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Magnesium in PDB 1cw3: Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+

All present enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+:
1.2.1.3;

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+, PDB code: 1cw3 was solved by L.Ni, J.Zhou, T.D.Hurley, H.Weiner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 2.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.400, 176.300, 102.000, 90.00, 94.70, 90.00
R / Rfree (%) 17.5 / 24.2

Other elements in 1cw3:

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+ also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+ (pdb code 1cw3). 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 Nad+ and MN2+, PDB code: 1cw3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1cw3

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Magnesium binding site 1 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+


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 Nad+ and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1501

b:27.5
occ:1.00
 O A:GLN196 2.2 33.9 1.0
O A:VAL40 2.7 37.1 1.0
O A:ASP109 2.8 29.3 1.0
O A:HOH1508 2.8 27.8 1.0
OD1 A:ASP109 2.8 30.2 1.0
C A:GLN196 3.4 30.6 1.0
OG1 A:THR39 3.4 26.0 1.0
C A:VAL40 3.8 31.3 1.0
C A:ASP109 3.9 29.0 1.0
N A:VAL40 3.9 30.5 1.0
CG A:ASP109 3.9 30.7 1.0
CA A:GLN196 4.1 25.7 1.0
CA A:VAL40 4.3 31.7 1.0
CG2 A:THR197 4.4 32.6 1.0
CD A:PRO42 4.4 33.0 1.0
CA A:ASP109 4.4 29.2 1.0
O A:VAL345 4.4 39.0 1.0
CB A:GLN196 4.4 19.4 1.0
N A:THR197 4.4 30.1 1.0
C A:THR39 4.7 29.5 1.0
CA A:THR197 4.7 27.0 1.0
OD2 A:ASP109 4.7 27.5 1.0
CB A:THR39 4.7 24.3 1.0
CG2 A:VAL345 4.7 23.9 1.0
CB A:ASP109 4.7 26.8 1.0
CA A:THR39 4.9 29.3 1.0
N A:ASN41 4.9 26.5 1.0
CB A:VAL40 4.9 32.8 1.0

Magnesium binding site 2 out of 8 in 1cw3

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Magnesium binding site 2 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+


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 Nad+ and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2501

b:23.7
occ:1.00
 O B:GLN196 2.3 35.5 1.0
OD1 B:ASP109 2.4 40.9 1.0
O B:VAL40 2.6 44.9 1.0
O B:HOH2508 2.6 23.4 1.0
OG1 B:THR39 2.7 22.2 1.0
O B:ASP109 2.9 20.7 1.0
CG B:ASP109 3.3 38.3 1.0
C B:GLN196 3.5 34.9 1.0
N B:VAL40 3.6 39.1 1.0
C B:VAL40 3.6 41.7 1.0
C B:ASP109 3.8 19.9 1.0
OD2 B:ASP109 4.0 41.8 1.0
CA B:ASP109 4.0 25.6 1.0
CB B:THR39 4.0 32.9 1.0
C B:THR39 4.1 36.2 1.0
CA B:VAL40 4.1 39.3 1.0
CB B:ASP109 4.2 31.3 1.0
CA B:THR39 4.3 35.9 1.0
N B:THR197 4.4 36.6 1.0
CA B:GLN196 4.4 31.8 1.0
CG2 B:THR197 4.4 28.6 1.0
CA B:THR197 4.5 33.1 1.0
CD1 B:ILE48 4.6 34.7 1.0
N B:ASN41 4.7 39.1 1.0
CD B:PRO42 4.8 31.4 1.0
O B:THR39 4.9 36.7 1.0
O B:HOH2552 4.9 33.4 1.0
CG2 B:THR39 4.9 18.4 1.0
N B:ASN110 5.0 21.3 1.0

Magnesium binding site 3 out of 8 in 1cw3

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Magnesium binding site 3 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+


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 Nad+ and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3501

b:38.0
occ:1.00
 O C:VAL40 2.3 37.1 1.0
O C:HOH3511 2.4 26.9 1.0
O C:GLN196 2.5 32.1 1.0
OD1 C:ASP109 2.6 31.0 1.0
O C:ASP109 2.8 32.9 1.0
OG1 C:THR39 3.1 25.4 1.0
C C:VAL40 3.3 35.7 1.0
N C:VAL40 3.4 35.1 1.0
CG C:ASP109 3.7 33.3 1.0
C C:GLN196 3.7 31.6 1.0
C C:ASP109 3.9 29.8 1.0
CA C:VAL40 3.9 35.5 1.0
C C:THR39 4.1 32.1 1.0
CA C:ASP109 4.2 25.4 1.0
CB C:THR39 4.3 33.6 1.0
CA C:THR39 4.4 30.6 1.0
CD C:PRO42 4.4 35.4 1.0
N C:ASN41 4.5 35.3 1.0
CA C:GLN196 4.5 33.5 1.0
OD2 C:ASP109 4.5 41.8 1.0
CB C:ASP109 4.6 23.4 1.0
CB C:VAL40 4.6 36.9 1.0
N C:THR197 4.8 32.8 1.0
CG2 C:THR197 4.8 22.0 1.0
CD1 C:ILE48 4.8 28.8 1.0
O C:VAL345 4.9 38.2 1.0
O C:THR39 4.9 33.8 1.0
CA C:THR197 4.9 31.5 1.0
CA C:ASN41 4.9 37.6 1.0

