Magnesium in PDB 6vjf: The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse
Protein crystallography data
The structure of The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse, PDB code: 6vjf
was solved by
B.A.Tornabene,
N.V.Varlakhanova,
J.S.Chappie,
M.G.J.Ford,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
80.38 /
2.47
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.873,
119.032,
84.576,
90.00,
100.95,
90.00
|
R / Rfree (%)
|
18.9 /
23.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse
(pdb code 6vjf). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse, PDB code: 6vjf:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6vjf
Go back to
Magnesium Binding Sites List in 6vjf
Magnesium binding site 1 out
of 4 in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg702
b:43.0
occ:1.00
|
OG
|
A:SER57
|
1.8
|
28.9
|
1.0
|
O2G
|
A:GCP701
|
2.0
|
34.7
|
1.0
|
O
|
A:HOH804
|
2.0
|
37.4
|
1.0
|
OG1
|
A:THR77
|
2.1
|
32.1
|
1.0
|
O
|
A:HOH801
|
2.2
|
43.9
|
1.0
|
O2B
|
A:GCP701
|
2.2
|
23.4
|
1.0
|
CB
|
A:SER57
|
3.0
|
30.2
|
1.0
|
CB
|
A:THR77
|
3.3
|
32.2
|
1.0
|
PG
|
A:GCP701
|
3.3
|
34.5
|
1.0
|
PB
|
A:GCP701
|
3.4
|
30.5
|
1.0
|
C3B
|
A:GCP701
|
3.5
|
33.4
|
1.0
|
N
|
A:SER57
|
3.7
|
31.5
|
1.0
|
OD2
|
A:ASP170
|
3.8
|
49.4
|
1.0
|
CA
|
A:SER57
|
3.9
|
30.4
|
1.0
|
N
|
A:THR77
|
4.0
|
33.3
|
1.0
|
OD1
|
A:ASP170
|
4.1
|
47.4
|
1.0
|
O3G
|
A:GCP701
|
4.1
|
35.6
|
1.0
|
O2A
|
A:GCP701
|
4.2
|
32.0
|
1.0
|
CG2
|
A:THR77
|
4.2
|
31.2
|
1.0
|
O
|
A:HOH806
|
4.2
|
52.8
|
1.0
|
CA
|
A:THR77
|
4.3
|
31.9
|
1.0
|
O1B
|
A:GCP701
|
4.3
|
34.5
|
1.0
|
CG
|
A:ASP170
|
4.3
|
47.7
|
1.0
|
O1G
|
A:GCP701
|
4.4
|
34.4
|
1.0
|
O3A
|
A:GCP701
|
4.4
|
31.4
|
1.0
|
O
|
A:PRO70
|
4.4
|
36.8
|
1.0
|
PA
|
A:GCP701
|
4.7
|
30.8
|
1.0
|
O1A
|
A:GCP701
|
4.7
|
32.2
|
1.0
|
CB
|
A:VAL76
|
4.8
|
36.6
|
1.0
|
O
|
A:LEU171
|
4.8
|
37.2
|
1.0
|
CG1
|
A:VAL76
|
4.8
|
38.0
|
1.0
|
C
|
A:ALA56
|
4.9
|
32.4
|
1.0
|
CB
|
A:ALA56
|
4.9
|
33.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6vjf
Go back to
Magnesium Binding Sites List in 6vjf
Magnesium binding site 2 out
of 4 in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg702
b:38.5
occ:1.00
|
OG
|
B:SER57
|
1.8
|
23.5
|
1.0
|
O3G
|
B:GCP701
|
2.1
|
26.9
|
1.0
|
OG1
|
B:THR77
|
2.1
|
37.6
|
1.0
|
O
|
B:HOH804
|
2.1
|
36.1
|
1.0
|
O2B
|
B:GCP701
|
2.1
|
25.6
|
1.0
|
O
|
B:HOH805
|
2.1
|
41.8
|
1.0
|
CB
|
B:SER57
|
2.9
|
28.3
|
1.0
|
CB
|
B:THR77
|
3.2
|
31.6
|
1.0
|
PG
|
B:GCP701
|
3.4
|
33.2
|
1.0
|
PB
|
B:GCP701
|
3.4
|
30.2
|
1.0
|
C3B
|
B:GCP701
|
3.5
|
36.7
|
1.0
|
N
|
B:SER57
|
3.8
|
27.2
|
1.0
|
OD2
|
B:ASP170
|
3.8
|
33.7
|
1.0
|
CA
|
B:SER57
|
3.9
|
26.7
|
1.0
|
N
|
B:THR77
|
3.9
|
31.4
|
1.0
|
O2A
|
B:GCP701
|
4.1
|
29.6
|
1.0
|
CA
|
B:THR77
|
4.1
|
32.9
|
1.0
|
OD1
|
B:ASP170
|
4.2
|
39.7
|
1.0
|
CG2
|
B:THR77
|
4.2
|
30.8
|
1.0
|
O1G
|
B:GCP701
|
4.3
|
29.7
|
1.0
|
O1B
|
B:GCP701
|
4.4
|
32.2
|
1.0
|
O3A
|
B:GCP701
|
4.4
|
32.5
|
1.0
|
O
|
B:PRO70
|
4.4
|
32.6
|
1.0
|
CG
|
B:ASP170
|
4.4
|
34.0
|
1.0
|
O2G
|
B:GCP701
|
4.6
|
37.5
|
1.0
|
CB
|
B:VAL76
|
4.7
|
41.5
|
1.0
|
PA
|
B:GCP701
|
4.7
|
31.2
|
1.0
|
O
|
B:LEU171
|
4.9
|
28.7
|
1.0
|
C
|
B:VAL76
|
4.9
|
33.9
|
1.0
|
C
|
B:ALA56
|
4.9
|
27.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6vjf
Go back to
Magnesium Binding Sites List in 6vjf
Magnesium binding site 3 out
of 4 in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg702
b:41.6
occ:1.00
|
OG
|
C:SER57
|
2.0
|
32.4
|
1.0
|
O2G
|
C:GCP701
|
2.0
|
34.0
|
1.0
|
O
|
C:HOH802
|
2.1
|
39.5
|
1.0
|
O2B
|
C:GCP701
|
2.1
|
29.3
|
1.0
|
OG1
|
C:THR77
|
2.2
|
34.0
|
1.0
|
O
|
C:HOH805
|
2.2
|
44.3
|
1.0
|
CB
|
C:SER57
|
3.0
|
35.6
|
1.0
|
PG
|
C:GCP701
|
3.2
|
35.0
|
1.0
|
CB
|
C:THR77
|
3.3
|
38.0
|
1.0
|
C3B
|
C:GCP701
|
3.3
|
37.3
|
1.0
|
PB
|
C:GCP701
|
3.3
|
33.1
|
1.0
|
N
|
C:SER57
|
3.9
|
38.7
|
1.0
|
O3G
|
C:GCP701
|
3.9
|
37.5
|
1.0
|
OD2
|
C:ASP170
|
3.9
|
48.5
|
1.0
|
N
|
C:THR77
|
3.9
|
35.9
|
1.0
|
CA
|
C:SER57
|
4.0
|
36.1
|
1.0
|
O2A
|
C:GCP701
|
4.1
|
32.7
|
1.0
|
CA
|
C:THR77
|
4.2
|
36.0
|
1.0
|
OD1
|
C:ASP170
|
4.3
|
49.5
|
1.0
|
CG2
|
C:THR77
|
4.3
|
37.5
|
1.0
|
O3A
|
C:GCP701
|
4.3
|
33.4
|
1.0
|
O1B
|
C:GCP701
|
4.4
|
38.9
|
1.0
|
O1G
|
C:GCP701
|
4.4
|
39.8
|
1.0
|
O
|
C:PRO70
|
4.4
|
39.1
|
1.0
|
CG
|
C:ASP170
|
4.5
|
49.0
|
1.0
|
PA
|
C:GCP701
|
4.6
|
32.0
|
1.0
|
CB
|
C:VAL76
|
4.6
|
41.5
|
1.0
|
O
|
C:LEU171
|
4.8
|
40.6
|
1.0
|
CG1
|
C:VAL76
|
4.9
|
42.0
|
1.0
|
C
|
C:VAL76
|
5.0
|
37.2
|
1.0
|
O1A
|
C:GCP701
|
5.0
|
34.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6vjf
Go back to
Magnesium Binding Sites List in 6vjf
Magnesium binding site 4 out
of 4 in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg702
b:45.1
occ:1.00
|
O2G
|
D:GCP701
|
1.9
|
25.8
|
1.0
|
OG
|
D:SER57
|
2.0
|
28.2
|
1.0
|
O
|
D:HOH809
|
2.0
|
35.9
|
1.0
|
O2B
|
D:GCP701
|
2.0
|
26.6
|
1.0
|
OG1
|
D:THR77
|
2.1
|
37.0
|
1.0
|
O
|
D:HOH804
|
2.2
|
43.4
|
1.0
|
CB
|
D:SER57
|
3.1
|
26.7
|
1.0
|
PG
|
D:GCP701
|
3.2
|
28.4
|
1.0
|
CB
|
D:THR77
|
3.2
|
33.2
|
1.0
|
PB
|
D:GCP701
|
3.3
|
29.1
|
1.0
|
C3B
|
D:GCP701
|
3.4
|
32.1
|
1.0
|
N
|
D:SER57
|
3.8
|
25.9
|
1.0
|
OD2
|
D:ASP170
|
3.9
|
35.8
|
1.0
|
N
|
D:THR77
|
3.9
|
33.5
|
1.0
|
O3G
|
D:GCP701
|
4.0
|
34.1
|
1.0
|
CA
|
D:SER57
|
4.0
|
25.5
|
1.0
|
O2A
|
D:GCP701
|
4.1
|
31.5
|
1.0
|
OD1
|
D:ASP170
|
4.1
|
40.1
|
1.0
|
CA
|
D:THR77
|
4.2
|
33.0
|
1.0
|
CG2
|
D:THR77
|
4.2
|
33.5
|
1.0
|
O1B
|
D:GCP701
|
4.3
|
31.9
|
1.0
|
O3A
|
D:GCP701
|
4.3
|
31.9
|
1.0
|
O1G
|
D:GCP701
|
4.4
|
32.9
|
1.0
|
CG
|
D:ASP170
|
4.4
|
36.9
|
1.0
|
O
|
D:PRO70
|
4.5
|
28.1
|
1.0
|
PA
|
D:GCP701
|
4.6
|
32.3
|
1.0
|
O
|
D:LEU171
|
4.8
|
31.9
|
1.0
|
CB
|
D:VAL76
|
4.8
|
33.6
|
1.0
|
CB
|
D:ALA56
|
4.9
|
27.3
|
1.0
|
C
|
D:ALA56
|
4.9
|
30.5
|
1.0
|
|
Reference:
B.A.Tornabene,
N.V.Varlakhanova,
C.J.Hosford,
J.S.Chappie,
M.G.J.Ford.
Structural and Functional Characterization of the Dominant Negative P-Loop Lysine Mutation in the Dynamin Superfamily Protein VPS1. Protein Sci. 2020.
ISSN: ESSN 1469-896X
PubMed: 31981262
DOI: 10.1002/PRO.3830
Page generated: Tue Oct 1 22:05:49 2024
|