Magnesium in PDB 6jws: Crystal Structure of Plasmodium Falciparum Hppk-Dhps A437G with Pteroate
Protein crystallography data
The structure of Crystal Structure of Plasmodium Falciparum Hppk-Dhps A437G with Pteroate, PDB code: 6jws
was solved by
P.Chitnumsub,
A.Jaruwat,
Y.Yuthavong,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.58 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.909,
136.761,
138.958,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.7 /
23.3
|
Other elements in 6jws:
The structure of Crystal Structure of Plasmodium Falciparum Hppk-Dhps A437G with Pteroate also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Falciparum Hppk-Dhps A437G with Pteroate
(pdb code 6jws). 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 Hppk-Dhps A437G with Pteroate, PDB code: 6jws:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 6jws
Go back to
Magnesium Binding Sites List in 6jws
Magnesium binding site 1 out
of 3 in the Crystal Structure of Plasmodium Falciparum Hppk-Dhps A437G with Pteroate
![](/pictures/MG/pdb/jw/6jws-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/jw/6jws-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 Crystal Structure of Plasmodium Falciparum Hppk-Dhps A437G with Pteroate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg803
b:21.7
occ:1.00
|
O1A
|
A:ATP802
|
1.9
|
98.6
|
1.0
|
OD2
|
A:ASP208
|
2.2
|
30.1
|
1.0
|
OD1
|
A:ASP210
|
2.3
|
32.1
|
1.0
|
O
|
A:HOH954
|
2.3
|
42.0
|
1.0
|
O3G
|
A:ATP802
|
2.4
|
97.5
|
1.0
|
OD1
|
A:ASP208
|
2.4
|
31.2
|
1.0
|
O
|
A:HOH913
|
2.5
|
42.7
|
1.0
|
CG
|
A:ASP208
|
2.6
|
27.4
|
1.0
|
CG
|
A:ASP210
|
3.0
|
31.6
|
1.0
|
OD2
|
A:ASP210
|
3.1
|
31.4
|
1.0
|
PA
|
A:ATP802
|
3.3
|
92.0
|
1.0
|
O2B
|
A:ATP802
|
3.5
|
0.7
|
1.0
|
PG
|
A:ATP802
|
3.6
|
0.0
|
1.0
|
O3B
|
A:ATP802
|
3.7
|
0.9
|
1.0
|
O3A
|
A:ATP802
|
3.8
|
89.8
|
1.0
|
C5'
|
A:ATP802
|
3.9
|
76.4
|
1.0
|
PB
|
A:ATP802
|
3.9
|
0.1
|
1.0
|
O5'
|
A:ATP802
|
4.1
|
87.9
|
1.0
|
CB
|
A:ASP208
|
4.2
|
25.5
|
1.0
|
O1G
|
A:ATP802
|
4.3
|
0.6
|
1.0
|
O
|
A:HOH1010
|
4.3
|
38.8
|
1.0
|
O2A
|
A:ATP802
|
4.4
|
93.9
|
1.0
|
CB
|
A:ASP210
|
4.5
|
28.2
|
1.0
|
NE2
|
A:HIS320
|
4.5
|
26.8
|
1.0
|
O
|
A:HOH984
|
4.7
|
47.8
|
1.0
|
O2G
|
A:ATP802
|
4.8
|
92.7
|
1.0
|
C2
|
A:ATP802
|
5.0
|
34.6
|
1.0
|
N3
|
A:ATP802
|
5.0
|
33.7
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 6jws
Go back to
Magnesium Binding Sites List in 6jws
Magnesium binding site 2 out
of 3 in the Crystal Structure of Plasmodium Falciparum Hppk-Dhps A437G with Pteroate
![](/pictures/MG/pdb/jw/6jws-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/jw/6jws-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 Crystal Structure of Plasmodium Falciparum Hppk-Dhps A437G with Pteroate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg803
b:25.5
occ:1.00
|
O1A
|
B:ATP802
|
2.0
|
87.2
|
1.0
|
O
|
B:HOH942
|
2.3
|
49.8
|
1.0
|
OD1
|
B:ASP210
|
2.3
|
33.2
|
1.0
|
O3G
|
B:ATP802
|
2.4
|
81.2
|
1.0
|
OD1
|
B:ASP208
|
2.4
|
35.3
|
1.0
|
OD2
|
B:ASP208
|
2.7
|
37.8
|
1.0
|
CG
|
B:ASP208
|
2.9
|
34.3
|
1.0
|
O3A
|
B:ATP802
|
2.9
|
79.6
|
1.0
|
PA
|
B:ATP802
|
3.0
|
88.2
|
1.0
|
CG
|
B:ASP210
|
3.1
|
31.6
|
1.0
|
PG
|
B:ATP802
|
3.1
|
96.3
|
1.0
|
OD2
|
B:ASP210
|
3.2
|
33.2
|
1.0
|
O1G
|
B:ATP802
|
3.3
|
95.1
|
1.0
|
O3B
|
B:ATP802
|
3.4
|
82.6
|
1.0
|
PB
|
B:ATP802
|
3.7
|
77.4
|
1.0
|
O5'
|
B:ATP802
|
3.9
|
75.9
|
1.0
|
O2B
|
B:ATP802
|
4.0
|
81.1
|
1.0
|
C5'
|
B:ATP802
|
4.0
|
66.6
|
1.0
|
O2A
|
B:ATP802
|
4.1
|
88.5
|
1.0
|
CB
|
B:ASP208
|
4.4
|
32.9
|
1.0
|
CB
|
B:ASP210
|
4.6
|
29.1
|
1.0
|
O2G
|
B:ATP802
|
4.6
|
81.8
|
1.0
|
O
|
B:HOH974
|
4.6
|
42.6
|
1.0
|
NE2
|
B:HIS320
|
4.6
|
21.8
|
1.0
|
C2
|
B:ATP802
|
5.0
|
30.0
|
1.0
|
N3
|
B:ATP802
|
5.0
|
32.5
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 6jws
Go back to
Magnesium Binding Sites List in 6jws
Magnesium binding site 3 out
of 3 in the Crystal Structure of Plasmodium Falciparum Hppk-Dhps A437G with Pteroate
![](/pictures/MG/pdb/jw/6jws-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/jw/6jws-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 Crystal Structure of Plasmodium Falciparum Hppk-Dhps A437G with Pteroate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg807
b:12.4
occ:1.00
|
O
|
B:HOH910
|
2.2
|
17.4
|
1.0
|
OE2
|
B:GLU692
|
2.2
|
17.6
|
1.0
|
O
|
B:MET648
|
2.2
|
32.4
|
1.0
|
OD1
|
B:ASP689
|
2.3
|
15.5
|
1.0
|
O
|
B:HOH1044
|
2.4
|
42.7
|
1.0
|
CD
|
B:GLU692
|
3.2
|
16.1
|
1.0
|
C
|
B:MET648
|
3.4
|
35.5
|
1.0
|
CG
|
B:ASP689
|
3.4
|
15.3
|
1.0
|
OE1
|
B:GLU692
|
3.6
|
15.1
|
1.0
|
CB
|
B:ASP689
|
3.8
|
14.2
|
1.0
|
CA
|
B:MET648
|
4.0
|
36.9
|
1.0
|
NH2
|
B:ARG608
|
4.1
|
15.7
|
1.0
|
CB
|
B:MET648
|
4.2
|
37.8
|
1.0
|
CA
|
B:ASP689
|
4.3
|
14.4
|
1.0
|
OD2
|
B:ASP689
|
4.5
|
14.8
|
1.0
|
N
|
B:PHE649
|
4.5
|
36.4
|
1.0
|
CG
|
B:GLU692
|
4.6
|
14.6
|
1.0
|
CA
|
B:PHE649
|
4.8
|
42.0
|
1.0
|
CD1
|
B:ILE667
|
4.9
|
19.5
|
1.0
|
O
|
B:HOH915
|
5.0
|
22.2
|
1.0
|
|
Reference:
P.Chitnumsub,
A.Jaruwat,
Y.Talawanich,
K.Noytanom,
B.Liwnaree,
S.Poen,
Y.Yuthavong.
The Structure of Plasmodium Falciparum Hydroxymethyldihydropterin Pyrophosphokinase-Dihydropteroate Synthase Reveals the Basis of Sulfa Resistance. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31883412
DOI: 10.1111/FEBS.15196
Page generated: Mon Dec 14 23:03:30 2020
|