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Magnesium in PDB 7pt3: Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493A Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp

Enzymatic activity of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493A 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) Mutant E493A 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) Mutant E493A Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp, PDB code: 7pt3 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) 87.21 / 1.63
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 103.915, 146.718, 174.413, 90, 90, 90
R / Rfree (%) 15.4 / 18.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493A Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp (pdb code 7pt3). 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) Mutant E493A Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp, PDB code: 7pt3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7pt3

Go back to Magnesium Binding Sites List in 7pt3
Magnesium binding site 1 out of 3 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493A 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) Mutant E493A 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:20.0
occ:1.00
 H21 A:TPW701 1.8 17.2 0.0
OD1 A:ASP460 2.0 18.8 1.0
O21 A:TPW701 2.0 17.3 1.0
O A:HOH894 2.1 18.6 1.0
O A:ALA489 2.1 18.8 1.0
O13 A:TPW701 2.1 19.3 1.0
OD1 A:ASN487 2.2 20.6 1.0
HD21 A:ASN487 2.9 20.1 1.0
CG A:ASN487 3.1 20.3 1.0
P2 A:TPW701 3.2 20.0 1.0
P1 A:TPW701 3.2 19.1 1.0
H A:ASP460 3.2 17.1 1.0
CG A:ASP460 3.2 18.1 1.0
H A:GLY461 3.3 18.1 1.0
C A:ALA489 3.3 19.7 1.0
H A:ASN491 3.3 21.6 1.0
ND2 A:ASN487 3.4 20.1 1.0
O11 A:TPW701 3.4 18.6 1.0
H A:ALA489 3.4 20.2 1.0
H A:ASN487 3.6 19.7 1.0
O22 A:TPW701 3.8 20.2 1.0
HA A:TRP490 3.8 19.6 1.0
OD2 A:ASP460 3.8 18.6 1.0
HB2 A:ASN491 3.8 22.1 1.0
N A:ASP460 3.9 16.9 1.0
O5G A:TPW701 4.0 19.4 1.0
O A:SER485 4.1 22.9 1.0
N A:ASN491 4.1 21.7 1.0
HA2 A:GLY459 4.1 17.0 1.0
N A:GLY461 4.2 18.2 1.0
N A:ALA489 4.2 20.3 1.0
HA3 A:GLY459 4.2 16.9 1.0
HD22 A:ASN487 4.2 20.2 1.0
CA A:ALA489 4.3 20.7 1.0
N A:TRP490 4.3 19.0 1.0
HB3 A:ALA489 4.3 21.5 1.0
CB A:ASP460 4.4 17.2 1.0
O23 A:TPW701 4.4 20.1 1.0
CA A:TRP490 4.4 19.6 1.0
N A:ASN487 4.4 19.6 1.0
O12 A:TPW701 4.4 17.4 1.0
CB A:ASN487 4.4 20.4 1.0
CA A:GLY459 4.5 16.6 1.0
CA A:ASP460 4.6 17.1 1.0
CB A:ASN491 4.6 22.0 1.0
HD11 A:LEU509 4.7 22.1 1.0
C A:GLY459 4.7 16.8 1.0
HA3 A:GLY461 4.7 17.9 1.0
HB3 A:ASN491 4.7 22.2 1.0
CA A:ASN487 4.8 19.9 1.0
C A:TRP490 4.8 20.8 1.0
CB A:ALA489 4.8 21.8 1.0
HB3 A:ASP460 4.8 17.4 1.0
C A:ASN487 4.8 20.1 1.0
C A:ASP460 4.9 17.7 1.0
H A:ARG488 4.9 20.0 1.0
HB3 A:ASN487 4.9 20.3 1.0
CA A:ASN491 5.0 22.6 1.0
N A:ARG488 5.0 19.8 1.0

