Magnesium in PDB 6s02: Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain - Adp Bound State
Protein crystallography data
The structure of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain - Adp Bound State, PDB code: 6s02
was solved by
I.Vakonakis,
J.Day,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
72.51 /
1.87
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.115,
101.796,
103.310,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.2 /
25.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain - Adp Bound State
(pdb code 6s02). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain - Adp Bound State, PDB code: 6s02:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6s02
Go back to
Magnesium Binding Sites List in 6s02
Magnesium binding site 1 out
of 2 in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain - Adp Bound State
![](/pictures/MG/pdb/s0/6s02-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/s0/6s02-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 Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain - Adp Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg451
b:49.1
occ:1.00
|
O1B
|
A:ADP450
|
2.3
|
50.4
|
1.0
|
O
|
A:HOH599
|
2.4
|
27.4
|
1.0
|
O
|
A:TYR44
|
2.4
|
24.4
|
1.0
|
HA3
|
A:GLY41
|
2.8
|
31.8
|
1.0
|
OD2
|
A:ASP39
|
2.9
|
28.8
|
1.0
|
O
|
A:HOH525
|
2.9
|
42.3
|
1.0
|
O3B
|
A:ADP450
|
3.2
|
40.5
|
1.0
|
PB
|
A:ADP450
|
3.2
|
41.8
|
1.0
|
O
|
A:HOH538
|
3.5
|
45.3
|
1.0
|
C
|
A:TYR44
|
3.5
|
25.1
|
1.0
|
O2A
|
A:ADP450
|
3.6
|
31.8
|
1.0
|
HB2
|
A:TYR44
|
3.7
|
32.3
|
1.0
|
CA
|
A:GLY41
|
3.7
|
26.5
|
1.0
|
CG
|
A:ASP39
|
3.7
|
28.7
|
1.0
|
H
|
A:TYR44
|
3.8
|
30.8
|
1.0
|
O1A
|
A:ADP450
|
3.9
|
36.6
|
1.0
|
HA2
|
A:GLY41
|
3.9
|
31.8
|
1.0
|
PA
|
A:ADP450
|
3.9
|
28.7
|
1.0
|
HA
|
A:SER45
|
4.0
|
33.2
|
1.0
|
O3A
|
A:ADP450
|
4.0
|
41.9
|
1.0
|
OD1
|
A:ASP39
|
4.0
|
30.0
|
1.0
|
O
|
A:HOH585
|
4.1
|
42.5
|
1.0
|
H
|
A:GLY41
|
4.3
|
30.1
|
1.0
|
CA
|
A:TYR44
|
4.3
|
26.1
|
1.0
|
CB
|
A:TYR44
|
4.3
|
26.9
|
1.0
|
N
|
A:TYR44
|
4.4
|
25.6
|
1.0
|
N
|
A:GLY41
|
4.4
|
25.0
|
1.0
|
N
|
A:SER45
|
4.5
|
27.8
|
1.0
|
HB3
|
A:TYR44
|
4.5
|
32.3
|
1.0
|
O2B
|
A:ADP450
|
4.5
|
46.8
|
1.0
|
CA
|
A:SER45
|
4.6
|
27.6
|
1.0
|
H
|
A:THR42
|
4.7
|
31.8
|
1.0
|
C
|
A:GLY41
|
4.7
|
26.4
|
1.0
|
O
|
A:ASP397
|
4.7
|
24.0
|
1.0
|
HB2
|
A:ASP397
|
4.8
|
34.8
|
1.0
|
O
|
A:HOH561
|
4.8
|
21.2
|
1.0
|
H
|
A:THR43
|
4.9
|
29.4
|
1.0
|
HB3
|
A:ASP39
|
4.9
|
31.3
|
1.0
|
HB2
|
A:CYS46
|
4.9
|
31.6
|
1.0
|
N
|
A:THR42
|
5.0
|
26.4
|
1.0
|
CB
|
A:ASP39
|
5.0
|
26.1
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6s02
Go back to
Magnesium Binding Sites List in 6s02
Magnesium binding site 2 out
of 2 in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain - Adp Bound State
![](/pictures/MG/pdb/s0/6s02-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/s0/6s02-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 Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain - Adp Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg452
b:59.9
occ:1.00
|
OD2
|
B:ASP39
|
2.8
|
34.3
|
1.0
|
O3B
|
B:ADP450
|
3.0
|
48.1
|
1.0
|
HA3
|
B:GLY41
|
3.0
|
37.0
|
1.0
|
O2B
|
B:ADP450
|
3.1
|
48.8
|
1.0
|
O
|
B:HOH533
|
3.1
|
36.8
|
1.0
|
O
|
B:TYR44
|
3.1
|
31.1
|
1.0
|
PB
|
B:ADP450
|
3.4
|
48.4
|
1.0
|
O1A
|
B:ADP450
|
3.5
|
50.2
|
1.0
|
CG
|
B:ASP39
|
3.6
|
34.0
|
1.0
|
OD1
|
B:ASP39
|
3.8
|
33.8
|
1.0
|
HA2
|
B:GLY41
|
3.8
|
37.0
|
1.0
|
CA
|
B:GLY41
|
3.9
|
30.8
|
1.0
|
PA
|
B:ADP450
|
3.9
|
45.3
|
1.0
|
O3A
|
B:ADP450
|
4.0
|
50.4
|
1.0
|
O2A
|
B:ADP450
|
4.0
|
46.3
|
1.0
|
H
|
B:TYR44
|
4.2
|
39.9
|
1.0
|
HB2
|
B:TYR44
|
4.2
|
42.9
|
1.0
|
O
|
B:HOH586
|
4.2
|
36.5
|
1.0
|
C
|
B:TYR44
|
4.3
|
31.7
|
1.0
|
H
|
B:THR42
|
4.4
|
38.8
|
1.0
|
HA
|
B:SER45
|
4.5
|
34.1
|
1.0
|
N
|
B:GLY41
|
4.7
|
28.6
|
1.0
|
H
|
B:GLY41
|
4.7
|
34.4
|
1.0
|
HB3
|
B:ASP39
|
4.8
|
38.2
|
1.0
|
C
|
B:GLY41
|
4.8
|
30.2
|
1.0
|
O
|
B:HOH569
|
4.8
|
32.4
|
1.0
|
CB
|
B:ASP39
|
4.9
|
31.8
|
1.0
|
O
|
B:ASP397
|
4.9
|
36.8
|
1.0
|
HA
|
B:ASP397
|
4.9
|
47.1
|
1.0
|
N
|
B:THR42
|
4.9
|
32.3
|
1.0
|
O1B
|
B:ADP450
|
4.9
|
51.3
|
1.0
|
N
|
B:TYR44
|
4.9
|
33.2
|
1.0
|
CB
|
B:TYR44
|
5.0
|
35.7
|
1.0
|
CA
|
B:TYR44
|
5.0
|
33.0
|
1.0
|
|
Reference:
J.Day,
A.Passecker,
H.P.Beck,
I.Vakonakis.
Theplasmodium FALCIPARUMHSP70-X Chaperone Assists the Heat Stress Response of the Malaria Parasite. Faseb J. 1741R 2019.
ISSN: ESSN 1530-6860
PubMed: 31690116
DOI: 10.1096/FJ.201901741R
Page generated: Tue Oct 1 17:35:36 2024
|