Atomistry » Magnesium » PDB 1nzz-1oev » 1o02
Atomistry »
  Magnesium »
    PDB 1nzz-1oev »
      1o02 »

Magnesium in PDB 1o02: Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of MG2+

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

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

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of MG2+, PDB code: 1o02 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) 24.97 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.492, 150.873, 177.195, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.3

Other elements in 1o02:

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 MG2+ (pdb code 1o02). 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 MG2+, PDB code: 1o02:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1o02

Go back to Magnesium Binding Sites List in 1o02
Magnesium binding site 1 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4601

b:32.1
occ:1.00
O2A A:NAI4606 2.1 23.4 1.0
O A:HOH4866 2.1 26.6 1.0
O A:HOH4731 2.2 33.9 1.0
O A:HOH4733 2.2 32.9 1.0
O A:HOH4867 2.2 28.2 1.0
O1N A:NAI4606 2.2 21.9 1.0
PA A:NAI4606 3.3 23.6 1.0
PN A:NAI4606 3.4 24.3 1.0
O3 A:NAI4606 3.5 23.8 1.0
O A:HOH4865 4.2 33.1 1.0
O A:HOH4734 4.2 38.7 1.0
O1A A:NAI4606 4.2 21.6 1.0
O5B A:NAI4606 4.3 22.5 1.0
O A:HOH4732 4.3 47.5 1.0
C5D A:NAI4606 4.3 24.9 1.0
O2N A:NAI4606 4.4 23.9 1.0
CG1 A:ILE249 4.4 26.7 1.0
O5D A:NAI4606 4.4 23.9 1.0
C8A A:NAI4606 4.7 23.9 1.0
OG A:SER246 4.7 20.7 1.0
OE2 A:GLU248 4.8 47.4 1.0
CD1 A:ILE249 4.9 26.2 1.0
N7A A:NAI4606 5.0 24.6 1.0

Magnesium binding site 2 out of 8 in 1o02

Go back to Magnesium Binding Sites List in 1o02
Magnesium binding site 2 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:29.2
occ:1.00
O B:HOH788 2.0 32.2 1.0
O1N B:NAI606 2.0 23.6 1.0
O B:HOH787 2.1 32.5 1.0
O B:HOH786 2.2 41.5 1.0
O B:HOH785 2.2 28.8 1.0
O2A B:NAI606 2.2 22.9 1.0
PN B:NAI606 3.3 24.7 1.0
PA B:NAI606 3.3 22.9 1.0
O3 B:NAI606 3.5 22.9 1.0
O B:HOH789 4.0 30.6 1.0
O B:HOH775 4.2 31.8 1.0
C5D B:NAI606 4.2 23.0 1.0
O2N B:NAI606 4.3 23.6 1.0
O5D B:NAI606 4.3 23.1 1.0
O5B B:NAI606 4.3 22.5 1.0
O1A B:NAI606 4.3 21.6 1.0
O B:HOH784 4.5 41.2 1.0
CG1 B:ILE249 4.5 23.1 1.0
O B:HOH782 4.7 48.0 1.0
C8A B:NAI606 4.8 21.1 1.0
OG B:SER246 4.8 20.5 1.0
O B:HOH783 4.8 44.1 1.0
OE2 B:GLU248 4.9 44.3 1.0

Magnesium binding site 3 out of 8 in 1o02

Go back to Magnesium Binding Sites List in 1o02
Magnesium binding site 3 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:27.2
occ:1.00
O C:HOH1039 2.0 30.1 1.0
O C:HOH1066 2.1 32.0 1.0
O2A C:NAI606 2.1 20.4 1.0
O1N C:NAI606 2.2 21.0 1.0
O C:HOH1040 2.3 36.3 1.0
O C:HOH1067 2.4 31.8 1.0
PA C:NAI606 3.3 19.6 1.0
PN C:NAI606 3.4 21.4 1.0
O3 C:NAI606 3.6 21.4 1.0
O C:HOH1037 4.0 29.2 1.0
O C:HOH1068 4.2 31.4 1.0
O1A C:NAI606 4.2 20.9 1.0
C5D C:NAI606 4.3 20.9 1.0
O5D C:NAI606 4.3 22.2 1.0
O5B C:NAI606 4.3 20.1 1.0
CG1 C:ILE249 4.4 21.9 1.0
O2N C:NAI606 4.4 23.6 1.0
O C:HOH1041 4.4 32.3 1.0
OG C:SER246 4.6 19.4 1.0
C8A C:NAI606 4.8 17.7 1.0
CD1 C:ILE249 4.9 23.1 1.0

Magnesium binding site 4 out of 8 in 1o02

Go back to Magnesium Binding Sites List in 1o02
Magnesium binding site 4 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:27.7
occ:1.00
O D:HOH720 2.0 30.8 1.0
O2A D:NAI606 2.1 20.2 1.0
O D:HOH717 2.2 28.6 1.0
O1N D:NAI606 2.3 24.7 1.0
O D:HOH719 2.3 31.6 1.0
O D:HOH718 2.5 47.8 1.0
PA D:NAI606 3.3 21.9 1.0
PN D:NAI606 3.5 24.3 1.0
O3 D:NAI606 3.7 23.1 1.0
O D:HOH716 3.9 32.8 1.0
O D:HOH721 4.1 28.1 1.0
O1A D:NAI606 4.3 22.2 1.0
CG1 D:ILE249 4.3 20.5 1.0
C5D D:NAI606 4.4 24.7 1.0
O5B D:NAI606 4.4 21.7 1.0
O5D D:NAI606 4.4 25.4 1.0
OG D:SER246 4.5 21.9 1.0
O2N D:NAI606 4.5 26.1 1.0
C8A D:NAI606 4.7 19.8 1.0
OE2 D:GLU248 4.7 42.2 1.0
CD1 D:ILE249 4.9 22.2 1.0
N7A D:NAI606 5.0 19.0 1.0

Magnesium binding site 5 out of 8 in 1o02

Go back to Magnesium Binding Sites List in 1o02
Magnesium binding site 5 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:31.0
occ:1.00
O E:HOH921 1.9 29.7 1.0
O2A E:NAI606 2.1 18.2 1.0
O1N E:NAI606 2.1 22.4 1.0
O E:HOH920 2.2 30.1 1.0
O E:HOH788 2.3 33.6 1.0
O E:HOH787 2.4 31.3 1.0
PA E:NAI606 3.3 20.3 1.0
PN E:NAI606 3.3 23.7 1.0
O3 E:NAI606 3.6 20.8 1.0
O E:HOH922 3.8 28.9 1.0
O E:HOH789 4.0 40.1 1.0
O1A E:NAI606 4.2 18.2 1.0
O5B E:NAI606 4.3 19.3 1.0
O2N E:NAI606 4.3 21.8 1.0
O5D E:NAI606 4.3 24.1 1.0
C5D E:NAI606 4.4 22.1 1.0
O E:HOH926 4.4 47.7 1.0
CG1 E:ILE249 4.5 20.7 1.0
OG E:SER246 4.7 17.5 1.0
C8A E:NAI606 4.7 17.6 1.0
OE1 E:GLU248 4.9 39.6 1.0

Magnesium binding site 6 out of 8 in 1o02

Go back to Magnesium Binding Sites List in 1o02
Magnesium binding site 6 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:25.7
occ:1.00
O F:HOH784 1.9 26.9 1.0
O2A F:NAI607 2.0 16.9 1.0
O F:HOH783 2.1 28.0 1.0
O1N F:NAI607 2.2 17.8 1.0
O F:HOH817 2.3 31.5 1.0
O F:HOH816 2.3 24.9 1.0
PA F:NAI607 3.2 17.9 1.0
PN F:NAI607 3.4 19.5 1.0
O3 F:NAI607 3.5 17.4 1.0
O F:HOH785 3.9 25.9 1.0
O1A F:NAI607 4.1 15.4 1.0
O F:HOH782 4.2 30.9 1.0
O5B F:NAI607 4.3 16.2 1.0
C5D F:NAI607 4.3 17.1 1.0
O5D F:NAI607 4.3 18.5 1.0
CG1 F:ILE249 4.4 20.1 1.0
O2N F:NAI607 4.4 18.1 1.0
OG F:SER246 4.6 22.5 1.0
C8A F:NAI607 4.8 15.8 1.0
CD1 F:ILE249 4.9 23.1 1.0

Magnesium binding site 7 out of 8 in 1o02

Go back to Magnesium Binding Sites List in 1o02
Magnesium binding site 7 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:28.8
occ:1.00
O2A G:NAI606 1.9 24.6 1.0
O1N G:NAI606 2.1 26.7 1.0
O G:HOH706 2.1 33.0 1.0
O G:HOH707 2.2 36.1 1.0
O G:HOH709 2.2 34.5 1.0
O G:HOH708 2.4 38.4 1.0
PA G:NAI606 3.1 25.0 1.0
PN G:NAI606 3.2 27.9 1.0
O3 G:NAI606 3.4 25.2 1.0
O G:HOH710 4.0 42.2 1.0
O5B G:NAI606 4.1 23.8 1.0
O1A G:NAI606 4.2 24.0 1.0
O2N G:NAI606 4.3 25.4 1.0
O5D G:NAI606 4.3 25.8 1.0
O G:HOH705 4.3 46.9 1.0
C5D G:NAI606 4.4 25.0 1.0
CG1 G:ILE249 4.4 24.8 1.0
C8A G:NAI606 4.6 23.7 1.0
OG G:SER246 4.6 22.2 1.0
CD1 G:ILE249 4.8 23.1 1.0
O G:HOH742 4.9 44.6 1.0
N7A G:NAI606 4.9 24.5 1.0

Magnesium binding site 8 out of 8 in 1o02

Go back to Magnesium Binding Sites List in 1o02
Magnesium binding site 8 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:31.8
occ:1.00
O H:HOH763 2.0 48.6 1.0
O2A H:NAI605 2.0 27.7 1.0
O1N H:NAI605 2.2 28.4 1.0
O H:HOH768 2.2 42.7 1.0
O H:HOH770 2.4 33.6 1.0
O H:HOH769 2.4 37.5 1.0
PA H:NAI605 3.2 26.7 1.0
PN H:NAI605 3.3 28.5 1.0
O3 H:NAI605 3.5 27.6 1.0
O H:HOH762 3.8 44.7 1.0
O H:HOH767 4.1 35.3 1.0
O5B H:NAI605 4.2 25.1 1.0
O1A H:NAI605 4.2 26.3 1.0
O H:HOH764 4.2 46.6 1.0
C5D H:NAI605 4.3 29.8 1.0
O2N H:NAI605 4.3 26.3 1.0
O5D H:NAI605 4.3 28.6 1.0
CG1 H:ILE249 4.4 26.5 1.0
OG H:SER246 4.5 25.1 1.0
C8A H:NAI605 4.8 27.0 1.0
OE2 H:GLU248 5.0 44.7 1.0
CD1 H:ILE249 5.0 25.5 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: Mon Dec 14 06:34:13 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy