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Magnesium in PDB 1o04: CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+

Enzymatic activity of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+

All present enzymatic activity of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+:
1.2.1.3;

Protein crystallography data

The structure of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+, PDB code: 1o04 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) 50.00 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.211, 152.487, 177.200, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.1

Other elements in 1o04:

The structure of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ (pdb code 1o04). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+, PDB code: 1o04:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1o04

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Magnesium binding site 1 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg6701

b:18.6
occ:1.00
 O2A A:NAD6501 2.0 17.0 1.0
O A:HOH7059 2.1 25.3 1.0
O A:HOH7060 2.1 21.3 1.0
O A:HOH7062 2.1 25.7 1.0
O A:HOH7257 2.1 24.1 1.0
O A:HOH7058 2.2 21.9 1.0
PA A:NAD6501 3.5 16.1 1.0
O5B A:NAD6501 4.0 15.4 1.0
O1N A:NAD6501 4.1 21.7 1.0
O A:HOH7061 4.1 19.0 1.0
O A:HOH7259 4.2 30.8 1.0
O A:HOH7057 4.3 20.4 1.0
O A:HOH7256 4.4 26.7 1.0
O3 A:NAD6501 4.4 16.7 1.0
O1A A:NAD6501 4.5 14.6 1.0
O A:HOH7063 4.5 29.9 1.0
O A:HOH7055 4.6 30.6 1.0
O A:HOH7258 4.6 33.3 1.0
PN A:NAD6501 4.6 18.5 1.0
C8A A:NAD6501 4.6 16.0 1.0
NE2 A:GLN196 4.8 20.5 1.0
OE2 A:GLU195 4.8 23.4 1.0
O2N A:NAD6501 5.0 18.4 1.0

Magnesium binding site 2 out of 8 in 1o04

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Magnesium binding site 2 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg6702

b:16.3
occ:1.00
 O2A B:NAD6502 2.0 16.9 1.0
O B:HOH7430 2.0 20.3 1.0
O B:HOH7194 2.1 22.1 1.0
O B:HOH7011 2.1 18.9 1.0
O B:HOH7191 2.1 23.0 1.0
O B:HOH7013 2.2 17.4 1.0
PA B:NAD6502 3.5 15.6 1.0
O B:HOH7190 4.0 25.7 1.0
O B:HOH7012 4.0 15.9 1.0
O5B B:NAD6502 4.0 16.3 1.0
O1N B:NAD6502 4.0 17.5 1.0
O B:HOH7193 4.1 38.9 1.0
O B:HOH7429 4.2 25.0 1.0
O B:HOH7014 4.2 20.1 1.0
O B:HOH7192 4.3 34.4 1.0
O3 B:NAD6502 4.4 15.2 1.0
O1A B:NAD6502 4.5 14.9 1.0
O B:HOH7195 4.5 32.8 1.0
O B:HOH7016 4.5 25.5 1.0
C8A B:NAD6502 4.6 14.8 1.0
PN B:NAD6502 4.6 15.6 1.0
NE2 B:GLN196 4.7 15.1 1.0
OE2 B:GLU195 4.7 20.0 1.0
O2N B:NAD6502 5.0 17.4 1.0

Magnesium binding site 3 out of 8 in 1o04

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Magnesium binding site 3 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg6703

b:18.0
occ:1.00
 O2A C:NAD6503 2.0 14.9 1.0
O C:HOH7220 2.0 21.8 1.0
O C:HOH7221 2.1 19.1 1.0
O C:HOH7257 2.2 26.9 1.0
O C:HOH7223 2.2 19.1 1.0
O C:HOH7000 2.3 20.3 1.0
PA C:NAD6503 3.5 14.1 1.0
O5B C:NAD6503 4.0 13.5 1.0
O1N C:NAD6503 4.0 17.4 1.0
O C:HOH7222 4.1 14.9 1.0
O C:HOH6999 4.1 31.9 1.0
O C:HOH7001 4.2 37.5 1.0
O C:HOH7217 4.2 19.6 1.0
O C:HOH7224 4.2 32.5 1.0
O3 C:NAD6503 4.4 15.1 1.0
O C:HOH7219 4.4 29.0 1.0
O1A C:NAD6503 4.5 13.6 1.0
C8A C:NAD6503 4.6 12.8 1.0
PN C:NAD6503 4.7 15.9 1.0
NE2 C:GLN196 4.7 13.8 1.0
OE2 C:GLU195 4.7 16.4 1.0

Magnesium binding site 4 out of 8 in 1o04

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Magnesium binding site 4 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg6704

b:15.9
occ:1.00
 O2A D:NAD6504 2.0 16.3 1.0
O D:HOH7070 2.1 20.5 1.0
O D:HOH7072 2.1 25.8 1.0
O D:HOH7069 2.1 20.6 1.0
O D:HOH7531 2.1 21.4 1.0
O D:HOH7447 2.2 20.5 1.0
PA D:NAD6504 3.4 14.9 1.0
O5B D:NAD6504 4.0 13.1 1.0
O1N D:NAD6504 4.0 17.3 1.0
O D:HOH7068 4.1 19.6 1.0
O D:HOH7448 4.1 28.5 1.0
O D:HOH6983 4.2 30.6 1.0
O D:HOH6984 4.3 21.1 1.0
O3 D:NAD6504 4.3 14.4 1.0
O D:HOH7071 4.4 32.7 1.0
O1A D:NAD6504 4.4 12.6 1.0
O D:HOH7446 4.5 35.6 1.0
O D:HOH7073 4.5 32.7 1.0
O D:HOH6986 4.6 31.3 1.0
C8A D:NAD6504 4.6 14.9 1.0
PN D:NAD6504 4.6 15.8 1.0
OE2 D:GLU195 4.8 22.8 1.0
NE2 D:GLN196 4.9 15.9 1.0
O2N D:NAD6504 5.0 17.0 1.0

