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Magnesium in PDB 6o4e: Structure of ALDH7A1 Mutant N167S Complexed with Nad

Enzymatic activity of Structure of ALDH7A1 Mutant N167S Complexed with Nad

All present enzymatic activity of Structure of ALDH7A1 Mutant N167S Complexed with Nad:
1.2.1.3; 1.2.1.31; 1.2.1.8;

Protein crystallography data

The structure of Structure of ALDH7A1 Mutant N167S Complexed with Nad, PDB code: 6o4e was solved by J.J.Tanner, D.A.Korasick, A.R.Laciak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.09 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.920, 161.730, 158.410, 90.00, 94.65, 90.00
R / Rfree (%) 16.8 / 20.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of ALDH7A1 Mutant N167S Complexed with Nad (pdb code 6o4e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of ALDH7A1 Mutant N167S Complexed with Nad, PDB code: 6o4e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6o4e

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Magnesium binding site 1 out of 6 in the Structure of ALDH7A1 Mutant N167S Complexed with Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of ALDH7A1 Mutant N167S Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:43.9
occ:1.00
 O2N B:NAD601 2.2 36.6 1.0
O B:HOH848 2.2 36.7 1.0
O B:HOH856 2.2 36.0 1.0
O2A B:NAD601 2.3 28.1 1.0
O B:HOH823 2.3 44.1 1.0
O B:HOH931 2.5 48.9 1.0
PN B:NAD601 3.4 33.5 1.0
PA B:NAD601 3.4 28.3 1.0
O3 B:NAD601 3.5 29.6 1.0
O B:HOH934 4.0 43.5 1.0
O B:HOH830 4.1 44.6 1.0
O1N B:NAD601 4.3 31.1 1.0
O1A B:NAD601 4.4 24.8 1.0
O5B B:NAD601 4.5 25.0 1.0
O5D B:NAD601 4.5 33.6 1.0
O B:HOH844 4.6 30.6 1.0
O B:HOH947 4.6 38.1 1.0
C5D B:NAD601 4.6 37.9 1.0

Magnesium binding site 2 out of 6 in 6o4e

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Magnesium binding site 2 out of 6 in the Structure of ALDH7A1 Mutant N167S Complexed with Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of ALDH7A1 Mutant N167S Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:48.5
occ:1.00
 O1N C:NAD601 2.1 35.6 0.9
O C:HOH906 2.1 44.9 1.0
O2A C:NAD601 2.6 30.1 0.9
PN C:NAD601 3.3 34.0 0.9
O3 C:NAD601 3.5 33.7 0.9
PA C:NAD601 3.6 27.2 0.9
O2N C:NAD601 4.2 33.1 0.9
O C:HOH775 4.4 32.0 1.0
O5D C:NAD601 4.5 40.9 0.9
C5D C:NAD601 4.6 37.2 0.9
O5B C:NAD601 4.6 23.6 0.9
O C:HOH933 4.6 39.1 1.0
O1A C:NAD601 4.7 27.0 0.9
O C:HOH800 4.9 39.6 1.0
CE2 C:PHE166 4.9 29.1 1.0

Magnesium binding site 3 out of 6 in 6o4e

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Magnesium binding site 3 out of 6 in the Structure of ALDH7A1 Mutant N167S Complexed with Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of ALDH7A1 Mutant N167S Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:48.5
occ:1.00
 O1N D:NAD601 2.2 36.4 0.9
O2A D:NAD601 2.4 27.8 0.9
O D:HOH783 2.4 41.5 1.0
PN D:NAD601 3.3 37.0 0.9
O3 D:NAD601 3.3 33.0 0.9
PA D:NAD601 3.4 29.4 0.9
O2N D:NAD601 4.2 34.6 0.9
O1A D:NAD601 4.4 28.8 0.9
O5D D:NAD601 4.4 38.8 0.9
O5B D:NAD601 4.5 27.5 0.9
C5D D:NAD601 4.5 40.6 0.9
O D:HOH748 4.7 32.0 1.0

Magnesium binding site 4 out of 6 in 6o4e

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Magnesium binding site 4 out of 6 in the Structure of ALDH7A1 Mutant N167S Complexed with Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of ALDH7A1 Mutant N167S Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg603

b:39.2
occ:1.00
 O1N F:NAD601 1.9 29.9 0.9
O F:HOH877 2.1 40.2 1.0
O F:HOH754 2.1 35.3 1.0
O2A F:NAD601 2.2 29.8 0.9
O F:HOH889 2.2 36.2 1.0
PN F:NAD601 3.2 29.0 0.9
PA F:NAD601 3.3 27.5 0.9
O3 F:NAD601 3.3 27.5 0.9
O F:HOH927 3.8 36.1 1.0
O2N F:NAD601 4.0 27.8 0.9
O F:HOH748 4.2 34.5 1.0
O F:HOH941 4.3 44.0 1.0
O5D F:NAD601 4.3 29.3 0.9
O1A F:NAD601 4.3 23.9 0.9
O5B F:NAD601 4.4 27.2 0.9
C5D F:NAD601 4.4 34.0 0.9

Magnesium binding site 5 out of 6 in 6o4e

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Magnesium binding site 5 out of 6 in the Structure of ALDH7A1 Mutant N167S Complexed with Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of ALDH7A1 Mutant N167S Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:44.6
occ:1.00
 O G:HOH937 2.1 43.2 1.0
O1N G:NAD601 2.1 35.3 1.0
O G:HOH771 2.1 42.4 1.0
O G:HOH927 2.2 45.9 1.0
O2A G:NAD601 2.3 29.9 1.0
O G:HOH946 2.5 58.0 1.0
PN G:NAD601 3.4 34.0 1.0
PA G:NAD601 3.5 28.4 1.0
O3 G:NAD601 3.6 30.6 1.0
O G:HOH703 3.7 47.6 1.0
O G:HOH956 4.0 33.3 1.0
O2N G:NAD601 4.2 31.1 1.0
O G:HOH776 4.4 31.4 1.0
O5B G:NAD601 4.5 23.9 1.0
O5D G:NAD601 4.5 32.8 1.0
O1A G:NAD601 4.6 30.6 1.0
C5D G:NAD601 4.6 37.6 1.0
CE2 G:PHE166 5.0 28.6 1.0

Magnesium binding site 6 out of 6 in 6o4e

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Magnesium binding site 6 out of 6 in the Structure of ALDH7A1 Mutant N167S Complexed with Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of ALDH7A1 Mutant N167S Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:47.3
occ:1.00
 O1N H:NAD601 2.0 34.3 0.9
O H:HOH935 2.1 38.6 1.0
O2A H:NAD601 2.3 29.8 0.9
PN H:NAD601 3.2 30.9 0.9
O3 H:NAD601 3.3 30.0 0.9
PA H:NAD601 3.3 26.1 0.9
O2N H:NAD601 4.1 33.8 0.9
O5D H:NAD601 4.3 31.4 0.9
C5D H:NAD601 4.4 37.9 0.9
O1A H:NAD601 4.4 24.5 0.9
O5B H:NAD601 4.4 26.3 0.9
O H:HOH761 4.5 37.6 1.0
O H:HOH899 4.7 34.7 1.0

Reference:

A.R.Laciak, D.A.Korasick, J.W.Wyatt, K.S.Gates, J.J.Tanner. Structural and Biochemical Consequences of Pyridoxine-Dependent Epilepsy Mutations That Target the Aldehyde Binding Site of Aldehyde Dehydrogenase ALDH7A1. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31302938
DOI: 10.1111/FEBS.14997
Page generated: Tue Oct 1 13:16:06 2024

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