Magnesium binding site 4 out of 8 in 1cw3

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Magnesium binding site 4 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+


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 Nad+ and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4501

b:24.4
occ:1.00
 O D:VAL40 2.4 23.3 1.0
O D:GLN196 2.5 19.1 1.0
O D:ASP109 2.6 30.8 1.0
O D:HOH4568 3.1 33.8 1.0
OD1 D:ASP109 3.1 33.3 1.0
C D:VAL40 3.5 24.6 1.0
C D:GLN196 3.6 19.5 1.0
C D:ASP109 3.7 28.4 1.0
OG1 D:THR39 3.8 31.1 1.0
N D:VAL40 3.9 21.4 1.0
CD D:PRO42 4.0 23.9 1.0
CG D:ASP109 4.1 30.4 1.0
CA D:VAL40 4.2 20.4 1.0
CA D:ASP109 4.2 28.5 1.0
O D:VAL345 4.3 30.5 1.0
CA D:GLN196 4.3 20.7 1.0
CG2 D:THR197 4.4 19.2 1.0
CB D:GLN196 4.6 23.4 1.0
N D:ASN41 4.6 19.5 1.0
C D:THR39 4.7 21.3 1.0
N D:THR197 4.7 20.2 1.0
CB D:ASP109 4.7 25.1 1.0
CB D:VAL40 4.7 20.3 1.0
CG2 D:VAL345 4.8 17.6 1.0
N D:ASN110 4.8 24.9 1.0
OD2 D:ASP109 4.9 33.1 1.0
CG D:PRO42 4.9 21.2 1.0
N D:PRO42 4.9 24.2 1.0
CA D:THR197 4.9 20.1 1.0
CA D:ASN41 5.0 20.5 1.0

Magnesium binding site 5 out of 8 in 1cw3

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Magnesium binding site 5 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+


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 Nad+ and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg5501

b:38.4
occ:1.00
 O E:VAL40 2.4 45.7 1.0
O E:GLN196 2.4 29.0 1.0
O E:HOH9219 2.5 26.2 1.0
OD1 E:ASP109 2.7 41.9 1.0
O E:ASP109 2.8 28.8 1.0
OG1 E:THR39 3.2 43.4 1.0
O E:HOH9193 3.4 11.8 1.0
C E:VAL40 3.5 41.3 1.0
N E:VAL40 3.6 33.6 1.0
C E:GLN196 3.6 27.8 1.0
CG E:ASP109 3.7 41.5 1.0
C E:ASP109 3.8 30.3 1.0
CA E:VAL40 4.0 39.0 1.0
CA E:ASP109 4.2 33.0 1.0
C E:THR39 4.2 33.0 1.0
CB E:THR39 4.4 42.6 1.0
CA E:GLN196 4.4 27.8 1.0
CD E:PRO42 4.4 40.7 1.0
OD2 E:ASP109 4.5 40.4 1.0
CG2 E:THR197 4.5 20.7 1.0
CA E:THR39 4.5 39.6 1.0
CB E:ASP109 4.5 35.4 1.0
N E:THR197 4.6 30.8 1.0
N E:ASN41 4.6 35.4 1.0
CA E:THR197 4.7 30.7 1.0
CB E:VAL40 4.8 41.6 1.0
CG E:PRO42 4.8 36.4 1.0
CD1 E:ILE48 4.8 31.0 1.0
O E:VAL345 4.9 24.7 1.0
O E:THR39 5.0 28.5 1.0
CB E:GLN196 5.0 19.9 1.0

Magnesium binding site 6 out of 8 in 1cw3

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Magnesium binding site 6 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+


