Magnesium in PDB 5y1w: Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc

Protein crystallography data

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc, PDB code: 5y1w was solved by A.K.Marapaka, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.67 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.421, 109.205, 112.477, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.6

Other elements in 5y1w:

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc 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 with Magnesium Bound to Active Site Zinc (pdb code 5y1w). 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 with Magnesium Bound to Active Site Zinc, PDB code: 5y1w:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5y1w

Go back to Magnesium Binding Sites List in 5y1w
Magnesium binding site 1 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc


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 with Magnesium Bound to Active Site Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:25.8
occ:1.00
O A:HOH1219 1.9 30.6 1.0
O A:HOH1238 1.9 14.7 1.0
O A:HOH1265 2.1 16.0 1.0
O A:HOH1703 2.1 26.4 1.0
O A:HOH1397 2.2 16.9 1.0
O A:HOH1346 2.4 18.7 1.0
O A:HOH1202 2.7 20.6 1.0
ZN A:ZN1101 3.2 14.8 1.0
OH A:TYR580 3.5 15.6 1.0
O A:ALA461 3.7 15.1 1.0
OE2 A:GLU519 3.8 14.7 1.0
OE1 A:GLU463 4.0 13.2 1.0
OE2 A:GLU497 4.1 16.5 1.0
OE1 A:GLU497 4.3 15.4 1.0
NE2 A:HIS496 4.4 12.3 1.0
O A:HOH1777 4.4 29.3 1.0
OE1 A:GLU519 4.5 13.7 1.0
CD A:GLU519 4.5 14.1 1.0
OE1 A:GLU319 4.5 17.4 1.0
NE2 A:HIS500 4.6 12.7 1.0
CZ A:TYR580 4.7 15.4 1.0
CD A:GLU497 4.7 14.6 1.0
C A:ALA461 4.7 12.1 1.0
CD2 A:HIS496 4.8 14.2 1.0
CE2 A:TYR580 4.9 14.2 1.0
O A:HOH1709 4.9 30.9 1.0
O A:HOH1817 4.9 26.0 1.0

Magnesium binding site 2 out of 3 in 5y1w

Go back to Magnesium Binding Sites List in 5y1w
Magnesium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc


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 with Magnesium Bound to Active Site Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:25.1
occ:1.00
O A:HOH1380 2.0 22.3 1.0
O A:HOH1823 2.1 30.7 1.0
O A:HOH1883 2.1 26.8 1.0
O A:HOH1870 2.1 31.7 1.0
O A:HOH1508 2.1 24.6 1.0
O A:HOH1248 2.2 25.5 1.0
OE2 A:GLU957 3.7 18.2 1.0
ND2 A:ASN992 4.2 19.4 1.0
O A:HOH1381 4.2 27.2 1.0
O A:HOH1891 4.2 23.4 1.0
OD2 A:ASP995 4.2 21.1 1.0
O A:HOH1814 4.3 35.7 1.0
CD A:GLU957 4.5 19.3 1.0
O A:HOH1301 4.5 25.2 1.0
O A:HOH1465 4.6 21.2 1.0
CG A:GLU957 4.8 23.7 1.0
O A:HOH1836 4.9 34.1 1.0
CE A:LYS311 5.0 20.8 1.0

Magnesium binding site 3 out of 3 in 5y1w

Go back to Magnesium Binding Sites List in 5y1w
Magnesium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc


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 with Magnesium Bound to Active Site Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:24.4
occ:1.00
O A:GLY250 2.1 16.3 1.0
O A:HOH1733 2.1 24.3 1.0
O A:HOH1731 2.1 25.1 1.0
C A:GLY250 3.2 16.9 1.0
CA A:GLY250 3.9 18.6 1.0
O A:HOH1434 4.0 20.3 1.0
N A:LEU251 4.3 15.6 1.0
CA A:LEU251 4.6 16.0 1.0
O A:ILE295 4.6 15.4 1.0
O A:HOH1773 4.8 20.3 1.0
CD2 A:HIS297 4.8 23.6 1.0
CA A:ILE296 4.8 15.0 1.0
C A:LEU251 5.0 16.8 1.0

Reference:

A.K.Marapaka, A.Addlagatta. Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc To Be Published.
Page generated: Mon Dec 14 22:12:52 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy