Magnesium in PDB 6ci9: Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure

Enzymatic activity of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure

All present enzymatic activity of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure:
1.1.1.100;

Protein crystallography data

The structure of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure, PDB code: 6ci9 was solved by E.Mallette, M.S.Kimber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.50 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 131.770, 129.060, 145.790, 90.00, 107.88, 90.00
R / Rfree (%) 20.4 / 23.3

Other elements in 6ci9:

The structure of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure also contains other interesting chemical elements:

Chlorine (Cl) 17 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure (pdb code 6ci9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure, PDB code: 6ci9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6ci9

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Magnesium binding site 1 out of 8 in the Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:43.6
occ:1.00
 O A:HOH527 2.2 43.3 1.0
O A:HOH410 2.3 50.1 1.0
OE2 A:GLU6 4.0 55.2 1.0
OD1 A:ASP33 4.2 30.0 1.0
O A:GLY31 4.3 29.9 1.0
O A:ARG55 4.3 33.2 1.0
OD2 A:ASP33 4.5 38.6 1.0
CG A:GLU6 4.6 42.5 1.0
N A:GLY7 4.7 25.6 1.0
CD A:GLU6 4.8 52.3 1.0
CA A:GLY7 4.8 26.5 1.0
CG A:ASP33 4.8 32.5 1.0

Magnesium binding site 2 out of 8 in 6ci9

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Magnesium binding site 2 out of 8 in the Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:24.8
occ:1.00
 O3X C:NAP301 1.9 19.9 0.9
O C:HOH415 2.1 25.3 1.0
O C:HOH520 2.2 22.6 1.0
P2B C:NAP301 3.1 23.2 0.9
O1X C:NAP301 3.3 23.9 0.9
O2B C:NAP301 3.8 24.6 0.9
NH2 C:ARG39 4.0 27.2 1.0
C2B C:NAP301 4.0 25.3 0.9
O C:HOH550 4.0 25.0 1.0
O2X C:NAP301 4.3 21.0 0.9
O C:HOH464 4.3 28.1 1.0
NZ C:LYS17 4.4 50.8 1.0
O C:HOH545 4.4 28.3 1.0
OD1 C:ASP43 4.5 42.4 1.0
CD C:LYS17 4.5 40.8 1.0
C3B C:NAP301 4.7 25.9 0.9
O C:HOH506 4.7 46.2 1.0
O C:HOH579 4.8 40.8 1.0
CE C:LYS17 4.9 47.4 1.0

Magnesium binding site 3 out of 8 in 6ci9

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Magnesium binding site 3 out of 8 in the Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg304

b:52.6
occ:1.00
 O F:HOH516 1.9 51.1 1.0
O F:HOH530 2.0 50.7 1.0
O F:HOH412 2.7 43.0 1.0
O F:ARG55 3.7 38.1 1.0
OE2 F:GLU6 3.9 62.3 1.0
NH1 F:ARG55 4.2 67.6 1.0
O F:GLY31 4.3 31.1 1.0
OD2 F:ASP33 4.4 31.7 1.0
CG F:GLU6 4.6 46.6 1.0
C F:ARG55 4.6 37.9 1.0
CD F:GLU6 4.7 58.1 1.0
OD1 F:ASP33 4.8 35.0 1.0
CG F:ARG55 4.8 52.0 1.0
CA F:GLY56 4.8 34.7 1.0

Magnesium binding site 4 out of 8 in 6ci9

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Magnesium binding site 4 out of 8 in the Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg304

b:28.3
occ:1.00
 O3X H:NAP301 1.9 21.7 0.9
O H:HOH551 2.1 26.2 1.0
O H:HOH528 2.1 26.1 1.0
O H:HOH457 2.1 29.5 1.0
O H:HOH416 2.2 27.2 1.0
P2B H:NAP301 3.1 21.8 0.9
O1X H:NAP301 3.4 22.4 0.9
O2B H:NAP301 3.8 25.3 0.9
C2B H:NAP301 4.0 22.7 0.9
NH2 H:ARG39 4.0 25.5 1.0
O H:HOH573 4.1 21.4 1.0
NZ H:LYS17 4.2 45.0 1.0
O H:HOH477 4.4 29.8 1.0
O2X H:NAP301 4.4 18.6 0.9
OD2 H:ASP43 4.4 41.8 1.0
O H:HOH576 4.5 30.3 1.0
O H:HOH599 4.5 40.7 1.0
CD H:LYS17 4.5 40.2 1.0
C3B H:NAP301 4.6 25.2 0.9
CE H:LYS17 4.8 43.7 1.0