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 Nad+ and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg6501

b:33.2
occ:1.00
 O F:GLN196 2.3 44.2 1.0
OD1 F:ASP109 2.5 46.2 1.0
O F:ASP109 2.5 32.5 1.0
O F:VAL40 2.6 41.4 1.0
OG1 F:THR39 3.1 37.5 1.0
CG F:ASP109 3.4 41.3 1.0
C F:ASP109 3.5 28.6 1.0
C F:GLN196 3.5 40.7 1.0
C F:VAL40 3.8 44.2 1.0
CA F:ASP109 3.9 33.1 1.0
N F:VAL40 3.9 43.0 1.0
O F:HOH9249 4.0 23.5 1.0
OD2 F:ASP109 4.2 37.1 1.0
CB F:ASP109 4.2 35.0 1.0
CG2 F:THR197 4.3 37.2 1.0
O F:HOH9248 4.3 34.3 1.0
CA F:GLN196 4.4 35.2 1.0
CA F:VAL40 4.4 44.7 1.0
N F:THR197 4.4 36.4 1.0
CD F:PRO42 4.5 41.5 1.0
CB F:THR39 4.5 40.2 1.0
CA F:THR197 4.5 37.3 1.0
C F:THR39 4.5 42.1 1.0
N F:ASN110 4.7 27.0 1.0
CD1 F:ILE48 4.7 39.5 1.0
CA F:THR39 4.8 41.0 1.0
N F:ASN41 4.8 43.8 1.0
CB F:GLN196 4.8 34.0 1.0
O F:VAL345 5.0 44.8 1.0

Magnesium binding site 7 out of 8 in 1cw3

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Magnesium binding site 7 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+


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 Nad+ and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg7501

b:32.7
occ:1.00
 O G:GLN196 2.3 24.4 1.0
O G:VAL40 2.5 34.2 1.0
O G:ASP109 2.7 36.9 1.0
OD1 G:ASP109 2.9 42.2 1.0
O G:HOH9290 3.1 29.6 1.0
C G:GLN196 3.5 26.8 1.0
OG1 G:THR39 3.6 41.2 1.0
C G:VAL40 3.6 34.2 1.0
N G:VAL40 3.8 37.2 1.0
C G:ASP109 3.8 35.6 1.0
CG G:ASP109 3.9 43.5 1.0
CA G:VAL40 4.2 35.2 1.0
CD G:PRO42 4.2 33.7 1.0
CA G:GLN196 4.2 29.1 1.0
O G:VAL345 4.3 31.0 1.0
CA G:ASP109 4.4 36.0 1.0
CG2 G:THR197 4.4 23.8 1.0
C G:THR39 4.5 40.3 1.0
N G:THR197 4.6 30.2 1.0
CB G:GLN196 4.6 30.0 1.0
OD2 G:ASP109 4.7 46.1 1.0
CB G:ASP109 4.7 42.5 1.0
N G:ASN41 4.7 35.3 1.0
CA G:THR197 4.8 28.1 1.0
CB G:THR39 4.8 37.1 1.0
CB G:VAL40 4.8 33.2 1.0
CA G:THR39 4.9 41.2 1.0
CG2 G:VAL345 4.9 25.9 1.0
N G:ASN110 5.0 32.6 1.0
O G:HOH9399 5.0 19.3 1.0

Magnesium binding site 8 out of 8 in 1cw3

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Magnesium binding site 8 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MN2+


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 Nad+ and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg8501

b:31.7
occ:1.00
 O H:GLN196 2.3 29.8 1.0
O H:HOH8604 2.3 30.2 1.0
O H:VAL40 2.6 20.1 1.0
OD1 H:ASP109 2.6 35.6 1.0
OG1 H:THR39 2.7 28.7 1.0
O H:ASP109 2.8 28.1 1.0
O H:HOH8574 3.3 35.9 1.0
CG H:ASP109 3.4 26.3 1.0
C H:GLN196 3.5 25.7 1.0
N H:VAL40 3.6 26.7 1.0
C H:VAL40 3.6 23.4 1.0
C H:ASP109 3.8 25.8 1.0
CA H:ASP109 4.0 19.4 1.0
CB H:THR39 4.0 27.0 1.0
OD2 H:ASP109 4.0 23.5 1.0
C H:THR39 4.1 24.1 1.0
CA H:VAL40 4.1 27.5 1.0
CB H:ASP109 4.2 23.7 1.0
CA H:THR39 4.3 22.9 1.0
CA H:GLN196 4.4 22.6 1.0
N H:THR197 4.4 27.0 1.0
CA H:THR197 4.5 25.5 1.0
CD1 H:ILE48 4.5 36.8 1.0
CG2 H:THR197 4.6 11.7 1.0
N H:ASN41 4.8 23.2 1.0
CD H:PRO42 4.8 30.2 1.0
CG2 H:THR39 4.9 18.0 1.0
O H:THR39 4.9 24.6 1.0
CD H:PRO198 5.0 33.9 1.0

Reference:

L.Ni, J.Zhou, T.D.Hurley, H.Weiner. Human Liver Mitochondrial Aldehyde Dehydrogenase: Three-Dimensional Structure and the Restoration of Solubility and Activity of Chimeric Forms. Protein Sci. V. 8 2784 1999.
ISSN: ISSN 0961-8368
PubMed: 10631996
Page generated: Tue Aug 13 02:32:21 2024

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