Atomistry » Magnesium » PDB 7psm-7q03 » 7pt4
Atomistry »
  Magnesium »
    PDB 7psm-7q03 »
      7pt4 »

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

Go back to Magnesium Binding Sites List in 7pt4
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

Last articles

Mn in 2G8I
Mn in 2GDF
Mn in 2GA2
Mn in 2G74
Mn in 2G73
Mn in 2FYD
Mn in 2G38
Mn in 2FEU
Mn in 2G4I
Mn in 2FFV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy