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Magnesium in PDB 8gju: Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp

Enzymatic activity of Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp

All present enzymatic activity of Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp:
5.4.99.2;

Protein crystallography data

The structure of Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp, PDB code: 8gju was solved by R.M.Mascarenhas, M.Ruetz, H.Gouda, M.Yaw, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.62 / 2.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.806, 221.872, 121.824, 90, 105.53, 90
R / Rfree (%) 22.9 / 27.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp (pdb code 8gju). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp, PDB code: 8gju:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8gju

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:83.5
occ:1.00
 O1B D:GDP501 2.1 52.9 1.0
OD1 D:ASP193 2.1 83.4 1.0
OG D:SER157 2.1 61.9 1.0
OE2 D:GLU242 2.1 60.4 1.0
O D:HOH601 2.1 68.2 1.0
O D:HOH603 2.2 69.2 1.0
CG D:ASP193 3.1 75.9 1.0
PB D:GDP501 3.1 55.4 1.0
CD D:GLU242 3.3 60.2 1.0
O2B D:GDP501 3.3 48.4 1.0
CB D:SER157 3.5 55.5 1.0
OD2 D:ASP193 3.6 65.6 1.0
OE1 D:GLU242 3.8 72.0 1.0
N D:SER157 3.9 54.7 1.0
O3A D:GDP501 4.0 39.3 1.0
O2A D:GDP501 4.0 64.2 1.0
CB D:ASP193 4.1 68.2 1.0
CA D:SER157 4.2 51.1 1.0
O3B D:GDP501 4.3 52.9 1.0
PA D:GDP501 4.4 53.5 1.0
CA D:ASP193 4.4 54.7 1.0
CG D:GLU242 4.5 50.4 1.0
O D:GLY192 4.7 58.3 1.0
CB D:LYS156 4.8 48.3 1.0
CE D:LYS156 4.8 53.8 1.0
OD1 D:ASP180 4.9 82.4 1.0
C D:LYS156 4.9 43.2 1.0

Magnesium binding site 2 out of 4 in 8gju

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:70.2
occ:1.00
 OD1 F:ASP193 2.0 66.9 1.0
O1B F:GDP601 2.1 57.9 1.0
OE2 F:GLU242 2.1 68.2 1.0
OG F:SER157 2.1 59.8 1.0
O F:HOH702 2.1 56.5 1.0
CG F:ASP193 3.1 68.8 1.0
PB F:GDP601 3.2 55.0 1.0
CD F:GLU242 3.2 58.8 1.0
CB F:SER157 3.4 53.8 1.0
O3B F:GDP601 3.4 45.6 1.0
OE1 F:GLU242 3.8 58.1 1.0
OD2 F:ASP193 3.9 74.0 1.0
CB F:ASP193 4.0 61.9 1.0
N F:SER157 4.1 56.2 1.0
O3A F:GDP601 4.2 38.5 1.0
CA F:ASP193 4.3 65.6 1.0
O1A F:GDP601 4.3 54.2 1.0
CA F:SER157 4.3 50.9 1.0
CG F:GLU242 4.4 53.0 1.0
OD2 F:ASP180 4.5 85.7 1.0
O2B F:GDP601 4.5 52.6 1.0
PA F:GDP601 4.7 61.2 1.0
NZ F:LYS156 4.7 49.2 1.0
OD1 F:ASP180 4.9 74.9 1.0
N F:ASP193 4.9 71.3 1.0
CB F:LYS156 4.9 51.5 1.0

Magnesium binding site 3 out of 4 in 8gju

Go back to Magnesium Binding Sites List in 8gju
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:61.2
occ:1.00
 O2B A:GDP501 2.1 47.0 1.0
OD1 A:ASP193 2.1 62.7 1.0
OG A:SER157 2.1 61.3 1.0
OE2 A:GLU242 2.1 53.2 1.0
O A:HOH602 2.2 63.0 1.0
CG A:ASP193 3.0 63.4 1.0
CD A:GLU242 3.1 47.7 1.0
PB A:GDP501 3.2 63.9 1.0
O A:HOH603 3.4 43.6 1.0
CB A:SER157 3.5 59.5 1.0
OE1 A:GLU242 3.6 47.9 1.0
O1B A:GDP501 3.6 45.8 1.0
OD2 A:ASP193 3.6 57.2 1.0
CB A:ASP193 3.9 55.8 1.0
N A:SER157 3.9 49.8 1.0
CA A:SER157 4.2 43.2 1.0
O3A A:GDP501 4.2 37.2 1.0
CA A:ASP193 4.2 46.8 1.0
O3B A:GDP501 4.4 59.2 1.0
OD1 A:ASP180 4.4 61.8 1.0
CG A:GLU242 4.4 43.2 1.0
O1A A:GDP501 4.6 56.8 1.0
PA A:GDP501 4.7 68.9 1.0
CB A:LYS156 4.7 37.3 1.0
NZ A:LYS156 4.8 29.7 1.0
O A:GLY192 4.8 45.4 1.0
C A:LYS156 4.9 46.7 1.0
N A:ASP193 5.0 53.4 1.0

Magnesium binding site 4 out of 4 in 8gju

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Methylmalonyl-Coa Mutase (Mmut) in Complex with Methylmalonic Acidemia Type A Protein (Mmaa), Coenzyme A, and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:68.2
occ:1.00
 OD1 B:ASP193 2.0 64.5 1.0
OG B:SER157 2.1 48.2 1.0
OE2 B:GLU242 2.1 49.4 1.0
O2B B:GDP501 2.1 51.9 1.0
O B:HOH603 2.1 64.4 1.0
O B:HOH602 2.8 55.2 1.0
CG B:ASP193 3.1 57.6 1.0
CB B:SER157 3.2 49.6 1.0
CD B:GLU242 3.2 45.1 1.0
PB B:GDP501 3.2 48.1 1.0
O3B B:GDP501 3.5 42.5 1.0
OE1 B:GLU242 3.7 44.9 1.0
N B:SER157 3.7 46.4 1.0
OD2 B:ASP193 3.8 67.2 1.0
CB B:ASP193 4.0 39.5 1.0
CA B:SER157 4.0 43.8 1.0
CA B:ASP193 4.2 52.5 1.0
O3A B:GDP501 4.3 32.6 1.0
O1B B:GDP501 4.3 33.0 1.0
CG B:GLU242 4.4 45.3 1.0
O B:HOH604 4.6 41.4 1.0
CB B:LYS156 4.7 35.5 1.0
O B:GLY192 4.7 60.0 1.0
NZ B:LYS156 4.8 38.8 1.0
PA B:GDP501 4.8 85.0 1.0
C B:LYS156 4.8 43.3 1.0
CE B:LYS156 4.8 46.2 1.0
O2A B:GDP501 4.9 48.1 1.0
N B:ASP193 5.0 57.7 1.0
OD1 B:ASP180 5.0 60.2 1.0

Reference:

R.Mascarenhas, M.Ruetz, H.Gouda, N.Heitman, M.Yaw, R.Banerjee. Architecture of the Human G-Protein-Methylmalonyl-Coa Mutase Nanoassembly For B 12 Delivery and Repair. Nat Commun V. 14 4332 2023.
ISSN: ESSN 2041-1723
PubMed: 37468522
DOI: 10.1038/S41467-023-40077-4
Page generated: Thu Dec 28 09:06:22 2023

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