Magnesium in PDB 6ee3: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) and Catalytic Zinc Ion
Protein crystallography data
The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) and Catalytic Zinc Ion, PDB code: 6ee3
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)
|
46.40 /
1.82
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.960,
108.601,
118.160,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.1 /
19.6
|
Other elements in 6ee3:
The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) 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 (6K) and Catalytic Zinc Ion
(pdb code 6ee3). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) and Catalytic Zinc Ion, PDB code: 6ee3:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6ee3
Go back to
Magnesium Binding Sites List in 6ee3
Magnesium binding site 1 out
of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) and Catalytic Zinc Ion
![](/pictures/MG/pdb/ee/6ee3-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/ee/6ee3-MG-sphere_01_stereo.jpg) 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 (6K) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1106
b:16.3
occ:1.00
|
O
|
A:GLY250
|
2.0
|
9.8
|
1.0
|
O
|
A:HOH1679
|
2.1
|
12.6
|
1.0
|
O
|
A:HOH1457
|
2.1
|
10.1
|
1.0
|
O
|
A:HOH1777
|
2.1
|
17.4
|
1.0
|
O
|
A:HOH1944
|
2.2
|
15.1
|
1.0
|
O
|
A:HOH1671
|
2.2
|
10.6
|
1.0
|
C
|
A:GLY250
|
3.2
|
9.5
|
1.0
|
CA
|
A:GLY250
|
3.8
|
9.8
|
1.0
|
O
|
A:HOH2294
|
3.9
|
16.1
|
1.0
|
O
|
A:HOH1481
|
4.2
|
8.7
|
1.0
|
N
|
A:LEU251
|
4.2
|
10.2
|
1.0
|
ND1
|
A:HIS297
|
4.2
|
14.0
|
1.0
|
O
|
A:HOH2139
|
4.3
|
21.5
|
1.0
|
O
|
A:HOH1366
|
4.3
|
22.9
|
1.0
|
O
|
A:ILE295
|
4.4
|
10.1
|
1.0
|
O
|
A:HOH2103
|
4.5
|
8.7
|
1.0
|
CA
|
A:LEU251
|
4.5
|
10.3
|
1.0
|
CA
|
A:ILE296
|
4.7
|
11.0
|
1.0
|
C
|
A:LEU251
|
4.8
|
11.7
|
1.0
|
CE1
|
A:HIS297
|
4.8
|
15.6
|
1.0
|
N
|
A:LYS252
|
4.9
|
10.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6ee3
Go back to
Magnesium Binding Sites List in 6ee3
Magnesium binding site 2 out
of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) and Catalytic Zinc Ion
![](/pictures/MG/pdb/ee/6ee3-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/ee/6ee3-MG-sphere_02_stereo.jpg) 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 (6K) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1107
b:27.4
occ:1.00
|
O
|
A:HOH2343
|
2.0
|
28.1
|
1.0
|
O
|
A:HOH1576
|
2.1
|
12.9
|
1.0
|
O
|
A:HOH2129
|
2.1
|
21.7
|
1.0
|
O
|
A:HOH1922
|
2.2
|
19.9
|
1.0
|
O
|
A:HOH2472
|
2.2
|
35.0
|
1.0
|
O
|
A:HOH1296
|
2.4
|
22.1
|
1.0
|
OD1
|
A:ASP438
|
3.9
|
18.8
|
1.0
|
O
|
A:HOH1434
|
4.0
|
15.1
|
1.0
|
O
|
A:HOH2157
|
4.1
|
51.3
|
1.0
|
OD2
|
A:ASP438
|
4.1
|
19.3
|
1.0
|
OE1
|
A:GLU437
|
4.4
|
14.7
|
1.0
|
CG
|
A:ASP438
|
4.4
|
18.1
|
1.0
|
OH
|
A:TYR399
|
4.5
|
12.0
|
1.0
|
CB
|
A:ALA434
|
4.5
|
9.8
|
1.0
|
CD
|
A:LYS402
|
4.6
|
14.2
|
1.0
|
O
|
A:HOH2410
|
4.7
|
41.0
|
1.0
|
CE
|
A:LYS402
|
4.9
|
16.2
|
1.0
|
CG
|
A:LYS402
|
4.9
|
15.3
|
1.0
|
CA
|
A:ALA434
|
5.0
|
10.6
|
1.0
|
O
|
A:HOH2119
|
5.0
|
30.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6ee3
Go back to
Magnesium Binding Sites List in 6ee3
Magnesium binding site 3 out
of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) and Catalytic Zinc Ion
![](/pictures/MG/pdb/ee/6ee3-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/ee/6ee3-MG-sphere_03_stereo.jpg) 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 (6K) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1108
b:31.5
occ:1.00
|
O
|
A:HOH2382
|
2.1
|
21.2
|
1.0
|
O
|
A:HOH2341
|
2.2
|
23.6
|
1.0
|
O
|
A:HOH1386
|
2.2
|
21.6
|
1.0
|
O
|
A:HOH1793
|
2.2
|
14.7
|
1.0
|
O
|
A:HOH2211
|
2.3
|
24.0
|
1.0
|
O
|
A:HOH1279
|
2.3
|
17.1
|
1.0
|
OE2
|
A:GLU957
|
3.7
|
13.7
|
1.0
|
O
|
A:HOH2188
|
4.0
|
32.8
|
1.0
|
O
|
A:HOH1733
|
4.1
|
28.1
|
1.0
|
O
|
A:HOH1232
|
4.1
|
21.3
|
1.0
|
ND2
|
A:ASN992
|
4.2
|
14.5
|
1.0
|
O
|
A:HOH2378
|
4.2
|
22.5
|
1.0
|
OD2
|
A:ASP995
|
4.3
|
10.4
|
1.0
|
O
|
A:HOH2131
|
4.3
|
24.1
|
1.0
|
CD
|
A:GLU957
|
4.4
|
15.8
|
1.0
|
O
|
A:HOH1749
|
4.5
|
14.1
|
1.0
|
CG
|
A:GLU957
|
4.6
|
20.0
|
1.0
|
O
|
A:HOH1280
|
4.7
|
19.5
|
1.0
|
CE
|
A:LYS311
|
4.9
|
13.9
|
1.0
|
O
|
A:HOH2305
|
4.9
|
32.6
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6ee3
Go back to
Magnesium Binding Sites List in 6ee3
Magnesium binding site 4 out
of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) and Catalytic Zinc Ion
![](/pictures/MG/pdb/ee/6ee3-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/ee/6ee3-MG-sphere_04_stereo.jpg) 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 (6K) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1109
b:29.0
occ:1.00
|
OD1
|
A:ASN1083
|
2.0
|
14.3
|
1.0
|
O
|
A:HOH1962
|
2.0
|
26.2
|
1.0
|
O
|
A:HOH1332
|
2.0
|
25.8
|
1.0
|
O
|
A:HOH2311
|
2.1
|
32.7
|
1.0
|
O
|
A:HOH1740
|
2.3
|
13.8
|
1.0
|
O
|
A:HOH1271
|
2.3
|
14.8
|
1.0
|
O
|
A:HOH2323
|
3.1
|
25.1
|
1.0
|
CG
|
A:ASN1083
|
3.2
|
14.1
|
1.0
|
O
|
A:HOH2329
|
3.6
|
29.1
|
1.0
|
CA
|
A:ASN1083
|
3.9
|
15.6
|
1.0
|
CB
|
A:ASN1083
|
4.0
|
14.4
|
1.0
|
CG
|
A:GLU679
|
4.0
|
39.1
|
1.0
|
ND2
|
A:ASN1083
|
4.2
|
16.6
|
1.0
|
O
|
A:ARG1080
|
4.3
|
13.2
|
1.0
|
O
|
A:PRO558
|
4.4
|
11.7
|
1.0
|
O
|
A:HOH1940
|
4.5
|
17.2
|
1.0
|
CD
|
A:GLU679
|
4.5
|
49.5
|
1.0
|
O
|
A:HOH1204
|
4.6
|
45.6
|
1.0
|
CB
|
A:PRO558
|
4.7
|
7.6
|
1.0
|
O
|
A:HOH1876
|
4.8
|
40.3
|
1.0
|
N
|
A:ASN1083
|
4.8
|
11.7
|
1.0
|
O
|
A:HOH2454
|
4.8
|
37.0
|
1.0
|
C
|
A:ASN1083
|
4.8
|
24.0
|
1.0
|
OE2
|
A:GLU679
|
4.8
|
50.9
|
1.0
|
CB
|
A:GLU679
|
4.9
|
29.4
|
1.0
|
OE1
|
A:GLU679
|
5.0
|
55.7
|
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 23:53:41 2024
|