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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

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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

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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

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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: Wed Aug 13 05:41:05 2025

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