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:
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
|