Magnesium binding site 2 out of 3 in 7pt3

Go back to Magnesium Binding Sites List in 7pt3
Magnesium binding site 2 out of 3 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493A 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) Mutant E493A 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:21.5
occ:1.00
 O B:HOH941 2.2 19.4 1.0
O B:HOH1070 2.3 16.8 1.0
O A:HOH1094 2.3 18.6 1.0
O B:HOH883 2.3 20.1 1.0
O A:HOH880 2.3 20.6 1.0
O A:HOH845 2.4 21.1 1.0
OD2 B:ASP64 4.0 18.3 1.0
OD2 A:ASP64 4.0 18.8 1.0
HA B:ASN95 4.1 15.0 1.0
HA A:ASN95 4.1 14.3 1.0
O B:HOH1083 4.3 31.9 1.0
O A:HOH1135 4.3 24.7 1.0
O B:ASN95 4.3 14.2 1.0
OD1 B:ASN95 4.4 15.4 1.0
O A:HOH1126 4.4 21.5 1.0
O B:HOH1175 4.4 27.8 1.0
OD1 B:ASP64 4.4 19.6 1.0
OD1 A:ASN95 4.4 15.7 1.0
O A:ASN95 4.4 15.6 1.0
O A:HOH987 4.4 17.6 1.0
OD1 A:ASP64 4.5 20.1 1.0
O B:HOH1110 4.5 19.4 1.0
CG B:ASP64 4.6 18.5 1.0
CG A:ASP64 4.6 18.1 1.0
HB3 B:ASN95 4.7 15.2 1.0
O A:HOH1233 4.7 29.5 1.0
O B:HOH1231 4.7 32.8 1.0
HB3 A:ASN95 4.7 14.8 1.0
CG B:ASN95 4.8 15.2 1.0
CA B:ASN95 4.9 14.9 1.0
CG A:ASN95 4.9 15.7 1.0
CA A:ASN95 4.9 14.2 1.0

Magnesium binding site 3 out of 3 in 7pt3

Go back to Magnesium Binding Sites List in 7pt3
Magnesium binding site 3 out of 3 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493A 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) Mutant E493A 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:14.9
occ:1.00
 O B:ALA489 1.9 13.8 1.0
O22 B:TPW701 2.0 16.0 1.0
OD1 B:ASP460 2.0 16.2 1.0
O13 B:TPW701 2.1 15.1 1.0
OD1 B:ASN487 2.1 18.5 1.0
O B:HOH936 2.2 14.6 1.0
HD21 B:ASN487 3.0 17.9 1.0
CG B:ASN487 3.0 18.0 1.0
C B:ALA489 3.2 15.4 1.0
CG B:ASP460 3.2 16.6 1.0
P2 B:TPW701 3.2 16.4 1.0
P1 B:TPW701 3.3 15.7 1.0
H B:ASN491 3.3 17.1 1.0
H B:ASP460 3.3 15.9 1.0
H B:GLY461 3.3 16.7 1.0
ND2 B:ASN487 3.4 17.9 1.0
H B:ALA489 3.4 16.7 1.0
O11 B:TPW701 3.5 15.4 1.0
H B:ASN487 3.6 16.5 1.0
HB2 B:ASN491 3.7 18.5 1.0
HA B:TRP490 3.8 15.6 1.0
H23 B:TPW701 3.8 15.8 0.0
OD2 B:ASP460 3.8 18.4 1.0
O5G B:TPW701 3.9 15.1 1.0
O23 B:TPW701 4.0 15.8 1.0
N B:ASP460 4.0 15.6 1.0
N B:ASN491 4.0 17.1 1.0
N B:ALA489 4.1 16.9 1.0
CA B:ALA489 4.1 16.3 1.0
O B:SER485 4.1 17.4 1.0
N B:TRP490 4.2 15.0 1.0
HB3 B:ALA489 4.2 16.9 1.0
N B:GLY461 4.2 16.8 1.0
HD22 B:ASN487 4.2 17.9 1.0
HA2 B:GLY459 4.3 16.2 1.0
HA3 B:GLY459 4.3 16.1 1.0
CA B:TRP490 4.4 15.4 1.0
CB B:ASP460 4.4 16.1 1.0
CB B:ASN487 4.4 17.1 1.0
N B:ASN487 4.4 16.5 1.0
O12 B:TPW701 4.5 14.8 1.0
O21 B:TPW701 4.5 16.3 1.0
HD11 B:LEU509 4.5 19.8 1.0
CB B:ASN491 4.6 18.4 1.0
H21 B:TPW701 4.6 16.3 0.0
CA B:ASP460 4.6 16.4 1.0
CB B:ALA489 4.7 17.1 1.0
CA B:GLY459 4.7 15.9 1.0
HA3 B:GLY461 4.7 16.3 1.0
HB3 B:ASN491 4.7 18.5 1.0
C B:TRP490 4.7 16.8 1.0
CA B:ASN487 4.7 16.7 1.0
C B:ASN487 4.8 16.6 1.0
C B:GLY459 4.8 16.1 1.0
H B:ARG488 4.8 16.8 1.0
HB3 B:ASP460 4.9 16.4 1.0
CA B:ASN491 4.9 17.5 1.0
N B:ARG488 4.9 16.4 1.0
C B:ASP460 4.9 16.9 1.0
HB1 B:ALA489 4.9 16.8 1.0
HB3 B:ASN487 4.9 17.3 1.0
HA B:ALA489 5.0 16.4 1.0
HB2 B:ASN487 5.0 17.2 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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