Magnesium in PDB 7cor: Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat
Enzymatic activity of Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat
All present enzymatic activity of Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat:
7.2.2.1;
Protein crystallography data
The structure of Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat, PDB code: 7cor
was solved by
T.Kosugi,
M.Tanabe,
N.Koga,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.62 /
2.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
119.763,
126.726,
123.806,
90,
94.17,
90
|
R / Rfree (%)
|
23.1 /
28.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat
(pdb code 7cor). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat, PDB code: 7cor:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 7cor
Go back to
Magnesium Binding Sites List in 7cor
Magnesium binding site 1 out
of 5 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:39.6
occ:1.00
|
O2
|
A:PO4602
|
2.0
|
54.3
|
1.0
|
OG1
|
A:THR239
|
2.3
|
44.0
|
1.0
|
O2B
|
A:ADP600
|
2.7
|
57.3
|
1.0
|
O
|
A:HOH713
|
3.0
|
37.7
|
1.0
|
P
|
A:PO4602
|
3.3
|
53.6
|
1.0
|
O4
|
A:PO4602
|
3.5
|
69.7
|
1.0
|
OE1
|
A:GLU265
|
3.6
|
54.4
|
1.0
|
NH1
|
A:ARG262
|
3.6
|
49.6
|
1.0
|
CB
|
A:THR239
|
3.7
|
43.7
|
1.0
|
NH1
|
A:ARG333
|
3.8
|
46.4
|
1.0
|
PB
|
A:ADP600
|
3.8
|
56.3
|
1.0
|
OD2
|
A:ASP329
|
3.9
|
42.1
|
1.0
|
OD1
|
A:ASP329
|
3.9
|
33.8
|
1.0
|
O3B
|
A:ADP600
|
3.9
|
52.6
|
1.0
|
NH2
|
A:ARG333
|
4.0
|
45.2
|
1.0
|
O3
|
A:PO4602
|
4.1
|
50.9
|
1.0
|
CG2
|
A:THR239
|
4.2
|
41.2
|
1.0
|
O1
|
A:PO4602
|
4.3
|
49.1
|
1.0
|
CG
|
A:ASP329
|
4.3
|
36.9
|
1.0
|
CZ
|
A:ARG333
|
4.4
|
44.0
|
1.0
|
CD
|
A:GLU265
|
4.5
|
51.9
|
1.0
|
OE2
|
A:GLU261
|
4.5
|
47.0
|
1.0
|
OE2
|
A:GLU265
|
4.5
|
58.6
|
1.0
|
CA
|
A:THR239
|
4.7
|
45.9
|
1.0
|
N
|
A:THR239
|
4.7
|
55.5
|
1.0
|
CZ
|
A:ARG262
|
4.7
|
47.9
|
1.0
|
CE
|
A:LYS238
|
4.7
|
59.6
|
1.0
|
O1B
|
A:ADP600
|
4.8
|
50.8
|
1.0
|
NH2
|
A:ARG262
|
4.8
|
44.0
|
1.0
|
O3A
|
A:ADP600
|
5.0
|
55.9
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 7cor
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Magnesium Binding Sites List in 7cor
Magnesium binding site 2 out
of 5 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:63.3
occ:1.00
|
OE1
|
B:GLU265
|
2.0
|
77.9
|
1.0
|
O1B
|
B:ADP600
|
2.3
|
74.4
|
1.0
|
OG1
|
B:THR239
|
2.4
|
70.6
|
1.0
|
PB
|
B:ADP600
|
3.2
|
79.7
|
1.0
|
CD
|
B:GLU265
|
3.3
|
78.1
|
1.0
|
O3B
|
B:ADP600
|
3.4
|
78.5
|
1.0
|
CB
|
B:THR239
|
3.5
|
68.9
|
1.0
|
OD2
|
B:ASP329
|
3.7
|
70.5
|
1.0
|
O2B
|
B:ADP600
|
3.9
|
75.5
|
1.0
|
OE2
|
B:GLU265
|
4.1
|
74.2
|
1.0
|
OE1
|
B:GLU261
|
4.1
|
56.7
|
1.0
|
CG2
|
B:THR239
|
4.3
|
68.4
|
1.0
|
CG
|
B:GLU265
|
4.3
|
74.0
|
1.0
|
OD1
|
B:ASP329
|
4.4
|
68.0
|
1.0
|
CG
|
B:ASP329
|
4.5
|
67.0
|
1.0
|
O2A
|
B:ADP600
|
4.5
|
69.0
|
1.0
|
N
|
B:THR239
|
4.5
|
65.1
|
1.0
|
O3A
|
B:ADP600
|
4.6
|
75.8
|
1.0
|
CA
|
B:THR239
|
4.7
|
69.1
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 7cor
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Magnesium Binding Sites List in 7cor
Magnesium binding site 3 out
of 5 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:48.8
