back to Magnesium Binding Sites List in 8vza
Magnesium binding site 4 out of 4 in the Crystal Structure of 2-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, 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-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, L-Lactyl-Coa, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:20.9
occ:1.00
 OD1 D:ASN472 1.9 23.0 1.0
OD1 D:ASP445 2.0 21.2 1.0
O D:GLY474 2.1 22.4 1.0
O1B D:8FL601 2.1 23.3 1.0
O1A D:8FL601 2.3 21.8 1.0
O D:HOH706 2.6 22.4 1.0
CG D:ASN472 2.9 22.7 1.0
CG D:ASP445 3.0 22.6 1.0
C D:GLY474 3.2 23.6 1.0
ND2 D:ASN472 3.3 20.7 1.0
OD2 D:ASP445 3.4 26.0 1.0
PB D:8FL601 3.4 18.9 1.0
PA D:8FL601 3.5 21.8 1.0
N D:GLY474 3.7 24.3 1.0
O3A D:8FL601 3.7 20.2 1.0
O7 D:8FL601 3.8 20.6 1.0
CA D:GLY474 4.1 23.6 1.0
N D:ASP445 4.1 18.2 1.0
N D:GLY476 4.1 25.0 1.0
N D:ASN472 4.2 20.6 1.0
O2B D:8FL601 4.2 24.5 1.0
N D:ILE475 4.2 23.9 1.0
CB D:ASN472 4.3 21.3 1.0
CB D:ASP445 4.4 19.8 1.0
N D:SER446 4.4 19.4 1.0
N D:GLY473 4.5 22.7 1.0
CA D:ILE475 4.5 23.1 1.0
O3B D:8FL601 4.5 22.6 1.0
O D:LEU470 4.6 20.8 1.0
CA D:ASN472 4.6 21.6 1.0
C D:ASN472 4.7 22.8 1.0
CA D:ASP445 4.7 22.6 1.0
C D:ILE475 4.7 27.9 1.0
N D:MET477 4.8 28.8 1.0
O2A D:8FL601 4.8 23.6 1.0
C D:GLY473 4.9 24.6 1.0
C D:GLY444 4.9 17.6 1.0
CA D:GLY476 5.0 28.1 1.0
CA D:GLY444 5.0 17.1 1.0
CB D:SER446 5.0 20.4 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: Thu Oct 31 22:16:27 2024

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