Magnesium in PDB 5y3i: Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide

Protein crystallography data

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide, PDB code: 5y3i was solved by A.K.Marapaka, Y.Zhang, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.436, 109.267, 112.504, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.6

Other elements in 5y3i:

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide (pdb code 5y3i). 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 Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide, PDB code: 5y3i:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5y3i

Go back to Magnesium Binding Sites List in 5y3i
Magnesium binding site 1 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide


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 Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:26.8
occ:1.00
O A:HOH1691 2.0 25.0 1.0
O A:GLY250 2.1 15.5 1.0
O A:HOH1716 2.1 22.7 1.0
O A:HOH1317 2.2 18.4 1.0
C A:GLY250 3.3 17.6 1.0
CA A:GLY250 3.9 18.0 1.0
O A:HOH1424 3.9 18.4 1.0
N A:LEU251 4.3 14.9 1.0
CA A:LEU251 4.6 14.9 1.0
O A:ILE295 4.6 15.2 1.0
O A:HOH1732 4.7 17.9 1.0
CD2 A:HIS297 4.7 19.5 1.0
CA A:ILE296 4.8 13.1 1.0
O A:HOH1546 4.9 19.6 1.0

Magnesium binding site 2 out of 3 in 5y3i

Go back to Magnesium Binding Sites List in 5y3i
Magnesium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide


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 Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:23.2
occ:1.00
O A:HOH1577 2.0 21.2 1.0
O A:HOH1755 2.0 28.0 1.0
O A:HOH1804 2.1 22.9 1.0
O A:HOH1816 2.1 25.1 1.0
O A:HOH1589 2.1 22.8 1.0
O A:HOH1354 2.2 21.3 1.0
OE2 A:GLU957 3.7 17.4 1.0
O A:HOH1719 4.0 32.6 1.0
O A:HOH1416 4.1 22.0 1.0
ND2 A:ASN992 4.1 18.1 1.0
O A:HOH1814 4.2 21.0 1.0
OD2 A:ASP995 4.3 19.9 1.0
O A:HOH1763 4.4 29.5 1.0
O A:HOH1557 4.5 19.0 1.0
CD A:GLU957 4.6 20.3 1.0
O A:HOH1288 4.6 20.1 1.0
CG A:GLU957 4.8 25.6 1.0
CE A:LYS311 5.0 19.2 1.0
O A:HOH1774 5.0 30.3 1.0

Magnesium binding site 3 out of 3 in 5y3i

Go back to Magnesium Binding Sites List in 5y3i
Magnesium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide


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 Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:19.8
occ:1.00
O A:HOH1636 2.0 23.1 1.0
OE2 A:GLU526 2.0 16.8 1.0
O A:HOH1784 2.1 21.7 1.0
O A:HOH1239 2.1 20.0 1.0
O A:HOH1648 2.1 20.2 1.0
O A:HOH1436 2.2 22.2 1.0
CD A:GLU526 3.0 16.3 1.0
OE1 A:GLU526 3.4 12.6 1.0
C3 A:GOL1106 4.0 21.1 1.0
O A:HOH1249 4.1 23.0 1.0
OG1 A:THR492 4.1 17.0 1.0
O A:HOH1439 4.1 19.0 1.0
CB A:THR492 4.3 14.4 1.0
CG A:GLU526 4.4 15.3 1.0
O A:HOH1781 4.4 27.8 1.0
O3 A:GOL1106 4.5 33.5 1.0
OD1 A:ASN527 4.5 16.7 1.0
C2 A:GOL1106 4.7 14.1 1.0
CG2 A:THR492 4.8 15.5 1.0
O2 A:GOL1106 5.0 27.8 1.0

Reference:

A.K.Marapaka, A.Addlagatta. Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido) Pentanamide To Be Published.
Page generated: Mon Dec 14 22:13:01 2020

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