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Magnesium in PDB 1nzz: Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+

All present enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+:
1.2.1.3;

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+, PDB code: 1nzz was solved by S.J.Perez-Miller, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.307, 150.897, 177.031, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.8

Other elements in 1nzz:

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+ also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+ (pdb code 1nzz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+, PDB code: 1nzz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1nzz

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Magnesium binding site 1 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:54.5
occ:1.00
 O1N A:NAI1502 2.3 54.9 1.0
O A:HOH1787 2.4 59.1 1.0
O2A A:NAI1502 2.6 55.1 1.0
PN A:NAI1502 3.7 54.7 1.0
PA A:NAI1502 3.9 54.1 1.0
O3 A:NAI1502 4.2 55.4 1.0
O5B A:NAI1502 4.4 53.2 1.0
O2N A:NAI1502 4.4 55.8 1.0
O A:HOH1761 4.5 44.7 1.0
CG1 A:ILE249 4.6 47.5 1.0
C8A A:NAI1502 4.7 49.0 1.0
C5D A:NAI1502 4.7 54.1 1.0
O5D A:NAI1502 4.7 54.5 1.0
CD1 A:ILE249 4.9 46.5 1.0
OE1 A:GLU248 5.0 62.8 1.0
N7A A:NAI1502 5.0 49.1 1.0

Magnesium binding site 2 out of 8 in 1nzz

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Magnesium binding site 2 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1602

b:44.3
occ:1.00
 O2A B:NAI2502 2.1 51.4 1.0
O1N B:NAI2502 2.2 54.3 1.0
O B:HOH2632 2.8 48.8 1.0
PA B:NAI2502 3.3 50.9 1.0
PN B:NAI2502 3.5 55.2 1.0
O3 B:NAI2502 3.7 52.6 1.0
O5B B:NAI2502 4.0 50.6 1.0
C8A B:NAI2502 4.2 47.9 1.0
O2N B:NAI2502 4.2 54.6 1.0
CG1 B:ILE249 4.3 47.8 1.0
O1A B:NAI2502 4.5 50.9 1.0
N7A B:NAI2502 4.5 47.8 1.0
CD1 B:ILE249 4.6 45.2 1.0
O5D B:NAI2502 4.7 53.4 1.0
C5D B:NAI2502 4.8 53.9 1.0
OG B:SER246 4.9 41.0 1.0

Magnesium binding site 3 out of 8 in 1nzz

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Magnesium binding site 3 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1603

b:64.8
occ:1.00
 O1N C:NAI3502 2.2 40.7 1.0
O2A C:NAI3502 2.2 37.1 1.0
O C:HOH3633 2.4 49.0 1.0
PA C:NAI3502 3.5 37.8 1.0
PN C:NAI3502 3.6 40.2 1.0
O3 C:NAI3502 4.0 37.5 1.0
O5B C:NAI3502 4.3 36.7 1.0
O2N C:NAI3502 4.4 41.2 1.0
C8A C:NAI3502 4.4 27.7 1.0
O1A C:NAI3502 4.6 37.2 1.0
CG1 C:ILE249 4.6 40.5 1.0
O5D C:NAI3502 4.6 40.7 1.0
CD1 C:ILE249 4.7 42.4 1.0
C5D C:NAI3502 4.8 41.6 1.0
N7A C:NAI3502 4.8 28.3 1.0

Magnesium binding site 4 out of 8 in 1nzz

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Magnesium binding site 4 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:58.2
occ:1.00
 O1N D:NAI4502 2.1 53.2 1.0
O D:HOH4519 2.1 39.8 1.0
O2A D:NAI4502 2.2 47.9 1.0
O D:HOH4607 2.3 54.1 1.0
PN D:NAI4502 3.3 55.4 1.0
PA D:NAI4502 3.4 49.1 1.0
O3 D:NAI4502 3.7 52.1 1.0
O5B D:NAI4502 4.1 48.7 1.0
O2N D:NAI4502 4.3 55.4 1.0
O5D D:NAI4502 4.4 56.4 1.0
C8A D:NAI4502 4.5 43.2 1.0
CG1 D:ILE249 4.5 46.8 1.0
O1A D:NAI4502 4.5 48.7 1.0
C5D D:NAI4502 4.5 56.8 1.0
OG D:SER246 4.8 45.7 1.0
N7A D:NAI4502 4.9 42.1 1.0
CD1 D:ILE249 4.9 45.8 1.0

