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

Enzymatic activity of Crystal Structure of 2-Hydroxacyl-Coa Lyase/Synthase Apbhacs From Alphaproteobacteria Bacterium in the Complex with Thdp, D-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, D-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, D-Lactyl-Coa, and Adp, PDB code: 8vzb 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) 47.27 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.709, 178.005, 196.111, 90, 90, 90
R / Rfree (%) 17.9 / 21.8

Other elements in 8vzb:

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

Magnesium binding site 1 out of 4 in 8vzb

Go back to Magnesium Binding Sites List in 8vzb
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, D-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, D-Lactyl-Coa, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:15.5
occ:1.00
 OD1 A:ASP445 2.0 21.2 1.0
OD1 A:ASN472 2.1 22.2 1.0
O1A A:8FL602 2.1 21.6 1.0
O2B A:8FL602 2.1 18.7 1.0
O A:HOH790 2.1 20.9 1.0
O A:GLY474 2.2 21.5 1.0
CG A:ASN472 3.0 24.3 1.0
CG A:ASP445 3.2 23.7 1.0
PA A:8FL602 3.3 19.9 1.0
PB A:8FL602 3.3 20.9 1.0
ND2 A:ASN472 3.4 23.9 1.0
C A:GLY474 3.4 22.4 1.0
O3A A:8FL602 3.5 20.1 1.0
OD2 A:ASP445 3.7 22.5 1.0
O7 A:8FL602 3.8 19.0 1.0
N A:GLY474 3.9 23.1 1.0
O3B A:8FL602 3.9 19.7 1.0
N A:ASP445 4.0 18.4 1.0
N A:ASN472 4.2 21.8 1.0
N A:GLY476 4.3 21.9 1.0
CA A:GLY474 4.3 23.4 1.0
CB A:ASN472 4.3 24.0 1.0
N A:SER446 4.3 19.0 1.0
CB A:ASP445 4.4 21.2 1.0
O A:LEU470 4.4 22.6 1.0
N A:ILE475 4.4 23.4 1.0
N A:GLY473 4.5 23.1 1.0
O1B A:8FL602 4.6 20.6 1.0
O2A A:8FL602 4.6 20.9 1.0
CA A:ASN472 4.6 22.9 1.0
CA A:ILE475 4.6 22.2 1.0
CA A:ASP445 4.7 18.7 1.0
CA A:GLY444 4.8 17.7 1.0
C A:ASN472 4.8 23.8 1.0
C A:GLY444 4.8 18.5 1.0
C A:ILE475 4.9 22.5 1.0
OH A:TYR371 5.0 22.1 1.0
CB A:SER446 5.0 22.3 1.0

Magnesium binding site 2 out of 4 in 8vzb

Go back to Magnesium Binding Sites List in 8vzb
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, D-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, D-Lactyl-Coa, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:17.1
occ:1.00
 O1A B:8FL602 2.0 21.9 1.0
O2B B:8FL602 2.1 23.1 1.0
OD1 B:ASP445 2.1 22.6 1.0
OD1 B:ASN472 2.1 20.6 1.0
O B:GLY474 2.1 19.2 1.0
O B:HOH740 2.2 19.9 1.0
CG B:ASN472 3.1 21.6 1.0
CG B:ASP445 3.2 23.3 1.0
PA B:8FL602 3.2 21.8 1.0
PB B:8FL602 3.3 22.2 1.0
C B:GLY474 3.4 24.4 1.0
O3A B:8FL602 3.4 22.0 1.0
ND2 B:ASN472 3.5 21.7 1.0
OD2 B:ASP445 3.6 24.7 1.0
O7 B:8FL602 3.7 22.0 1.0
N B:GLY474 3.9 21.3 1.0
O3B B:8FL602 3.9 21.8 1.0
N B:ASP445 4.0 22.3 1.0
N B:GLY476 4.2 20.9 1.0
N B:ASN472 4.2 21.5 1.0
CA B:GLY474 4.2 22.3 1.0
N B:SER446 4.2 21.6 1.0
N B:ILE475 4.4 26.8 1.0
CB B:ASN472 4.4 22.9 1.0
CB B:ASP445 4.4 21.5 1.0
O B:LEU470 4.4 22.4 1.0
O2A B:8FL602 4.5 23.3 1.0
CA B:ILE475 4.5 23.5 1.0
O1B B:8FL602 4.5 24.6 1.0
N B:GLY473 4.6 22.7 1.0
CA B:ASP445 4.6 21.5 1.0
CA B:ASN472 4.7 22.8 1.0
C B:ILE475 4.8 24.4 1.0
CA B:GLY444 4.8 18.8 1.0
C B:GLY444 4.8 22.1 1.0
CB B:SER446 4.8 19.7 1.0
C B:ASN472 4.8 23.2 1.0
C B:ASP445 5.0 21.2 1.0
CA B:GLY476 5.0 26.1 1.0

