Atomistry » Magnesium » PDB 6e8s-6el0 » 6ee4
Atomistry »
  Magnesium »
    PDB 6e8s-6el0 »
      6ee4 »

Magnesium in PDB 6ee4: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion

Protein crystallography data

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion, PDB code: 6ee4 was solved by N.Drinkwater, S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.29 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.110, 108.860, 118.080, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.9

Other elements in 6ee4:

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion (pdb code 6ee4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion, PDB code: 6ee4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6ee4

Go back to Magnesium Binding Sites List in 6ee4
Magnesium binding site 1 out of 5 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1111

b:23.2
occ:1.00
 O A:HOH1404 2.1 17.3 1.0
O A:HOH2539 2.1 25.2 1.0
O A:HOH1804 2.1 17.2 1.0
O A:HOH2566 2.1 21.0 1.0
O A:HOH1621 2.1 23.3 1.0
O A:HOH2329 2.2 27.0 1.0
OE2 A:GLU957 3.6 13.6 1.0
O A:HOH1817 4.0 24.0 1.0
O A:HOH2690 4.0 43.6 1.0
O A:HOH1723 4.1 26.4 1.0
ND2 A:ASN992 4.2 15.1 1.0
O A:HOH2590 4.2 20.2 1.0
OD2 A:ASP995 4.3 12.9 1.0
O A:HOH2276 4.3 33.5 1.0
O A:HOH2142 4.4 29.4 1.0
CD A:GLU957 4.4 14.5 1.0
O A:HOH1736 4.5 16.5 1.0
CG A:GLU957 4.6 19.6 1.0
O A:HOH1467 4.7 22.2 1.0
NZ A:LYS311 5.0 16.1 1.0
CE A:LYS311 5.0 19.5 1.0
O A:HOH2434 5.0 28.8 1.0

Magnesium binding site 2 out of 5 in 6ee4

Go back to Magnesium Binding Sites List in 6ee4
Magnesium binding site 2 out of 5 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1112

b:29.3
occ:1.00
 O A:HOH2504 2.0 27.4 1.0
O A:HOH1658 2.0 19.2 1.0
O A:HOH2264 2.1 31.5 1.0
O A:HOH1862 2.3 28.5 1.0
O A:HOH2679 2.3 31.9 1.0
O A:HOH1586 2.3 31.0 1.0
OD1 A:ASP438 3.9 21.3 1.0
O A:HOH1576 3.9 19.8 1.0
O A:HOH2534 4.3 38.8 1.0
OD2 A:ASP438 4.3 19.1 1.0
OE1 A:GLU437 4.4 18.8 1.0
O A:HOH2597 4.4 45.4 1.0
O A:HOH2586 4.5 49.1 1.0
CG A:ASP438 4.5 18.4 1.0
OH A:TYR399 4.5 15.4 1.0
CB A:ALA434 4.6 13.9 1.0
CD A:LYS402 4.6 19.5 1.0
CG A:LYS402 4.9 20.6 1.0
CE A:LYS402 5.0 24.0 1.0
O A:HOH2183 5.0 35.8 1.0

Magnesium binding site 3 out of 5 in 6ee4

Go back to Magnesium Binding Sites List in 6ee4
Magnesium binding site 3 out of 5 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1113

b:19.1
occ:0.70
 O A:HOH2461 2.0 31.0 1.0
O A:HOH1699 2.1 20.2 1.0
O A:HOH2069 2.1 28.8 1.0
OE2 A:GLU526 2.1 15.3 0.7
O A:HOH1910 2.2 66.5 1.0
O A:HOH1856 2.2 26.6 1.0
CD A:GLU526 3.1 15.3 0.7
CG2 A:THR492 3.1 9.5 0.5
OE1 A:GLU526 3.4 8.1 0.3
OE1 A:GLU526 3.4 6.4 0.7
CD A:GLU526 4.0 10.4 0.3
O A:HOH1842 4.1 21.0 1.0
O4 A:PO41109 4.1 43.5 0.8
O A:HOH1236 4.2 38.2 1.0
O A:HOH1732 4.2 18.4 1.0
OG1 A:THR492 4.3 11.3 0.5
CB A:THR492 4.3 12.9 0.5
CB A:THR492 4.4 12.5 0.5
OG1 A:THR492 4.4 15.3 0.5
OE2 A:GLU526 4.4 10.0 0.3
CG A:GLU526 4.4 13.5 0.7
O3 A:PO41109 4.5 42.4 0.8
OD1 A:ASN527 4.6 21.6 1.0
O A:HOH1411 4.8 35.2 1.0
P A:PO41109 4.9 33.8 0.8
CG2 A:THR492 4.9 12.4 0.5
O A:HOH2224 4.9 45.2 1.0
CG A:GLU526 4.9 7.9 0.3
O A:HOH2087 5.0 26.5 1.0