Magnesium binding site 5 out of 8 in 1nzz

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Magnesium binding site 5 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1605

b:58.6
occ:1.00
 O1N E:NAI5502 2.1 47.2 1.0
O2A E:NAI5502 2.1 44.6 1.0
O E:HOH5597 2.3 55.5 1.0
PA E:NAI5502 3.3 45.0 1.0
PN E:NAI5502 3.4 48.5 1.0
O3 E:NAI5502 3.7 46.5 1.0
O5B E:NAI5502 4.0 43.8 1.0
O2N E:NAI5502 4.3 48.2 1.0
O5D E:NAI5502 4.4 48.2 1.0
C8A E:NAI5502 4.4 37.0 1.0
O1A E:NAI5502 4.5 44.3 1.0
C5D E:NAI5502 4.5 47.8 1.0
CG1 E:ILE249 4.6 39.1 1.0
N7A E:NAI5502 4.8 34.9 1.0
CD1 E:ILE249 4.9 37.0 1.0

Magnesium binding site 6 out of 8 in 1nzz

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Magnesium binding site 6 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1606

b:52.8
occ:1.00
 O1N F:NAI6502 2.3 37.2 1.0
O F:HOH6524 2.3 40.6 1.0
O2A F:NAI6502 2.4 34.0 1.0
PN F:NAI6502 3.6 37.6 1.0
PA F:NAI6502 3.7 34.5 1.0
O3 F:NAI6502 4.0 35.7 1.0
C5D F:NAI6502 4.3 40.2 1.0
O5D F:NAI6502 4.4 37.9 1.0
O1A F:NAI6502 4.6 34.6 1.0
CG1 F:ILE249 4.6 38.0 1.0
O2N F:NAI6502 4.6 36.0 1.0
O5B F:NAI6502 4.7 34.5 1.0
CD1 F:ILE249 4.8 38.3 1.0
OG F:SER246 4.9 35.9 1.0
C8A F:NAI6502 4.9 29.1 1.0

Magnesium binding site 7 out of 8 in 1nzz

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Magnesium binding site 7 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1607

b:57.9
occ:1.00
 O2A G:NAI7502 2.1 53.7 1.0
O1N G:NAI7502 2.3 53.6 1.0
O G:HOH7524 2.8 48.5 1.0
PA G:NAI7502 3.4 51.8 1.0
PN G:NAI7502 3.5 54.2 1.0
O3 G:NAI7502 3.8 52.4 1.0
O5B G:NAI7502 4.1 51.0 1.0
O2N G:NAI7502 4.3 52.9 1.0
C8A G:NAI7502 4.3 47.9 1.0
CG1 G:ILE249 4.4 38.5 1.0
O1A G:NAI7502 4.5 52.8 1.0
N7A G:NAI7502 4.5 47.8 1.0
CD1 G:ILE249 4.6 36.9 1.0
O5D G:NAI7502 4.8 53.7 1.0
C5D G:NAI7502 4.9 54.5 1.0

Magnesium binding site 8 out of 8 in 1nzz

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Magnesium binding site 8 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1608

b:62.9
occ:1.00
 O1N H:NAI8502 2.4 63.0 1.0
O2A H:NAI8502 2.4 60.6 1.0
O H:HOH8610 2.5 49.3 1.0
O H:HOH8590 2.9 47.6 1.0
PA H:NAI8502 3.7 59.4 1.0
PN H:NAI8502 3.7 63.2 1.0
O H:HOH8592 3.7 61.7 1.0
O3 H:NAI8502 4.1 61.0 1.0
O5B H:NAI8502 4.2 57.6 1.0
C8A H:NAI8502 4.4 55.0 1.0
O2N H:NAI8502 4.4 61.8 1.0
CG1 H:ILE249 4.4 50.5 1.0
N7A H:NAI8502 4.6 54.4 1.0
CD1 H:ILE249 4.6 51.0 1.0
OG H:SER246 4.8 50.9 1.0
O1A H:NAI8502 4.8 59.4 1.0
O5D H:NAI8502 4.9 61.4 1.0
C5D H:NAI8502 4.9 61.2 1.0

Reference:

S.J.Perez-Miller, T.D.Hurley. Coenzyme Isomerization Is Integral to Catalysis in Aldehyde Dehydrogenase Biochemistry V. 42 7100 2003.
ISSN: ISSN 0006-2960
PubMed: 12795606
DOI: 10.1021/BI034182W
Page generated: Tue Aug 13 10:29:59 2024

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