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Magnesium in PDB 7pt2: Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493Q Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp

Enzymatic activity of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493Q 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 E493Q 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 E493Q Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp, PDB code: 7pt2 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) 87.10 / 1.76
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 103.674, 145.481, 174.198, 90, 90, 90
R / Rfree (%) 14.7 / 18.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493Q Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp (pdb code 7pt2). 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) Mutant E493Q Structure in Complex with Substrate 2-Hib-Coa and Inactive Cofactor 3-Deaza-Thdp, PDB code: 7pt2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7pt2

Go back to Magnesium Binding Sites List in 7pt2
Magnesium binding site 1 out of 4 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493Q 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 E493Q 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:27.6
occ:1.00
 H21 A:TPW701 1.8 0.5 0.0
HD22 A:ASN487 1.9 26.4 1.0
O21 A:TPW701 2.0 22.7 1.0
OD1 A:ASP460 2.0 24.8 1.0
O A:ALA489 2.0 23.6 1.0
O13 A:TPW701 2.1 23.5 1.0
ND2 A:ASN487 2.2 26.6 1.0
O A:HOH876 2.2 23.2 1.0
HD21 A:ASN487 2.3 26.8 1.0
H A:ASP460 3.1 22.8 1.0
P2 A:TPW701 3.2 24.6 1.0
CG A:ASN487 3.2 27.5 1.0
P1 A:TPW701 3.2 25.2 1.0
CG A:ASP460 3.2 24.0 1.0
H A:GLY461 3.2 24.7 1.0
C A:ALA489 3.3 25.4 1.0
H A:ASN491 3.3 25.7 1.0
O11 A:TPW701 3.4 22.9 1.0
OD1 A:ASN487 3.4 28.5 1.0
H A:ALA489 3.5 26.3 1.0
HA A:TRP490 3.7 24.4 1.0
H A:ASN487 3.7 26.2 1.0
OD2 A:ASP460 3.8 25.8 1.0
HB2 A:ASN491 3.8 26.4 1.0
O22 A:TPW701 3.8 24.5 1.0
N A:ASP460 3.9 21.9 1.0
O5G A:TPW701 4.0 24.9 1.0
N A:ASN491 4.0 26.1 1.0
N A:GLY461 4.1 25.0 1.0
O A:SER485 4.1 25.7 1.0
N A:TRP490 4.2 24.2 1.0
N A:ALA489 4.2 27.1 1.0
HA3 A:GLY459 4.2 22.8 1.0
HA2 A:GLY459 4.2 23.2 1.0
CA A:ALA489 4.3 26.2 1.0
CA A:TRP490 4.3 25.0 1.0
O23 A:TPW701 4.4 24.8 1.0
CB A:ASP460 4.4 23.5 1.0
O12 A:TPW701 4.4 22.0 1.0
HB3 A:ALA489 4.4 27.5 1.0
HD11 A:LEU509 4.5 28.2 1.0
N A:ASN487 4.5 26.5 1.0
CB A:ASN487 4.5 28.9 1.0
CA A:ASP460 4.5 23.4 1.0
CA A:GLY459 4.6 22.8 1.0
CB A:ASN491 4.6 27.0 1.0
C A:GLY459 4.7 22.4 1.0
HA3 A:GLY461 4.7 23.4 1.0
HB3 A:ASN491 4.7 26.5 1.0
C A:TRP490 4.7 25.5 1.0
HB3 A:ASP460 4.8 23.8 1.0
CA A:ASN487 4.8 27.6 1.0
CB A:ALA489 4.8 27.7 1.0
C A:ASN487 4.9 27.6 1.0
C A:ASP460 4.9 24.6 1.0
CA A:ASN491 4.9 26.5 1.0
H A:ARG488 4.9 26.4 1.0