occ:1.00
|
OG1
|
C:THR239
|
2.0
|
62.6
|
1.0
|
O2B
|
C:ADP600
|
2.7
|
68.4
|
1.0
|
CB
|
C:THR239
|
3.4
|
60.4
|
1.0
|
O3B
|
C:ADP600
|
3.5
|
67.8
|
1.0
|
OE1
|
C:GLU265
|
3.5
|
63.7
|
1.0
|
NH1
|
C:ARG262
|
3.6
|
67.6
|
1.0
|
OE2
|
C:GLU261
|
3.6
|
54.3
|
1.0
|
PB
|
C:ADP600
|
3.6
|
71.2
|
1.0
|
OD2
|
C:ASP329
|
3.6
|
49.5
|
1.0
|
CG
|
C:GLU261
|
3.7
|
55.1
|
1.0
|
OD1
|
C:ASP329
|
3.8
|
52.0
|
1.0
|
CD
|
C:GLU261
|
3.8
|
53.0
|
1.0
|
CG
|
C:ASP329
|
4.0
|
49.7
|
1.0
|
OE2
|
C:GLU265
|
4.1
|
70.5
|
1.0
|
CG2
|
C:THR239
|
4.1
|
56.6
|
1.0
|
CD
|
C:GLU265
|
4.2
|
64.3
|
1.0
|
O3A
|
C:ADP600
|
4.2
|
72.3
|
1.0
|
N
|
C:THR239
|
4.3
|
60.7
|
1.0
|
CA
|
C:THR239
|
4.4
|
60.1
|
1.0
|
CZ
|
C:ARG262
|
4.5
|
58.7
|
1.0
|
NZ
|
C:LYS238
|
4.7
|
58.8
|
1.0
|
OE1
|
C:GLU261
|
4.7
|
44.4
|
1.0
|
O1B
|
C:ADP600
|
5.0
|
60.0
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 7cor
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Magnesium Binding Sites List in 7cor
Magnesium binding site 4 out
of 5 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:66.2
occ:1.00
|
O2A
|
D:ADP600
|
2.2
|
84.2
|
1.0
|
OG
|
D:SER158
|
2.4
|
58.9
|
1.0
|
OE2
|
D:GLU190
|
2.6
|
58.2
|
1.0
|
O3B
|
D:ADP600
|
2.8
|
75.6
|
1.0
|
OE2
|
D:GLU248
|
3.0
|
53.9
|
1.0
|
OE1
|
D:GLU248
|
3.3
|
60.7
|
1.0
|
PA
|
D:ADP600
|
3.4
|
91.3
|
1.0
|
CD
|
D:GLU248
|
3.4
|
51.1
|
1.0
|
O3A
|
D:ADP600
|
3.7
|
98.3
|
1.0
|
CB
|
D:SER158
|
3.8
|
61.3
|
1.0
|
PB
|
D:ADP600
|
3.9
|
94.4
|
1.0
|
CD
|
D:GLU190
|
3.9
|
47.8
|
1.0
|
OD2
|
D:ASP249
|
4.2
|
69.2
|
1.0
|
O1A
|
D:ADP600
|
4.3
|
90.5
|
1.0
|
N
|
D:SER158
|
4.4
|
54.3
|
1.0
|
CA
|
D:SER158
|
4.5
|
56.2
|
1.0
|
O1B
|
D:ADP600
|
4.6
|
73.2
|
1.0
|
O5'
|
D:ADP600
|
4.6
|
91.1
|
1.0
|
OE1
|
D:GLU190
|
4.6
|
39.5
|
1.0
|
CG
|
D:GLU248
|
4.8
|
47.2
|
1.0
|
CG
|
D:GLU190
|
4.9
|
44.4
|
1.0
|
CD
|
D:LYS157
|
5.0
|
56.2
|
1.0
|
CG2
|
D:ILE186
|
5.0
|
33.5
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 7cor
Go back to
Magnesium Binding Sites List in 7cor
Magnesium binding site 5 out
of 5 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Hexameric Ring Complex of Engineered V1-Atpase Bound to 5 Adps: A3(De)3_(Adp-Pi)1CAT(Adp)2CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg601
b:102.1
occ:1.00
|
OG
|
E:SER158
|
2.3
|
98.6
|
1.0
|
OE2
|
E:GLU190
|
2.3
|
111.0
|
1.0
|
CD
|
E:GLU190
|
2.5
|
100.0
|
1.0
|
O2A
|
E:ADP600
|
2.6
|
111.0
|
1.0
|
OE1
|
E:GLU190
|
2.7
|
101.7
|
1.0
|
O3A
|
E:ADP600
|
2.9
|
129.4
|
1.0
|
CB
|
E:SER158
|
3.0
|
105.0
|
1.0
|
PA
|
E:ADP600
|
3.3
|
120.0
|
1.0
|
CG
|
E:GLU190
|
3.5
|
90.2
|
1.0
|
C5'
|
E:ADP600
|
3.7
|
111.0
|
1.0
|
O5'
|
E:ADP600
|
4.0
|
109.6
|
1.0
|
OE2
|
E:GLU248
|
4.0
|
74.6
|
1.0
|
CB
|
E:GLU190
|
4.3
|
84.3
|
1.0
|
PB
|
E:ADP600
|
4.3
|
148.9
|
1.0
|
CA
|
E:SER158
|
4.4
|
105.5
|
1.0
|
O1B
|
E:ADP600
|
4.6
|
134.7
|
1.0
|
O3B
|
E:ADP600
|
4.7
|
146.9
|
1.0
|
O1A
|
E:ADP600
|
4.7
|
116.9
|
1.0
|
C4'
|
E:ADP600
|
4.9
|
110.0
|
1.0
|
N
|
E:SER158
|
4.9
|
102.9
|
1.0
|
|
Reference:
T.Kosugi,
T.Iida,
M.Tanabe,
R.Iino,
N.Koga.
De Novo Design of Allosteric Control Into Rotary Motor V1-Atpase By Restroing Lost Function To Be Published.
Page generated: Sat Aug 21 16:21:23 2021
|