Magnesium binding site 4 out of 5 in 6ee4

Go back to Magnesium Binding Sites List in 6ee4
Magnesium binding site 4 out of 5 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1114

b:15.7
occ:0.80
 O A:HOH2014 2.0 18.6 1.0
O A:GLY250 2.0 17.0 1.0
O A:HOH2388 2.1 19.3 1.0
O A:HOH1661 2.1 16.3 1.0
O A:HOH1819 2.2 16.5 1.0
C A:GLY250 3.1 13.0 1.0
CA A:GLY250 3.8 13.2 1.0
O A:HOH1646 4.1 13.1 1.0
O A:HOH1239 4.2 26.5 1.0
N A:LEU251 4.2 16.4 1.0
O A:HOH1382 4.3 23.9 1.0
CD2 A:HIS297 4.3 12.4 1.0
O A:HOH2392 4.3 21.9 1.0
O A:HOH2208 4.5 22.1 1.0
CA A:LEU251 4.5 12.0 1.0
O A:ILE295 4.6 14.1 1.0
O A:HOH2206 4.6 12.3 1.0
O4 A:PO41108 4.7 80.8 1.0
C A:LEU251 4.8 14.7 1.0
CA A:ILE296 4.9 12.9 1.0
N A:LYS252 4.9 14.2 1.0

Magnesium binding site 5 out of 5 in 6ee4

Go back to Magnesium Binding Sites List in 6ee4
Magnesium binding site 5 out of 5 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1115

b:29.0
occ:1.00
 OD1 A:ASN1083 2.0 18.1 1.0
O A:HOH1680 2.1 29.5 1.0
O A:HOH2160 2.1 29.4 1.0
O A:HOH1778 2.2 21.4 1.0
O A:HOH1366 2.2 21.0 1.0
O A:HOH2554 2.5 41.3 1.0
CG A:ASN1083 3.1 17.9 1.0
O A:HOH2506 3.4 47.2 1.0
CA A:ASN1083 3.9 19.0 1.0
CB A:ASN1083 3.9 21.2 1.0
O A:HOH2472 3.9 32.5 1.0
ND2 A:ASN1083 4.1 20.5 1.0
CG A:GLU679 4.2 26.9 1.0
O A:HOH2112 4.2 22.8 1.0
O A:ARG1080 4.3 14.3 1.0
O A:HOH2337 4.4 38.1 1.0
O A:PRO558 4.4 12.4 1.0
O A:HOH2683 4.5 55.8 1.0
CD A:GLU679 4.6 43.4 1.0
O A:HOH1223 4.6 43.6 1.0
CB A:PRO558 4.7 9.8 1.0
OE2 A:GLU679 4.7 45.9 1.0
N A:ASN1083 4.7 13.9 1.0
C A:ASN1083 4.8 26.9 1.0

Reference:

N.B.Vinh, N.Drinkwater, T.R.Malcolm, M.Kassiou, L.Lucantoni, P.M.Grin, G.S.Butler, S.Duffy, C.M.Overall, V.M.Avery, P.J.Scammells, S.Mcgowan. Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. V. 62 622 2019.
ISSN: ISSN 1520-4804
PubMed: 30537832
DOI: 10.1021/ACS.JMEDCHEM.8B01310
Page generated: Mon Sep 30 23:53:45 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy