Magnesium in PDB 5ksz: Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State
Protein crystallography data
The structure of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State, PDB code: 5ksz
was solved by
J.L.Klosowiak,
P.J.Focia,
S.E.Rice,
D.M.Freymann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.68 /
2.50
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.180,
74.180,
218.859,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.1 /
26.6
|
Other elements in 5ksz:
The structure of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State
(pdb code 5ksz). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State, PDB code: 5ksz:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 5ksz
Go back to
Magnesium Binding Sites List in 5ksz
Magnesium binding site 1 out
of 2 in the Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg701
b:52.6
occ:1.00
|
OD1
|
A:ASP199
|
2.0
|
77.7
|
1.0
|
O
|
A:HOH804
|
2.0
|
67.5
|
1.0
|
OE1
|
A:GLU208
|
2.1
|
57.8
|
1.0
|
OD1
|
A:ASP201
|
2.1
|
56.4
|
1.0
|
O
|
A:THR203
|
2.1
|
49.1
|
1.0
|
OD1
|
A:ASP197
|
2.1
|
69.2
|
1.0
|
CD
|
A:GLU208
|
3.0
|
64.7
|
1.0
|
CG
|
A:ASP199
|
3.0
|
78.0
|
1.0
|
CG
|
A:ASP201
|
3.2
|
73.4
|
1.0
|
OE2
|
A:GLU208
|
3.2
|
78.9
|
1.0
|
CG
|
A:ASP197
|
3.3
|
44.2
|
1.0
|
C
|
A:THR203
|
3.4
|
67.7
|
1.0
|
OD2
|
A:ASP199
|
3.4
|
80.4
|
1.0
|
OD2
|
A:ASP201
|
3.6
|
79.8
|
1.0
|
OD2
|
A:ASP197
|
4.1
|
56.5
|
1.0
|
N
|
A:ASN205
|
4.1
|
71.4
|
1.0
|
CA
|
A:LEU204
|
4.2
|
62.6
|
1.0
|
N
|
A:LEU204
|
4.2
|
67.6
|
1.0
|
CB
|
A:ASP197
|
4.2
|
28.6
|
1.0
|
CA
|
A:ASP197
|
4.2
|
43.6
|
1.0
|
N
|
A:ASP201
|
4.3
|
68.4
|
1.0
|
N
|
A:THR203
|
4.3
|
53.7
|
1.0
|
CB
|
A:ASP199
|
4.3
|
80.0
|
1.0
|
N
|
A:ASP199
|
4.4
|
58.9
|
1.0
|
CA
|
A:THR203
|
4.4
|
64.5
|
1.0
|
CB
|
A:ASP201
|
4.4
|
70.1
|
1.0
|
CG
|
A:GLU208
|
4.4
|
61.3
|
1.0
|
OG1
|
A:THR203
|
4.4
|
76.5
|
1.0
|
ND2
|
A:ASN205
|
4.5
|
76.1
|
1.0
|
N
|
A:ASN200
|
4.5
|
65.3
|
1.0
|
CG
|
A:ASN205
|
4.5
|
67.9
|
1.0
|
C
|
A:ASP197
|
4.5
|
64.7
|
1.0
|
OD1
|
A:ASN205
|
4.7
|
59.0
|
1.0
|
N
|
A:GLN198
|
4.7
|
65.9
|
1.0
|
C
|
A:LEU204
|
4.7
|
70.3
|
1.0
|
CA
|
A:ASP199
|
4.7
|
66.7
|
1.0
|
CB
|
A:GLU208
|
4.8
|
67.5
|
1.0
|
CA
|
A:ASP201
|
4.8
|
68.2
|
1.0
|
C
|
A:ASP199
|
4.8
|
69.7
|
1.0
|
N
|
A:GLY202
|
4.9
|
49.9
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 5ksz
Go back to
Magnesium Binding Sites List in 5ksz
Magnesium binding site 2 out
of 2 in the Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg702
b:65.0
occ:1.00
|
OD1
|
A:ASP319
|
2.0
|
67.6
|
1.0
|
O
|
A:ALA323
|
2.1
|
63.0
|
1.0
|
OE1
|
A:GLU328
|
2.1
|
61.7
|
1.0
|
OD1
|
A:ASP317
|
2.1
|
61.8
|
1.0
|
OD1
|
A:ASP321
|
2.1
|
58.4
|
1.0
|
O
|
A:HOH801
|
2.1
|
55.1
|
1.0
|
CG
|
A:ASP319
|
2.8
|
66.9
|
1.0
|
CD
|
A:GLU328
|
2.9
|
64.1
|
1.0
|
OD2
|
A:ASP319
|
2.9
|
74.4
|
1.0
|
OE2
|
A:GLU328
|
3.0
|
63.7
|
1.0
|
CG
|
A:ASP321
|
3.1
|
58.8
|
1.0
|
C
|
A:ALA323
|
3.3
|
53.4
|
1.0
|
CG
|
A:ASP317
|
3.3
|
56.5
|
1.0
|
OD2
|
A:ASP321
|
3.5
|
66.9
|
1.0
|
CA
|
A:ASP317
|
4.0
|
56.9
|
1.0
|
N
|
A:ALA323
|
4.1
|
69.7
|
1.0
|
N
|
A:LEU324
|
4.1
|
54.2
|
1.0
|
CA
|
A:LEU324
|
4.1
|
51.3
|
1.0
|
CB
|
A:ASP317
|
4.2
|
50.6
|
1.0
|
CA
|
A:ALA323
|
4.2
|
53.5
|
1.0
|
OD2
|
A:ASP317
|
4.2
|
63.0
|
1.0
|
CB
|
A:ASP319
|
4.3
|
56.8
|
1.0
|
N
|
A:SER325
|
4.3
|
53.8
|
1.0
|
CG
|
A:GLU328
|
4.3
|
45.0
|
1.0
|
N
|
A:ASP321
|
4.3
|
67.1
|
1.0
|
C
|
A:ASP317
|
4.4
|
60.1
|
1.0
|
CB
|
A:ASP321
|
4.4
|
58.1
|
1.0
|
N
|
A:ASP319
|
4.5
|
57.3
|
1.0
|
N
|
A:ARG320
|
4.7
|
60.6
|
1.0
|
C
|
A:LEU324
|
4.7
|
57.9
|
1.0
|
CB
|
A:ALA323
|
4.7
|
40.8
|
1.0
|
CA
|
A:ASP319
|
4.8
|
55.3
|
1.0
|
N
|
A:LEU318
|
4.8
|
65.0
|
1.0
|
CD2
|
A:LEU324
|
4.8
|
60.5
|
1.0
|
CA
|
A:ASP321
|
4.8
|
67.3
|
1.0
|
O
|
A:ASP317
|
4.9
|
60.2
|
1.0
|
C
|
A:ASP319
|
4.9
|
58.9
|
1.0
|
CB
|
A:GLU328
|
4.9
|
52.4
|
1.0
|
N
|
A:CYS322
|
4.9
|
63.6
|
1.0
|
|
Reference:
J.L.Klosowiak,
S.Park,
K.P.Smith,
M.E.French,
P.J.Focia,
D.M.Freymann,
S.E.Rice.
Structural Insights Into Parkin Substrate Lysine Targeting From Minimal Miro Substrates. Sci Rep V. 6 33019 2016.
ISSN: ESSN 2045-2322
PubMed: 27605430
DOI: 10.1038/SREP33019
Page generated: Mon Dec 14 20:38:22 2020
|