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 / R_free (%)*	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

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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

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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

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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: Thu Oct 3 15:44:38 2024

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