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Magnesium in PDB 4q15: Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp in Space Group P212121 at 2.35 A

Enzymatic activity of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp in Space Group P212121 at 2.35 A

All present enzymatic activity of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp in Space Group P212121 at 2.35 A:
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 Halofuginone and Amppnp in Space Group P212121 at 2.35 A, PDB code: 4q15 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) 37.33 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.580, 78.090, 167.820, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 21.9

Other elements in 4q15:

The structure of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp in Space Group P212121 at 2.35 A also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 2 atoms

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 Halofuginone and Amppnp in Space Group P212121 at 2.35 A (pdb code 4q15). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp in Space Group P212121 at 2.35 A, PDB code: 4q15:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4q15

Go back to Magnesium Binding Sites List in 4q15
Magnesium binding site 1 out of 2 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp in Space Group P212121 at 2.35 A


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 Halofuginone and Amppnp in Space Group P212121 at 2.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:38.8
occ:1.00
 O2G A:ANP802 1.9 29.9 1.0
O A:HOH925 2.0 41.1 1.0
O A:HOH923 2.0 36.4 1.0
O2B A:ANP802 2.1 31.2 1.0
O A:HOH1008 2.2 34.2 1.0
O A:HOH924 2.3 27.9 1.0
PG A:ANP802 3.2 34.0 1.0
PB A:ANP802 3.2 42.7 1.0
NH1 A:ARG390 3.6 37.8 1.0
O1B A:ANP802 3.6 44.7 1.0
O3G A:ANP802 3.8 42.4 1.0
N3B A:ANP802 3.8 68.9 1.0
N1 A:HFG803 4.0 36.4 1.0
C2 A:HFG803 4.2 37.0 1.0
OE2 A:GLU392 4.3 41.0 1.0
OE2 A:GLU338 4.3 46.9 1.0
NH1 A:ARG401 4.3 35.5 1.0
OE1 A:GLU338 4.4 44.4 1.0
O1G A:ANP802 4.4 36.4 1.0
N7 A:ANP802 4.5 32.2 1.0
O1A A:ANP802 4.5 41.2 1.0
OE1 A:GLU392 4.5 45.6 1.0
O A:HOH952 4.5 48.5 1.0
O3A A:ANP802 4.6 57.4 1.0
CZ A:ARG390 4.7 37.1 1.0
CE1 A:PHE335 4.7 77.8 1.0
CD A:ARG390 4.7 36.4 1.0
C8 A:ANP802 4.7 34.6 1.0
CD A:GLU338 4.8 44.8 1.0
CD A:GLU392 4.9 42.8 1.0

Magnesium binding site 2 out of 2 in 4q15

Go back to Magnesium Binding Sites List in 4q15
Magnesium binding site 2 out of 2 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp in Space Group P212121 at 2.35 A


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 Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp in Space Group P212121 at 2.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:38.1
occ:1.00
 O2G B:ANP802 1.9 47.2 1.0
O B:HOH932 2.0 33.5 1.0
O B:HOH930 2.0 29.5 1.0
O2B B:ANP802 2.1 31.7 1.0
O B:HOH933 2.1 41.5 1.0
O B:HOH931 2.1 36.6 1.0
PG B:ANP802 3.3 43.4 1.0
PB B:ANP802 3.5 39.1 1.0
O3G B:ANP802 3.9 79.0 1.0
N3B B:ANP802 4.0 86.6 1.0
NH1 B:ARG390 4.0 35.1 1.0
N1 B:HFG803 4.1 30.4 1.0
OE2 B:GLU338 4.1 48.8 1.0
OE1 B:GLU338 4.1 46.9 1.0
NZ B:LYS394 4.2 59.0 1.0
O1B B:ANP802 4.2 43.9 1.0
OE1 B:GLU392 4.2 44.9 1.0
NH1 B:ARG401 4.2 36.1 1.0
O B:HOH999 4.2 52.9 1.0
OE2 B:GLU392 4.4 46.1 1.0
O1G B:ANP802 4.4 42.1 1.0
C2 B:HFG803 4.5 32.4 1.0
N7 B:ANP802 4.5 34.6 1.0
CD B:GLU338 4.5 48.1 1.0
O3A B:ANP802 4.6 45.6 1.0
CE1 B:PHE335 4.7 69.0 1.0
CD B:ARG390 4.7 37.2 1.0
CD B:GLU392 4.7 45.3 1.0
CE B:LYS394 4.8 59.0 1.0
CZ B:ARG390 4.9 36.3 1.0
C8 B:ANP802 4.9 35.3 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: Mon Dec 14 19:21:21 2020

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