Magnesium binding site 5 out of 8 in 1o04

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Magnesium binding site 5 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg6705

b:15.4
occ:1.00
 O2A E:NAD6505 2.0 13.4 1.0
O E:HOH2627 2.0 18.5 1.0
O E:HOH2631 2.0 23.2 1.0
O E:HOH2628 2.1 19.2 1.0
O E:HOH2632 2.2 26.4 1.0
O E:HOH4785 2.2 18.2 1.0
PA E:NAD6505 3.5 14.5 1.0
O1N E:NAD6505 4.0 16.0 1.0
O5B E:NAD6505 4.0 13.1 1.0
O E:HOH2626 4.0 16.7 1.0
O E:HOH4784 4.2 27.9 1.0
O E:HOH4787 4.2 29.6 1.0
O E:HOH4786 4.2 19.7 1.0
O3 E:NAD6505 4.3 13.8 1.0
O E:HOH2633 4.4 29.8 1.0
O1A E:NAD6505 4.4 11.6 1.0
O E:HOH2629 4.5 35.3 1.0
O E:HOH2630 4.5 29.4 1.0
C8A E:NAD6505 4.6 12.1 1.0
PN E:NAD6505 4.6 15.3 1.0
O E:HOH3890 4.7 28.8 1.0
OE2 E:GLU195 4.7 19.7 1.0
NE2 E:GLN196 4.8 16.4 1.0
O2N E:NAD6505 5.0 15.1 1.0

Magnesium binding site 6 out of 8 in 1o04

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Magnesium binding site 6 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg6706

b:18.7
occ:1.00
 O2A F:NAD6506 1.9 15.3 1.0
O F:HOH2814 2.0 24.6 1.0
O F:HOH2834 2.1 16.6 1.0
O F:HOH2813 2.1 21.7 1.0
O F:HOH2815 2.2 22.3 1.0
O F:HOH2833 2.3 20.0 1.0
PA F:NAD6506 3.4 14.4 1.0
O5B F:NAD6506 3.9 12.8 1.0
O1N F:NAD6506 4.0 16.1 1.0
O F:HOH2835 4.1 15.8 1.0
O F:HOH3074 4.2 29.9 1.0
O F:HOH2832 4.2 17.6 1.0
O F:HOH2831 4.2 30.4 1.0
O F:HOH2816 4.3 35.0 1.0
O3 F:NAD6506 4.4 15.0 1.0
O1A F:NAD6506 4.4 13.9 1.0
O F:HOH2812 4.5 31.6 1.0
C8A F:NAD6506 4.5 13.2 1.0
O F:HOH2837 4.6 25.4 1.0
PN F:NAD6506 4.7 15.4 1.0
OE2 F:GLU195 4.7 17.5 1.0
NE2 F:GLN196 4.8 15.8 1.0
O2N F:NAD6506 5.0 14.4 1.0

Magnesium binding site 7 out of 8 in 1o04

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Magnesium binding site 7 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg6707

b:15.5
occ:1.00
 O2A G:NAD6507 2.0 15.1 1.0
O G:HOH4361 2.0 18.2 1.0
O G:HOH3210 2.1 20.4 1.0
O G:HOH3209 2.1 19.2 1.0
O G:HOH4359 2.1 20.2 1.0
O G:HOH4360 2.1 18.9 1.0
PA G:NAD6507 3.5 14.5 1.0
O5B G:NAD6507 4.0 13.9 1.0
O1N G:NAD6507 4.1 17.0 1.0
O G:HOH4358 4.1 27.1 1.0
O G:HOH3208 4.1 23.0 1.0
O G:HOH4362 4.1 16.7 1.0
O G:HOH3207 4.2 16.2 1.0
O3 G:NAD6507 4.4 14.2 1.0
O G:HOH4357 4.4 32.9 1.0
O1A G:NAD6507 4.4 13.9 1.0
O G:HOH3211 4.5 33.5 1.0
C8A G:NAD6507 4.6 14.0 1.0
PN G:NAD6507 4.7 14.3 1.0
O G:HOH3205 4.7 25.9 1.0
NE2 G:GLN196 4.7 14.9 1.0
OE2 G:GLU195 4.8 19.6 1.0
O2N G:NAD6507 5.0 14.2 1.0

Magnesium binding site 8 out of 8 in 1o04

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Magnesium binding site 8 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg6708

b:17.4
occ:1.00
 O2A H:NAD6508 1.9 17.2 1.0
O H:HOH2231 2.0 25.8 1.0
O H:HOH2235 2.1 19.1 1.0
O H:HOH2230 2.1 18.8 1.0
O H:HOH2228 2.1 22.5 1.0
O H:HOH2227 2.2 21.2 1.0
PA H:NAD6508 3.4 15.5 1.0
O5B H:NAD6508 3.9 14.0 1.0
O H:HOH2236 4.0 17.8 1.0
O1N H:NAD6508 4.0 17.5 1.0
O H:HOH2237 4.1 28.2 1.0
O H:HOH2229 4.1 23.9 1.0
O H:HOH2226 4.3 17.3 1.0
O3 H:NAD6508 4.3 14.8 1.0
O1A H:NAD6508 4.4 14.2 1.0
O H:HOH2232 4.5 27.6 1.0
C8A H:NAD6508 4.6 13.7 1.0
O H:HOH2233 4.6 39.5 1.0
PN H:NAD6508 4.6 16.5 1.0
O H:HOH2224 4.7 26.7 1.0
OE2 H:GLU195 4.8 20.2 1.0
NE2 H:GLN196 4.8 17.1 1.0
O2N H:NAD6508 5.0 18.0 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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