Magnesium in PDB 7ywm: Crystal Structure of Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp

All present enzymatic activity of Crystal Structure of Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp:
2.7.7.3;

The structure of Crystal Structure of Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp, PDB code: 7ywm was solved by S.E.Thomas, A.G.Coyne, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.85 / 1.62
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	75.827, 125.134, 119.083, 90, 90, 90
R / Rfree (%)	18.6 / 21.1

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp (pdb code 7ywm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp, PDB code: 7ywm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp


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 Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:36.9 occ:1.00 O2B A:ATP201 2.6 25.1 0.8 O A:HOH323 2.8 21.2 1.0 O A:HOH308 2.9 47.3 1.0 NH2 A:ARG90 3.0 34.3 1.0 O A:HOH376 3.3 29.9 1.0 NH1 A:ARG90 3.4 44.1 1.0 C8 A:ATP201 3.6 20.1 0.8 CZ A:ARG90 3.6 44.5 1.0 CB A:SER126 3.7 26.4 1.0 O2A A:ATP201 3.8 18.9 0.8 PB A:ATP201 3.8 23.3 0.8 O3B A:ATP201 4.0 28.4 0.8 O5' A:ATP201 4.1 17.4 0.8 N7 A:ATP201 4.2 24.0 0.8 C3' A:ATP201 4.3 20.3 0.8 PA A:ATP201 4.4 17.8 0.8 CA A:SER126 4.5 18.3 1.0 O3A A:ATP201 4.5 18.6 0.8 C2' A:ATP201 4.6 31.8 0.8 N9 A:ATP201 4.7 20.2 0.8 OG A:SER126 4.8 21.5 1.0 N A:SER127 4.8 18.9 1.0 NE A:ARG90 4.9 33.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp


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 Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:41.2 occ:1.00 O2B B:ATP201 2.1 28.7 0.8 O B:HOH308 2.7 43.1 1.0 O B:HOH314 3.1 33.9 1.0 O B:HOH311 3.1 23.0 1.0 PB B:ATP201 3.4 28.2 0.8 NH1 B:ARG90 3.4 41.7 1.0 O3B B:ATP201 3.5 31.8 0.8 NH2 B:ARG90 3.6 34.2 1.0 O2A B:ATP201 3.9 21.5 0.8 CB B:SER126 4.0 24.3 1.0 CZ B:ARG90 4.0 38.8 1.0 C8 B:ATP201 4.2 24.7 0.8 O3A B:ATP201 4.3 24.5 0.8 O5' B:ATP201 4.3 18.9 0.8 PA B:ATP201 4.4 20.6 0.8 O1B B:ATP201 4.6 37.0 0.8 C3' B:ATP201 4.6 21.8 0.8 CA B:SER126 4.8 18.4 1.0 PG B:ATP201 4.8 42.1 0.8 C2' B:ATP201 4.9 33.3 0.8 N7 B:ATP201 4.9 19.4 0.8 OG B:SER126 4.9 24.5 1.0 O3G B:ATP201 5.0 34.2 0.8

Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp


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 Mycobacterium Abcessus Phosphopantetheine Adenylyltransferase in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:38.6 occ:1.00 O1B C:ATP201 2.7 37.0 1.0 O C:HOH320 2.8 24.1 1.0 NH2 C:ARG90 3.0 43.2 1.0 O C:HOH357 3.3 29.0 1.0 O C:HOH326 3.3 40.3 1.0 C8 C:ATP201 3.6 31.5 1.0 CB C:SER126 3.7 27.5 1.0 O1A C:ATP201 3.8 27.1 1.0 PB C:ATP201 3.9 35.6 1.0 O3B C:ATP201 3.9 41.9 1.0 C2' C:ATP201 3.9 34.6 1.0 O5' C:ATP201 4.1 25.5 1.0 CZ C:ARG90 4.1 49.5 1.0 O C:HOH307 4.1 45.9 1.0 O2' C:ATP201 4.3 37.0 1.0 NH1 C:ARG90 4.3 45.6 1.0 N7 C:ATP201 4.4 26.7 1.0 CA C:SER126 4.4 17.9 1.0 PA C:ATP201 4.4 27.5 1.0 O3A C:ATP201 4.6 32.7 1.0 N9 C:ATP201 4.6 29.7 1.0 O C:HOH339 4.6 44.8 1.0 C3' C:ATP201 4.6 27.7 1.0 N C:SER127 4.8 21.6 1.0 OG C:SER126 4.8 26.7 1.0 C1' C:ATP201 4.9 28.8 1.0

S.E.Thomas, W.J.Mccarthy, J.El Bakali, K.P.Brown, S.Y.Kim, M.Blaszczyk, V.Mendes, C.Abell, R.A.Floto, A.G.Coyne, T.L.Blundell. Structural Characterization of Mycobacterium Abscessus Phosphopantetheine Adenylyl Transferase Ligand Interactions: Implications For Fragment-Based Drug Design. Front Mol Biosci V. 9 80432 2022.
ISSN: ESSN 2296-889X
PubMed: 35712348
DOI: 10.3389/FMOLB.2022.880432