Magnesium in PDB 7yy3: Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7

Enzymatic activity of Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7

All present enzymatic activity of Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7:
2.7.7.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7, PDB code: 7yy3 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) 57.05 / 1.54
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 75.931, 125.405, 119.364, 90, 90, 90
R / Rfree (%) 21 / 23.6

Other elements in 7yy3:

The structure of Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7 also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7 (pdb code 7yy3). 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 Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7, PDB code: 7yy3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7yy3

Go back to Magnesium Binding Sites List in 7yy3
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7


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 Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:30.0
occ:1.00
 N A:SER127 3.2 20.4 1.0
O A:HOH377 3.3 29.0 1.0
NE2 A:HIS17 3.3 22.4 1.0
O A:HOH308 3.4 24.9 1.0
CE1 A:HIS17 3.6 21.3 1.0
CA A:SER126 3.7 21.2 1.0
OG A:SER127 3.7 25.9 1.0
CB A:SER126 3.8 24.6 1.0
C A:SER126 4.0 22.6 1.0
NH1 A:ARG90 4.0 35.0 1.0
CB A:SER127 4.1 22.9 1.0
O A:HOH393 4.2 26.9 1.0
CA A:SER127 4.2 23.0 1.0
CD2 A:HIS17 4.6 20.6 1.0
ND1 A:HIS17 4.8 19.3 1.0

Magnesium binding site 2 out of 3 in 7yy3

Go back to Magnesium Binding Sites List in 7yy3
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7


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 Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:30.0
occ:1.00
 N B:SER127 3.3 22.1 1.0
O B:HOH367 3.3 30.2 1.0
NE2 B:HIS17 3.3 23.6 1.0
O B:HOH315 3.5 25.1 1.0
O B:HOH379 3.5 46.1 1.0
CE1 B:HIS17 3.6 21.1 1.0
CA B:SER126 3.7 21.3 1.0
OG B:SER127 3.7 23.9 1.0
CB B:SER126 3.8 21.4 1.0
C B:SER126 4.0 22.2 1.0
CB B:SER127 4.0 21.1 1.0
NH2 B:ARG90 4.1 27.9 0.5
CA B:SER127 4.3 20.9 1.0
O B:HOH372 4.4 24.0 1.0
CD2 B:HIS17 4.6 22.7 1.0
ND1 B:HIS17 4.9 21.8 1.0
O B:HOH342 4.9 30.7 1.0

Magnesium binding site 3 out of 3 in 7yy3

Go back to Magnesium Binding Sites List in 7yy3
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7


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 Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:30.0
occ:1.00
 O C:HOH373 3.3 28.5 1.0
N C:SER127 3.3 25.4 1.0
NE2 C:HIS17 3.4 24.2 1.0
O C:HOH309 3.5 28.7 1.0
CE1 C:HIS17 3.6 23.8 1.0
CA C:SER126 3.8 23.6 1.0
OG C:SER127 3.8 27.8 1.0
CB C:SER126 3.9 27.7 1.0
C C:SER126 4.0 23.9 1.0
NH2 C:ARG90 4.0 33.1 0.5
CB C:SER127 4.1 24.4 1.0
O C:HOH371 4.3 24.0 1.0
CA C:SER127 4.3 23.2 1.0
CD2 C:HIS17 4.6 21.8 1.0
ND1 C:HIS17 4.9 22.3 1.0

Reference:

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
Page generated: Fri Apr 7 03:35:51 2023

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