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Magnesium in PDB 7pt1: Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp

Enzymatic activity of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp

All present enzymatic activity of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp:
4.2.1.17;

Protein crystallography data

The structure of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp, PDB code: 7pt1 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) 87.37 / 1.55
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 103.95, 146.138, 174.749, 90, 90, 90
R / Rfree (%) 16 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp (pdb code 7pt1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp, PDB code: 7pt1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7pt1

Go back to Magnesium Binding Sites List in 7pt1
Magnesium binding site 1 out of 3 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp


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 Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:21.4
occ:1.00
 H21 A:TPW701 1.7 16.5 0.0
O21 A:TPW701 2.0 16.4 1.0
O A:ALA489 2.0 18.0 1.0
OD1 A:ASN487 2.1 18.6 1.0
OD1 A:ASP460 2.1 16.3 1.0
O13 A:TPW701 2.2 16.4 1.0
O A:HOH834 2.3 17.9 1.0
HD21 A:ASN487 2.9 19.1 1.0
CG A:ASN487 2.9 19.2 1.0
P2 A:TPW701 3.2 19.8 1.0
ND2 A:ASN487 3.2 19.1 1.0
H A:ASN491 3.2 20.4 1.0
CG A:ASP460 3.3 16.9 1.0
C A:ALA489 3.3 18.7 1.0
P1 A:TPW701 3.3 16.5 1.0
H A:ASP460 3.3 16.3 1.0
H A:GLY461 3.4 17.8 1.0
H A:ALA489 3.4 19.5 1.0
O11 A:TPW701 3.5 17.0 1.0
H A:ASN487 3.6 19.4 1.0
HB2 A:ASN491 3.7 21.0 1.0
HA A:TRP490 3.7 17.9 1.0
O22 A:TPW701 3.8 17.7 1.0
OD2 A:ASP460 3.8 18.8 1.0
N A:ASN491 4.0 20.6 1.0
HD22 A:ASN487 4.0 19.1 1.0
N A:ASP460 4.0 16.2 1.0
O5G A:TPW701 4.1 15.7 1.0
O A:SER485 4.1 20.2 1.0
N A:ALA489 4.1 19.5 1.0
N A:TRP490 4.2 17.6 1.0
CA A:ALA489 4.2 19.9 1.0
N A:GLY461 4.3 18.2 1.0
HA3 A:GLY459 4.3 15.9 1.0
HB3 A:ALA489 4.3 21.1 1.0
O23 A:TPW701 4.3 17.4 1.0
CB A:ASN487 4.3 19.5 1.0
CA A:TRP490 4.4 18.1 1.0
HA2 A:GLY459 4.4 16.0 1.0
N A:ASN487 4.4 19.7 1.0
CB A:ASP460 4.5 16.6 1.0
CB A:ASN491 4.5 21.3 1.0
O12 A:TPW701 4.5 16.1 1.0
HB3 A:ASN491 4.6 21.0 1.0
CA A:ASP460 4.7 16.1 1.0
CA A:GLY459 4.7 15.6 1.0
C A:TRP490 4.7 19.4 1.0
CA A:ASN487 4.7 18.8 1.0
HD11 A:LEU509 4.7 23.1 1.0
CB A:ALA489 4.8 21.5 1.0
C A:ASN487 4.8 19.4 1.0
HA3 A:GLY461 4.8 17.2 1.0
C A:GLY459 4.8 16.2 1.0
HB3 A:ASN487 4.9 19.3 1.0
H A:ARG488 4.9 18.8 1.0
CA A:ASN491 4.9 21.3 1.0
HB2 A:ASN487 4.9 19.4 1.0
N A:ARG488 4.9 18.3 1.0
HB3 A:ASP460 4.9 16.6 1.0

Magnesium binding site 2 out of 3 in 7pt1

Go back to Magnesium Binding Sites List in 7pt1
Magnesium binding site 2 out of 3 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp


