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Manganese 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:

Magnesium (Mg) 8 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 8 in 1cw3

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Manganese 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 Manganese with other atoms in the Mn 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:Mn1503

b:42.4
occ:0.50
 O2A A:NAD1502 2.0 47.4 1.0
O A:HOH1523 2.3 20.2 1.0
O A:HOH1567 2.5 61.7 1.0
O1N A:NAD1502 3.1 73.9 1.0
O A:HOH1524 3.1 32.6 1.0
O5D A:NAD1502 3.2 69.3 1.0
PA A:NAD1502 3.4 42.4 1.0
PN A:NAD1502 3.6 74.3 1.0
O3 A:NAD1502 3.8 60.2 1.0
O5B A:NAD1502 4.2 40.6 1.0
C5D A:NAD1502 4.4 70.9 1.0
O1A A:NAD1502 4.4 41.1 1.0
O A:HOH1579 4.6 38.8 1.0
C8A A:NAD1502 4.7 35.1 1.0
CG1 A:ILE249 4.9 22.7 1.0

Manganese binding site 2 out of 8 in 1cw3

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Manganese 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 Manganese with other atoms in the Mn 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:Mn2503

b:43.3
occ:0.60
 O2A B:NAD2502 1.9 48.6 1.0
O B:HOH2524 2.5 12.5 1.0
O B:HOH2522 2.7 41.4 1.0
O B:HOH2523 2.8 17.0 1.0
PA B:NAD2502 3.3 45.0 1.0
O5B B:NAD2502 3.6 31.9 1.0
O B:HOH2580 3.8 57.3 1.0
O3 B:NAD2502 3.9 59.3 1.0
O2N B:NAD2502 4.1 65.3 1.0
PN B:NAD2502 4.3 69.0 1.0
C8A B:NAD2502 4.4 36.1 1.0
O1A B:NAD2502 4.5 45.1 1.0
O1N B:NAD2502 4.5 61.1 1.0
C2B B:NAD2502 5.0 24.9 1.0
N7A B:NAD2502 5.0 32.3 1.0

Manganese binding site 3 out of 8 in 1cw3

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Manganese 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 Manganese with other atoms in the Mn 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:Mn3503

b:33.3
occ:0.60
 O C:HOH3524 2.1 15.6 1.0
O C:HOH3558 2.1 21.0 1.0
O2A C:NAD3502 2.2 28.0 1.0
O C:HOH3523 2.7 20.8 1.0
PA C:NAD3502 3.5 35.1 1.0
O5B C:NAD3502 3.9 30.9 1.0
O3 C:NAD3502 4.3 40.4 1.0
O2N C:NAD3502 4.4 54.3 1.0
C8A C:NAD3502 4.4 17.5 1.0
O1N C:NAD3502 4.5 50.0 1.0
PN C:NAD3502 4.6 52.7 1.0
O1A C:NAD3502 4.7 30.3 1.0

Manganese binding site 4 out of 8 in 1cw3

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Manganese 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 Manganese with other atoms in the Mn 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:Mn4503

b:28.1
occ:0.50
 O2A D:NAD4502 2.0 29.0 1.0
O D:HOH4578 2.1 27.0 1.0
O D:HOH4603 2.6 26.8 1.0
O1N D:NAD4502 2.8 55.3 1.0
O D:HOH4532 2.9 25.7 1.0
O5D D:NAD4502 3.2 59.7 1.0
PA D:NAD4502 3.4 25.1 1.0
PN D:NAD4502 3.5 53.4 1.0
O3 D:NAD4502 3.8 41.2 1.0
O5B D:NAD4502 4.0 27.0 1.0
C5D D:NAD4502 4.4 61.6 1.0
C8A D:NAD4502 4.5 17.6 1.0
O1A D:NAD4502 4.6 27.8 1.0
O2N D:NAD4502 4.9 49.7 1.0

Manganese binding site 5 out of 8 in 1cw3

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Manganese 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 Manganese with other atoms in the Mn 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:Mn5503

b:40.4
occ:0.80
 O E:HOH9022 2.1 31.2 1.0
O E:HOH9023 2.2 25.4 1.0
O2A E:NAD5502 2.2 47.8 1.0
O E:HOH9021 2.6 21.2 1.0
PA E:NAD5502 3.6 41.6 1.0
C8A E:NAD5502 3.9 36.4 1.0
O1N E:NAD5502 3.9 73.2 1.0
O5B E:NAD5502 4.0 30.4 1.0
O3 E:NAD5502 4.3 54.9 1.0
N7A E:NAD5502 4.4 33.5 1.0
O5D E:NAD5502 4.4 68.1 1.0
PN E:NAD5502 4.5 70.3 1.0
O1A E:NAD5502 4.6 35.2 1.0
C5D E:NAD5502 4.7 69.9 1.0
O E:HOH9438 4.7 48.8 1.0
CG1 E:ILE249 4.7 21.2 1.0

Manganese binding site 6 out of 8 in 1cw3

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Manganese 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 Manganese with other atoms in the Mn 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:Mn6503

b:59.3
occ:0.50
 O F:HOH9085 2.0 35.0 1.0
O F:HOH9387 2.2 52.4 1.0
O F:HOH9084 2.2 35.0 1.0
O2A F:NAD6502 2.4 53.5 1.0
O F:HOH9267 2.8 51.7 1.0
PA F:NAD6502 3.7 51.3 1.0
O5D F:NAD6502 3.8 71.8 1.0
O1N F:NAD6502 4.0 73.5 1.0
C8A F:NAD6502 4.0 35.5 1.0
O5B F:NAD6502 4.1 48.4 1.0
PN F:NAD6502 4.3 74.8 1.0
N7A F:NAD6502 4.4 33.9 1.0
O3 F:NAD6502 4.5 61.8 1.0
CG1 F:ILE249 4.6 34.6 1.0
CD1 F:ILE249 4.8 37.4 1.0
O1A F:NAD6502 4.8 51.6 1.0
C5D F:NAD6502 4.9 69.7 1.0

Manganese binding site 7 out of 8 in 1cw3

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Manganese 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 Manganese with other atoms in the Mn 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:Mn7503

b:36.9
occ:0.60
 O G:HOH9125 2.1 28.0 1.0
O G:HOH9306 2.4 40.7 1.0
O G:HOH9582 2.5 52.9 1.0
O2A G:NAD7502 2.6 41.5 1.0
PA G:NAD7502 3.9 37.3 1.0
O5B G:NAD7502 4.3 37.4 1.0
O3 G:NAD7502 4.5 47.1 1.0
O2N G:NAD7502 4.5 57.6 1.0
C8A G:NAD7502 4.7 24.9 1.0
O G:HOH9492 4.8 35.7 1.0
PN G:NAD7502 4.8 59.1 1.0
O1N G:NAD7502 4.8 56.0 1.0
O G:HOH9365 5.0 25.5 1.0

Manganese binding site 8 out of 8 in 1cw3

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Manganese 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 Manganese with other atoms in the Mn 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:Mn8503

b:35.5
occ:0.80
 O H:HOH8529 2.1 15.7 1.0
O2A H:NAD8502 2.2 45.5 1.0
O H:HOH8530 2.4 27.9 1.0
O H:HOH8600 2.4 25.1 1.0
PA H:NAD8502 3.7 41.0 1.0
O5D H:NAD8502 3.8 65.4 1.0
O1N H:NAD8502 4.0 61.2 1.0
O5B H:NAD8502 4.2 39.1 1.0
O H:HOH8528 4.3 17.0 1.0
PN H:NAD8502 4.4 63.2 1.0
O3 H:NAD8502 4.4 47.2 1.0
C8A H:NAD8502 4.5 26.2 1.0
O1A H:NAD8502 4.6 39.4 1.0
C5D H:NAD8502 4.9 69.1 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: Sat Oct 5 10:02:55 2024

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