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Magnesium in PDB 7pt4: Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone

Enzymatic activity of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone

All present enzymatic activity of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone:
4.2.1.17;

Protein crystallography data

The structure of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone, PDB code: 7pt4 was solved by M.Zahn, T.Rohwerder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.66 / 1.64
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 116.234, 116.234, 312.056, 90, 90, 120
R / Rfree (%) 14.5 / 17.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone (pdb code 7pt4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone, PDB code: 7pt4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7pt4

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Magnesium binding site 1 out of 4 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg716

b:26.6
occ:0.50
 O A:HOH938 2.1 14.3 1.0
O A:HOH1176 2.2 15.1 1.0
O A:HOH931 2.3 20.9 1.0
OD2 A:ASP64 4.0 16.3 1.0
HA A:ASN95 4.2 11.8 1.0
O A:HOH1116 4.2 11.6 1.0
O A:HOH1066 4.3 24.6 1.0
O A:ASN95 4.3 13.1 1.0
O A:HOH1115 4.4 22.8 1.0
OD1 A:ASP64 4.4 15.3 1.0
OD1 A:ASN95 4.6 12.4 1.0
CG A:ASP64 4.6 14.2 1.0
HB3 A:ASN95 4.7 12.1 1.0
O A:HOH1235 4.8 16.9 1.0
CA A:ASN95 4.9 11.6 1.0

Magnesium binding site 2 out of 4 in 7pt4

Go back to Magnesium Binding Sites List in 7pt4
Magnesium binding site 2 out of 4 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg717

b:14.2
occ:1.00
 OD1 A:ASP460 1.9 14.3 1.0
O2A A:TPP701 2.0 11.9 1.0
O2B A:TPP701 2.0 11.9 1.0
O A:ALA489 2.0 12.9 1.0
OD1 A:ASN487 2.1 12.5 1.0
O A:HOH884 2.1 9.2 1.0
HD21 A:ASN487 3.0 11.7 1.0
CG A:ASN487 3.1 11.7 1.0
H A:ASP460 3.2 11.8 1.0
CG A:ASP460 3.2 13.3 1.0
PB A:TPP701 3.2 13.0 1.0
PA A:TPP701 3.2 12.5 1.0
H A:GLY461 3.2 12.3 1.0
C A:ALA489 3.3 13.4 1.0
H A:ASN491 3.3 13.4 1.0
H A:ALA489 3.4 13.7 1.0
ND2 A:ASN487 3.4 11.7 1.0
O3A A:TPP701 3.4 12.1 1.0
H A:ASN487 3.7 12.6 1.0
HA A:TRP490 3.7 12.7 1.0
OD2 A:ASP460 3.8 16.2 1.0
HB2 A:ASN491 3.8 14.7 1.0
O1B A:TPP701 3.9 12.9 1.0
N A:ASP460 3.9 11.7 1.0
O7 A:TPP701 4.0 12.3 1.0
N A:ASN491 4.1 13.4 1.0
O A:SER485 4.1 15.3 1.0
N A:ALA489 4.1 14.1 1.0
N A:GLY461 4.1 12.3 1.0
N A:TRP490 4.2 12.9 1.0
HA3 A:GLY459 4.2 11.9 1.0
CA A:ALA489 4.2 13.5 1.0
HD22 A:ASN487 4.3 11.7 1.0
HA2 A:GLY459 4.3 12.0 1.0
HB3 A:ALA489 4.3 13.9 1.0
CA A:TRP490 4.4 12.6 1.0
CB A:ASP460 4.4 12.2 1.0
O1A A:TPP701 4.4 12.7 1.0
O3B A:TPP701 4.4 11.7 1.0
CB A:ASN487 4.4 12.1 1.0
HD11 A:LEU509 4.5 17.4 1.0
N A:ASN487 4.5 12.5 1.0
CA A:ASP460 4.6 11.9 1.0
CA A:GLY459 4.6 11.8 1.0
CB A:ASN491 4.6 14.7 1.0
C A:GLY459 4.7 11.8 1.0
H A:ARG488 4.7 13.1 1.0
HA3 A:GLY461 4.7 12.1 1.0
HB3 A:ASN491 4.7 14.7 1.0
HB3 A:ASP460 4.8 12.4 1.0
C A:TRP490 4.8 13.3 1.0
CB A:ALA489 4.8 14.1 1.0
CA A:ASN487 4.8 12.5 1.0
C A:ASP460 4.9 12.3 1.0
C A:ASN487 4.9 13.0 1.0
N A:ARG488 4.9 13.2 1.0
HB3 A:ASN487 4.9 12.1 1.0
CA A:ASN491 5.0 13.8 1.0

Magnesium binding site 3 out of 4 in 7pt4

Go back to Magnesium Binding Sites List in 7pt4
Magnesium binding site 3 out of 4 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg709

b:12.8
occ:1.00
 OD1 B:ASP460 2.0 13.5 1.0
O1A B:OXT701 2.0 12.2 1.0
O1B B:OXT701 2.0 13.7 1.0
O B:ALA489 2.0 11.1 1.0
OD1 B:ASN487 2.1 13.8 1.0
O B:HOH886 2.2 10.3 1.0
HD21 B:ASN487 3.1 12.5 1.0
CG B:ASN487 3.1 13.4 1.0
CG B:ASP460 3.2 13.8 1.0
H B:ASP460 3.2 12.9 1.0
PB B:OXT701 3.2 14.0 1.0
PA B:OXT701 3.2 12.7 1.0
H B:GLY461 3.2 13.2 1.0
C B:ALA489 3.2 12.3 1.0
H B:ASN491 3.2 14.7 1.0
O3A B:OXT701 3.4 12.5 1.0
H B:ALA489 3.4 12.9 1.0
ND2 B:ASN487 3.5 12.1 1.0
HA B:TRP490 3.7 13.0 1.0
H B:ASN487 3.7 13.1 1.0
OD2 B:ASP460 3.8 15.8 1.0
O2B B:OXT701 3.9 14.6 1.0
HB2 B:ASN491 3.9 15.2 1.0
N B:ASP460 3.9 12.8 1.0
O76 B:OXT701 4.0 11.9 1.0
N B:ASN491 4.0 15.1 1.0
O B:SER485 4.1 13.3 1.0
N B:GLY461 4.1 13.3 1.0
N B:ALA489 4.1 12.8 1.0
N B:TRP490 4.1 12.7 1.0
HA3 B:GLY459 4.2 12.4 1.0
CA B:ALA489 4.2 12.8 1.0
HB3 B:ALA489 4.3 13.2 1.0
CA B:TRP490 4.3 13.0 1.0
HA2 B:GLY459 4.3 12.5 1.0
HD22 B:ASN487 4.3 12.5 1.0
CB B:ASP460 4.4 13.8 1.0
O2A B:OXT701 4.4 11.0 1.0
O3B B:OXT701 4.4 14.9 1.0
HD11 B:LEU509 4.5 15.6 1.0
CB B:ASN487 4.5 12.7 1.0
N B:ASN487 4.5 13.0 1.0
CA B:ASP460 4.6 13.4 1.0
CA B:GLY459 4.6 12.4 1.0
HA3 B:GLY461 4.7 13.3 1.0
CB B:ASN491 4.7 15.2 1.0
C B:GLY459 4.7 12.6 1.0
C B:TRP490 4.7 14.1 1.0
CB B:ALA489 4.8 13.4 1.0
HB3 B:ASP460 4.8 13.7 1.0
HB3 B:ASN491 4.8 15.2 1.0
CA B:ASN487 4.8 13.3 1.0
H B:ARG488 4.8 13.0 1.0
C B:ASP460 4.8 13.0 1.0
C B:ASN487 4.9 13.4 1.0
HB3 B:ASN487 5.0 13.0 1.0
N B:ARG488 5.0 13.1 1.0
CA B:ASN491 5.0 14.8 1.0

Magnesium binding site 4 out of 4 in 7pt4

Go back to Magnesium Binding Sites List in 7pt4
Magnesium binding site 4 out of 4 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with A Covalently Bound Reaction Intermediate As Well As Products Formyl-Coa and Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg710

b:33.8
occ:0.50
 O B:HOH879 2.1 13.9 1.0
O B:HOH866 2.3 17.7 1.0
O B:HOH1103 2.3 15.2 1.0
OD2 B:ASP64 3.8 18.4 1.0
HA B:ASN95 4.2 11.3 1.0
O B:HOH1224 4.3 24.0 1.0
OD1 B:ASP64 4.3 16.9 1.0
O B:HOH1101 4.3 14.9 1.0
O B:HOH1146 4.4 24.4 1.0
O B:ASN95 4.4 11.3 1.0
OD1 B:ASN95 4.5 11.7 1.0
CG B:ASP64 4.5 16.9 1.0
HB3 B:ASN95 4.7 11.7 1.0
CG B:ASN95 4.9 11.6 1.0
CA B:ASN95 4.9 11.4 1.0
O B:HOH1253 4.9 20.8 1.0

Reference:

M.Zahn, G.Konig, H.V.C.Pham, B.Seroka, R.Lazny, G.Yang, O.Ouerfelli, Z.Lotowski, T.Rohwerder. Mechanistic Details of the Actinobacterial Lyase-Catalyzed Degradation Reaction of 2-Hydroxyisobutyryl-Coa. J.Biol.Chem. V. 298 01522 2022.
ISSN: ESSN 1083-351X
PubMed: 34952003
DOI: 10.1016/J.JBC.2021.101522
Page generated: Thu Oct 3 04:45:53 2024

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