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 Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:18.6
occ:1.00
 O A:HOH921 2.2 18.8 1.0
O B:HOH833 2.3 17.6 1.0
O A:HOH1048 2.3 14.2 1.0
O A:HOH980 2.3 17.6 1.0
O B:HOH925 2.3 13.1 1.0
O B:HOH923 2.4 21.1 1.0
OD2 B:ASP64 4.0 16.9 1.0
OD2 A:ASP64 4.1 16.2 1.0
HA B:ASN95 4.1 14.8 1.0
HA A:ASN95 4.1 14.1 1.0
O A:HOH1120 4.2 24.5 1.0
O B:HOH1147 4.2 29.2 1.0
O B:ASN95 4.3 14.7 1.0
OD1 A:ASN95 4.3 13.7 1.0
O A:HOH1132 4.3 21.7 1.0
OD1 B:ASN95 4.4 14.3 1.0
O A:ASN95 4.4 13.4 1.0
O B:HOH1191 4.4 29.2 1.0
OD1 A:ASP64 4.4 16.1 1.0
OD1 B:ASP64 4.5 15.7 1.0
O B:HOH954 4.5 18.4 1.0
O A:HOH930 4.5 18.5 1.0
CG A:ASP64 4.6 15.7 1.0
HB3 A:ASN95 4.6 14.4 1.0
CG B:ASP64 4.7 16.2 1.0
O B:HOH1272 4.7 25.1 1.0
HB3 B:ASN95 4.8 14.8 1.0
CG A:ASN95 4.8 14.6 1.0
O A:HOH1237 4.8 27.4 1.0
CG B:ASN95 4.9 14.5 1.0
CA A:ASN95 4.9 14.1 1.0
CA B:ASN95 4.9 14.6 1.0

Magnesium binding site 3 out of 3 in 7pt1

Go back to Magnesium Binding Sites List in 7pt1
Magnesium binding site 3 out of 3 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp


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 Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:13.9
occ:1.00
 O22 B:TPW701 2.0 13.3 1.0
O B:ALA489 2.0 15.0 1.0
OD1 B:ASP460 2.0 16.1 1.0
O13 B:TPW701 2.1 14.9 1.0
OD1 B:ASN487 2.1 15.7 1.0
O B:HOH972 2.1 15.3 1.0
HD21 B:ASN487 2.9 16.3 1.0
CG B:ASN487 3.0 16.3 1.0
CG B:ASP460 3.2 15.4 1.0
H B:ASP460 3.2 14.9 1.0
H B:ASN491 3.2 14.4 1.0
C B:ALA489 3.2 14.9 1.0
ND2 B:ASN487 3.3 16.4 1.0
P2 B:TPW701 3.3 14.9 1.0
P1 B:TPW701 3.3 15.9 1.0
H B:GLY461 3.3 15.0 1.0
H B:ALA489 3.4 15.1 1.0
H B:ASN487 3.6 16.7 1.0
O11 B:TPW701 3.6 14.9 1.0
H23 B:TPW701 3.7 13.6 0.0
OD2 B:ASP460 3.8 18.4 1.0
HA B:TRP490 3.8 14.0 1.0
HB2 B:ASN491 3.8 15.9 1.0
O23 B:TPW701 3.9 13.6 1.0
N B:ASP460 3.9 14.8 1.0
O5G B:TPW701 4.0 14.3 1.0
N B:ASN491 4.0 14.1 1.0
HD22 B:ASN487 4.1 16.4 1.0
N B:ALA489 4.1 14.7 1.0
O B:SER485 4.1 15.7 1.0
N B:TRP490 4.2 14.7 1.0
CA B:ALA489 4.2 15.1 1.0
N B:GLY461 4.2 15.1 1.0
HB3 B:ALA489 4.2 16.1 1.0
HA3 B:GLY459 4.3 14.7 1.0
HA2 B:GLY459 4.4 14.7 1.0
CB B:ASP460 4.4 15.7 1.0
CA B:TRP490 4.4 13.7 1.0
CB B:ASN487 4.4 16.5 1.0
N B:ASN487 4.4 16.7 1.0
HD11 B:LEU509 4.5 17.2 1.0
O12 B:TPW701 4.5 15.9 1.0
O21 B:TPW701 4.6 14.2 1.0
CA B:ASP460 4.6 15.4 1.0
CB B:ASN491 4.6 15.8 1.0
CA B:GLY459 4.7 14.6 1.0
CB B:ALA489 4.7 16.6 1.0
H21 B:TPW701 4.7 14.3 0.0
CA B:ASN487 4.7 16.7 1.0
C B:GLY459 4.7 14.6 1.0
HB3 B:ASN491 4.8 15.9 1.0
C B:TRP490 4.8 14.1 1.0
H B:ARG488 4.8 16.3 1.0
C B:ASN487 4.8 16.4 1.0
HA3 B:GLY461 4.8 14.5 1.0
HB3 B:ASP460 4.8 15.6 1.0
N B:ARG488 4.9 16.1 1.0
HB3 B:ASN487 4.9 16.5 1.0
C B:ASP460 4.9 14.9 1.0
CA B:ASN491 4.9 15.4 1.0
HB1 B:ALA489 4.9 16.1 1.0
HB2 B:ASN487 5.0 16.5 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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