Magnesium binding site 5 out of 8 in 6ci9

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Magnesium binding site 5 out of 8 in the Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg304

b:42.5
occ:1.00
 O J:HOH429 2.1 43.3 1.0
O3X J:NAP301 2.1 38.2 0.9
O J:HOH467 2.2 41.9 1.0
P2B J:NAP301 3.2 34.4 0.9
O1X J:NAP301 3.4 33.5 0.9
O2B J:NAP301 3.9 34.4 0.9
O J:HOH499 4.2 40.0 1.0
C2B J:NAP301 4.2 34.3 0.9
NH2 J:ARG39 4.3 40.6 1.0
OD2 J:ASP43 4.4 56.0 1.0
O J:HOH417 4.4 41.2 1.0
O2X J:NAP301 4.5 34.0 0.9
O J:HOH508 4.5 59.2 1.0
NZ J:LYS17 4.7 69.5 1.0
C3B J:NAP301 4.8 35.1 0.9
CD J:LYS17 4.8 59.0 1.0
O J:HOH498 4.9 50.3 1.0

Magnesium binding site 6 out of 8 in 6ci9

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Magnesium binding site 6 out of 8 in the Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg304

b:66.1
occ:1.00
 O L:HOH422 2.0 66.4 1.0
O L:HOH499 2.1 69.4 1.0
O L:HOH484 2.2 56.0 1.0
OD1 L:ASP33 3.4 49.6 1.0
OD2 L:ASP33 3.8 50.4 1.0
O L:GLY31 3.9 40.8 1.0
CG L:ASP33 4.0 48.4 1.0
CA L:GLY7 4.2 42.2 1.0
N L:GLY7 4.3 41.2 1.0
OE1 L:GLU6 4.4 63.3 1.0
O L:ARG55 4.4 53.3 1.0
NZ L:LYS57 4.5 66.6 1.0
CA L:GLY56 4.6 49.7 1.0
CG L:GLU6 4.7 53.4 1.0
C L:GLY31 4.9 40.9 1.0

Magnesium binding site 7 out of 8 in 6ci9

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Magnesium binding site 7 out of 8 in the Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg304

b:71.5
occ:1.00
 O M:HOH489 2.1 70.6 1.0
OE1 M:GLU6 3.9 68.7 1.0
CG M:GLU6 4.3 59.0 1.0
O M:GLY31 4.5 50.2 1.0
N M:GLY7 4.5 49.1 1.0
CA M:GLY7 4.5 48.8 1.0
OD2 M:ASP33 4.5 55.8 1.0
OD1 M:ASP33 4.6 56.1 1.0
CD M:GLU6 4.6 66.0 1.0
O M:ARG55 5.0 62.3 1.0
CG M:ASP33 5.0 56.3 1.0

Magnesium binding site 8 out of 8 in 6ci9

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Magnesium binding site 8 out of 8 in the Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Rmm Microcompartment-Associated Aminopropanol Dehydrogenase Nadp + Aminoacetone Holo-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg304

b:45.3
occ:1.00
 O3X O:NAP301 1.9 43.8 1.0
O O:HOH509 1.9 44.3 1.0
O O:HOH504 2.0 43.0 1.0
O O:HOH483 2.2 47.8 1.0
O O:HOH436 2.2 37.8 1.0
O O:HOH506 2.3 45.1 1.0
P2B O:NAP301 3.1 42.2 1.0
O1X O:NAP301 3.4 45.1 1.0
O O:HOH516 3.4 42.8 1.0
O2B O:NAP301 3.6 43.8 1.0
C2B O:NAP301 3.7 39.7 1.0
NH2 O:ARG39 4.0 43.0 1.0
O2X O:NAP301 4.3 41.7 1.0
O O:HOH478 4.3 45.7 1.0
C3B O:NAP301 4.3 38.8 1.0
CD O:LYS17 4.5 49.8 1.0
O O:HOH514 4.7 49.1 1.0
C8A O:NAP301 4.8 35.4 1.0
OD2 O:ASP43 5.0 57.7 1.0
C1B O:NAP301 5.0 36.0 1.0

Reference:

E.Mallette, M.S.Kimber. Structure and Kinetics of the S-(+)-1-Amino-2-Propanol Dehydrogenase From the Rmm Microcompartment of Mycobacterium Smegmatis. Biochemistry V. 57 3780 2018.
ISSN: ISSN 1520-4995
PubMed: 29757625
DOI: 10.1021/ACS.BIOCHEM.8B00464
Page generated: Mon Dec 14 22:30:19 2020

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