Magnesium in PDB 4wi1: Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506

Enzymatic activity of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506

All present enzymatic activity of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506:
6.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506, PDB code: 4wi1 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	40.29 / 1.65
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	148.180, 91.340, 110.910, 90.00, 129.53, 90.00
*R / R_free (%)*	16.2 / 18.8

Other elements in 4wi1:

The structure of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 also contains other interesting chemical elements:

Fluorine	(F)	10 atoms
Chlorine	(Cl)	1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 (pdb code 4wi1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506, PDB code: 4wi1:

Magnesium binding site 1 out of 1 in 4wi1

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Magnesium Binding Sites List in 4wi1

Magnesium binding site 1 out of 1 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506

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 Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg809 b:35.8 occ:1.00	NE2	A:GLN384	2.7	12.6	0.5
	CD	A:GLN384	2.8	24.3	0.5
	OG1	A:THR362	2.8	21.3	1.0
	OE1	A:GLN384	2.8	15.0	0.5
	OE1	A:GLN384	2.9	18.6	0.5
	ND2	A:ASN386	3.2	27.3	1.0
	CD	A:GLU409	3.4	20.3	0.6
	OE2	A:GLU409	3.4	19.2	0.6
	CG2	A:THR362	3.5	19.1	1.0
	CD	A:GLN384	3.5	15.9	0.5
	CB	A:THR362	3.5	18.3	1.0
	CG	A:GLU409	3.6	16.2	0.6
	CB	A:GLN384	3.6	19.8	0.5
	CG	A:GLN384	3.6	27.8	0.5
	CG	A:GLN384	3.6	15.3	0.5
	CB	A:GLN384	3.7	16.9	0.5
	OD1	A:ASN386	3.9	23.2	1.0
	OE1	A:GLU409	3.9	18.3	0.6
	CG	A:ASN386	4.0	23.1	1.0
	CE2	A:PHE319	4.2	31.0	1.0
	OE1	A:GLU409	4.2	20.8	0.4
	CE	A:MET364	4.2	18.8	1.0
	CZ	A:PHE319	4.3	26.0	1.0
	O	A:HOH1042	4.5	31.7	1.0
	O	A:PHE316	4.6	18.2	1.0
	NE2	A:GLN384	4.7	10.4	0.5
	NE2	A:HIS411	4.7	19.2	1.0
	CB	A:PHE316	4.7	15.9	1.0
	CB	A:GLU409	4.9	14.6	0.4
	CA	A:THR362	5.0	16.1	1.0

Reference:

S.Nakazawa Hewitt, D.M.Dranow, B.G.Horst, J.A.Abendroth, B.Forte, I.Hallyburton, C.Jansen, B.Baragana, R.Choi, K.L.Rivas, M.A.Hulverson, M.Dumais, T.E.Edwards, D.D.Lorimer, A.H.Fairlamb, D.W.Gray, K.D.Read, A.M.Lehane, K.Kirk, P.J.Myler, A.Wernimont, C.S.Walpole, R.Stacy, L.K.Barrett, I.H.Gilbert, W.C.Van Voorhis. Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium Falciparum Drug Target, Prolyl-Trna-Synthetase. Acs Infect Dis. 2016.
ISSN: ESSN 2373-8227
PubMed: 27798837
DOI: 10.1021/ACSINFECDIS.6B00078

Page generated: Tue Aug 20 13:51:17 2024

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