Magnesium binding site 2 out of 4 in 7pt2

Go back to Magnesium Binding Sites List in 7pt2
Magnesium binding site 2 out of 4 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493Q 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 E493Q 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:25.5
occ:1.00
 O A:HOH896 2.2 18.9 1.0
O B:HOH909 2.3 20.4 1.0
O B:HOH995 2.3 23.5 1.0
O A:HOH1098 2.3 21.4 1.0
O A:HOH850 2.3 22.4 1.0
O B:HOH1012 2.4 20.1 1.0
OD2 A:ASP64 4.0 20.3 1.0
OD2 B:ASP64 4.0 21.2 1.0
HA A:ASN95 4.1 20.3 1.0
HA B:ASN95 4.2 19.7 1.0
O B:HOH1081 4.2 31.1 1.0
O A:HOH1143 4.2 28.0 1.0
O A:HOH1153 4.3 26.9 1.0
O A:ASN95 4.3 20.5 1.0
OD1 A:ASP64 4.3 22.6 1.0
O B:HOH1153 4.4 29.5 1.0
OD1 B:ASP64 4.4 22.6 1.0
O B:ASN95 4.4 18.6 1.0
OD1 A:ASN95 4.5 18.2 1.0
OD1 B:ASN95 4.5 18.1 1.0
O B:HOH1053 4.5 20.1 1.0
CG A:ASP64 4.5 21.7 1.0
O A:HOH959 4.6 21.8 1.0
CG B:ASP64 4.6 23.0 1.0
O B:HOH1256 4.7 33.5 1.0
HB3 A:ASN95 4.7 20.6 1.0
HB3 B:ASN95 4.8 20.0 1.0
CG A:ASN95 4.8 20.7 1.0
O A:HOH1229 4.8 26.4 1.0
CG B:ASN95 4.9 20.4 1.0
CA A:ASN95 4.9 20.1 1.0
O B:HOH829 4.9 28.1 1.0
CA B:ASN95 5.0 20.0 1.0

Magnesium binding site 3 out of 4 in 7pt2

Go back to Magnesium Binding Sites List in 7pt2
Magnesium binding site 3 out of 4 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493Q 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 E493Q 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:Mg705

b:39.4
occ:1.00
 O A:HOH1215 2.0 33.6 1.0
O A:HOH1114 2.1 33.9 1.0
O A:HOH828 2.4 25.2 1.0
OE2 A:GLU137 2.5 28.0 0.5
O A:GLU137 2.5 21.6 1.0
O A:THR140 2.6 18.2 1.0
HG2 A:GLU137 3.1 25.9 0.5
OE2 A:GLU137 3.2 30.5 0.5
CD A:GLU137 3.4 26.1 0.5
C A:GLU137 3.6 21.6 1.0
HG3 A:GLU137 3.6 24.8 0.5
H A:THR140 3.7 18.1 1.0
C A:THR140 3.7 18.1 1.0
CD A:GLU137 3.7 28.4 0.5
HA A:GLU137 3.8 21.5 0.5
HA A:GLU137 3.8 21.2 0.5
CG A:GLU137 3.8 26.0 0.5
O A:HOH1146 4.0 42.7 1.0
CG A:GLU137 4.0 25.0 0.5
HA A:ARG141 4.0 18.5 1.0
O A:HOH1083 4.1 21.9 1.0
CA A:GLU137 4.2 21.8 0.5
CA A:GLU137 4.2 21.5 0.5
OE1 A:GLU137 4.2 27.2 0.5
OG1 A:THR140 4.2 17.7 1.0
HA A:PRO138 4.3 22.2 1.0
N A:THR140 4.4 17.6 1.0
C A:ARG141 4.4 18.3 1.0
N A:ARG141 4.5 16.9 1.0
CA A:ARG141 4.5 18.8 1.0
O A:ARG141 4.6 17.7 1.0
HG3 A:GLU137 4.6 26.1 0.5
CA A:THR140 4.6 17.7 1.0
OE1 A:GLU137 4.6 29.6 0.5
N A:PRO138 4.6 22.2 1.0
CB A:GLU137 4.6 23.7 0.5
N A:LEU142 4.7 19.3 1.0
HA A:LEU142 4.7 20.6 1.0
CB A:GLU137 4.7 22.9 0.5
CA A:PRO138 4.8 21.8 1.0
C A:PRO138 4.8 21.8 1.0
HG1 A:THR140 4.8 0.5 0.0
HG2 A:GLU137 4.8 24.9 0.5
H A:LEU142 4.8 19.0 1.0
O A:HOH811 4.9 23.6 1.0