Magnesium binding site 3 out of 4 in 8vzb

Go back to Magnesium Binding Sites List in 8vzb
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, D-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, D-Lactyl-Coa, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:18.4
occ:1.00
 O2B C:8FL602 2.0 24.0 1.0
OD1 C:ASN472 2.1 24.1 1.0
OD1 C:ASP445 2.1 23.3 1.0
O1A C:8FL602 2.1 21.5 1.0
O C:GLY474 2.2 22.0 1.0
O C:HOH735 2.4 23.6 1.0
CG C:ASN472 3.0 24.4 1.0
PB C:8FL602 3.2 21.4 1.0
CG C:ASP445 3.2 23.3 1.0
PA C:8FL602 3.3 22.0 1.0
ND2 C:ASN472 3.3 23.9 1.0
C C:GLY474 3.4 25.1 1.0
O3A C:8FL602 3.4 23.3 1.0
O7 C:8FL602 3.7 22.9 1.0
OD2 C:ASP445 3.7 25.6 1.0
O3B C:8FL602 3.8 23.9 1.0
N C:GLY474 3.9 25.3 1.0
N C:ASP445 4.0 20.7 1.0
N C:GLY476 4.1 24.6 1.0
N C:ASN472 4.3 24.4 1.0
CA C:GLY474 4.3 25.1 1.0
N C:ILE475 4.3 25.1 1.0
N C:SER446 4.4 20.3 1.0
CB C:ASN472 4.4 25.1 1.0
O1B C:8FL602 4.4 21.8 1.0
CB C:ASP445 4.5 20.9 1.0
CA C:ILE475 4.5 21.3 1.0
O C:LEU470 4.5 23.2 1.0
O2A C:8FL602 4.6 24.1 1.0
N C:GLY473 4.7 25.1 1.0
CA C:ASN472 4.7 25.2 1.0
C C:ILE475 4.7 24.9 1.0
CA C:ASP445 4.7 22.7 1.0
CA C:GLY444 4.8 20.3 1.0
N C:MET477 4.8 30.7 1.0
C C:GLY444 4.8 20.9 1.0
C C:ASN472 4.9 25.9 1.0
OH C:TYR371 4.9 24.6 1.0
CA C:GLY476 4.9 24.3 1.0
CB C:SER446 4.9 20.7 1.0
C C:GLY476 5.0 27.5 1.0

Magnesium binding site 4 out of 4 in 8vzb

Go back to Magnesium Binding Sites List in 8vzb
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, D-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, D-Lactyl-Coa, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:19.3
occ:1.00
 OD1 D:ASN472 2.0 26.1 1.0
O2B D:8FL602 2.0 25.1 1.0
OD1 D:ASP445 2.1 22.9 1.0
O1A D:8FL602 2.1 23.5 1.0
O D:HOH731 2.2 21.9 1.0
O D:GLY474 2.2 23.0 1.0
CG D:ASN472 3.0 25.8 1.0
CG D:ASP445 3.1 24.6 1.0
PA D:8FL602 3.2 22.7 1.0
PB D:8FL602 3.2 26.0 1.0
ND2 D:ASN472 3.4 21.9 1.0
O3A D:8FL602 3.4 23.3 1.0
C D:GLY474 3.4 25.2 1.0
OD2 D:ASP445 3.6 28.1 1.0
O7 D:8FL602 3.7 23.5 1.0
O3B D:8FL602 3.9 22.7 1.0
N D:GLY474 3.9 23.6 1.0
N D:ASP445 3.9 21.5 1.0
N D:ASN472 4.2 23.1 1.0
N D:SER446 4.3 19.1 1.0
N D:GLY476 4.3 26.4 1.0
CA D:GLY474 4.3 24.1 1.0
CB D:ASN472 4.3 26.5 1.0
CB D:ASP445 4.4 24.8 1.0
O D:LEU470 4.4 23.5 1.0
N D:ILE475 4.4 26.0 1.0
O1B D:8FL602 4.5 26.0 1.0
O2A D:8FL602 4.5 24.8 1.0
N D:GLY473 4.6 26.5 1.0
CA D:ILE475 4.6 25.3 1.0
CA D:ASP445 4.6 21.5 1.0
CA D:ASN472 4.7 26.4 1.0
CA D:GLY444 4.7 22.4 1.0
C D:GLY444 4.8 22.3 1.0
C D:ASN472 4.8 26.4 1.0
C D:ILE475 4.9 26.5 1.0
CB D:SER446 4.9 21.2 1.0
OH D:TYR371 4.9 27.7 1.0
C D:ASP445 5.0 23.1 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 22:16:20 2024

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