Magnesium binding site 4 out of 4 in 7pt2

Go back to Magnesium Binding Sites List in 7pt2
Magnesium binding site 4 out of 4 in the Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493Q 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 4 of Actinobacterial 2-Hydroxyacyl-Coa Lyase (Achacl) Mutant E493Q 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:23.4
occ:1.00
 HD21 B:ASN487 1.5 21.6 1.0
OD1 B:ASP460 2.0 22.9 1.0
O B:ALA489 2.0 21.0 1.0
O13 B:TPW701 2.0 21.4 1.0
O22 B:TPW701 2.1 22.1 1.0
O B:HOH904 2.2 18.3 1.0
ND2 B:ASN487 2.2 21.5 1.0
HD22 B:ASN487 2.6 21.9 1.0
CG B:ASP460 3.2 23.2 1.0
P1 B:TPW701 3.2 22.2 1.0
H B:GLY461 3.2 21.7 1.0
H B:ASP460 3.2 21.8 1.0
P2 B:TPW701 3.2 22.9 1.0
CG B:ASN487 3.2 22.5 1.0
C B:ALA489 3.2 20.9 1.0
H B:ASN491 3.3 22.0 1.0
H B:ALA489 3.4 22.2 1.0
OD1 B:ASN487 3.5 24.1 1.0
O11 B:TPW701 3.5 20.4 1.0
HA B:TRP490 3.7 20.2 1.0
H B:ASN487 3.7 21.9 1.0
H23 B:TPW701 3.8 0.5 0.0
OD2 B:ASP460 3.8 25.6 1.0
HB2 B:ASN491 3.8 23.6 1.0
N B:ASP460 3.9 21.6 1.0
O23 B:TPW701 3.9 21.6 1.0
O5G B:TPW701 4.0 20.3 1.0
N B:ASN491 4.0 22.1 1.0
N B:GLY461 4.1 21.6 1.0
O B:SER485 4.1 25.5 1.0
N B:TRP490 4.2 20.5 1.0
N B:ALA489 4.2 22.6 1.0
HA3 B:GLY459 4.2 21.4 1.0
HA2 B:GLY459 4.2 21.8 1.0
CA B:ALA489 4.2 21.9 1.0
O12 B:TPW701 4.3 20.1 1.0
CA B:TRP490 4.3 20.1 1.0
CB B:ASP460 4.3 22.4 1.0
HD11 B:LEU509 4.3 23.7 1.0
HB3 B:ALA489 4.4 22.9 1.0
O21 B:TPW701 4.5 20.8 1.0
CA B:ASP460 4.5 21.6 1.0
N B:ASN487 4.6 22.0 1.0
CA B:GLY459 4.6 21.5 1.0
CB B:ASN487 4.6 22.8 1.0
HA3 B:GLY461 4.6 21.1 1.0
H21 B:TPW701 4.6 0.5 0.0
CB B:ASN491 4.6 23.8 1.0
C B:GLY459 4.7 21.5 1.0
C B:TRP490 4.7 21.6 1.0
HB3 B:ASN491 4.8 23.6 1.0
HB3 B:ASP460 4.8 22.7 1.0
C B:ASP460 4.8 21.5 1.0
CB B:ALA489 4.8 23.1 1.0
CA B:ASN487 4.9 22.8 1.0
C B:ASN487 4.9 22.3 1.0
H B:ARG488 4.9 22.6 1.0
CA B:GLY461 5.0 21.6 1.0
CA B:ASN491 5.0 22.7 1.0
H12 B:TPW701 5.0 0.5 0.0
N B:ARG488 5.0 22.7 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 Apr 6 19:17:31 2023

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