Magnesium in PDB 7cos: Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat
Enzymatic activity of Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat
All present enzymatic activity of Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat:
7.2.2.1;
Protein crystallography data
The structure of Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat, PDB code: 7cos
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)
|
48.83 /
3.95
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
179.441,
125.078,
180.973,
90,
93.84,
90
|
R / Rfree (%)
|
24.4 /
28.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat
(pdb code 7cos). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat, PDB code: 7cos:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 7cos
Go back to
Magnesium Binding Sites List in 7cos
Magnesium binding site 1 out
of 7 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,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 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:83.3
occ:1.00
|
O1B
|
A:ADP601
|
3.0
|
117.8
|
1.0
|
O3B
|
A:ADP601
|
3.0
|
102.3
|
1.0
|
PB
|
A:ADP601
|
3.4
|
109.1
|
1.0
|
OG1
|
A:THR239
|
3.6
|
94.0
|
1.0
|
NH2
|
A:ARG262
|
3.9
|
117.9
|
1.0
|
OG
|
A:SER391
|
4.0
|
103.0
|
1.0
|
O2B
|
A:ADP601
|
4.0
|
103.4
|
1.0
|
OE1
|
A:GLU265
|
4.1
|
93.1
|
1.0
|
OE2
|
A:GLU261
|
4.3
|
101.8
|
1.0
|
OD1
|
A:ASP329
|
4.4
|
77.0
|
1.0
|
OE1
|
A:GLU261
|
4.6
|
119.8
|
1.0
|
CD
|
A:LYS238
|
4.6
|
104.1
|
1.0
|
CD
|
A:GLU261
|
4.8
|
99.8
|
1.0
|
NZ
|
A:LYS238
|
4.8
|
132.2
|
1.0
|
O3A
|
A:ADP601
|
4.8
|
116.1
|
1.0
|
O
|
A:PHE234
|
4.9
|
128.6
|
1.0
|
OE2
|
A:GLU265
|
4.9
|
116.5
|
1.0
|
OD2
|
A:ASP329
|
4.9
|
89.4
|
1.0
|
CB
|
A:THR239
|
4.9
|
99.2
|
1.0
|
CD
|
A:GLU265
|
4.9
|
102.8
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 7cos
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Magnesium Binding Sites List in 7cos
Magnesium binding site 2 out
of 7 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,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 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg602
b:114.2
occ:1.00
|
O2B
|
C:ADP601
|
2.1
|
134.7
|
1.0
|
OG1
|
C:THR239
|
2.9
|
127.7
|
1.0
|
PB
|
C:ADP601
|
3.3
|
143.4
|
1.0
|
OE1
|
C:GLU265
|
3.6
|
160.6
|
1.0
|
O1B
|
C:ADP601
|
3.6
|
149.5
|
1.0
|
OE1
|
C:GLU261
|
3.6
|
149.0
|
1.0
|
CE
|
C:LYS238
|
3.8
|
142.6
|
1.0
|
CD
|
C:GLU261
|
4.0
|
134.3
|
1.0
|
OE2
|
C:GLU261
|
4.0
|
129.1
|
1.0
|
NZ
|
C:LYS238
|
4.1
|
151.9
|
1.0
|
O1A
|
C:ADP601
|
4.1
|
129.4
|
1.0
|
OD1
|
C:ASP329
|
4.2
|
122.0
|
1.0
|
CB
|
C:THR239
|
4.2
|
130.0
|
1.0
|
OD2
|
C:ASP329
|
4.2
|
105.7
|
1.0
|
O3B
|
C:ADP601
|
4.3
|
144.2
|
1.0
|
O3A
|
C:ADP601
|
4.5
|
133.1
|
1.0
|
CD
|
C:GLU265
|
4.5
|
159.2
|
1.0
|
CG
|
C:LYS238
|
4.5
|
133.2
|
1.0
|
OE2
|
C:GLU265
|
4.6
|
171.6
|
1.0
|
CG
|
C:ASP329
|
4.7
|
112.4
|
1.0
|
CD
|
C:LYS238
|
4.7
|
136.2
|
1.0
|
PA
|
C:ADP601
|
4.9
|
132.7
|
1.0
|
NH1
|
C:ARG262
|
5.0
|
178.2
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 7cos
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Magnesium Binding Sites List in 7cos
Magnesium binding site 3 out
of 7 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,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 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg602
b:135.0
occ:1.00
|
OG
|
D:SER158
|
2.2
|
153.1
|
1.0
|
CB
|
D:SER158
|
3.2
|
145.3
|
1.0
|
OE2
|
D:GLU248
|
3.3
|
119.1
|
1.0
|
CG
|
D:GLU190
|
3.3
|
126.3
|
1.0
|
CD
|
D:GLU190
|
3.4
|
133.7
|
1.0
|
O2A
|
D:ADP601
|
3.4
|
151.1
|
1.0
|
CB
|
D:GLU190
|
3.6
|
120.0
|
1.0
|
OE2
|
D:GLU190
|
3.6
|
154.9
|
1.0
|
OE1
|
D:GLU190
|
3.9
|
120.3
|
1.0
|
CD
|
D:GLU248
|
3.9
|
118.2
|
1.0
|
OE1
|
D:GLU248
|
4.0
|
138.8
|
1.0
|
CE2
|
D:PHE194
|
4.1
|
136.2
|
1.0
|
O3B
|
D:ADP601
|
4.1
|
155.7
|
1.0
|
CA
|
D:SER158
|
4.1
|
138.7
|
1.0
|
CZ
|
D:PHE194
|
4.2
|
141.2
|
1.0
|
O3A
|
D:ADP601
|
4.3
|
161.4
|
1.0
|
PA
|
D:ADP601
|
4.4
|
169.0
|
1.0
|
CG2
|
D:ILE186
|
4.6
|
105.4
|
1.0
|
CA
|
D:GLU190
|
4.7
|
119.3
|
1.0
|
PB
|
D:ADP601
|
4.8
|
162.5
|
1.0
|
N
|
D:SER158
|
4.9
|
133.5
|
1.0
|
O5'
|
D:ADP601
|
4.9
|
169.0
|
1.0
|
O2B
|
D:ADP601
|
5.0
|
142.7
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 7cos
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Magnesium Binding Sites List in 7cos
Magnesium binding site 4 out
of 7 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,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 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg602
b:124.6
occ:1.00
|
O1B
|
G:ADP601
|
2.5
|
157.3
|
1.0
|
OE1
|
G:GLU265
|
2.6
|
137.4
|
1.0
|
O2B
|
G:ADP601
|
3.0
|
174.2
|
1.0
|
PB
|
G:ADP601
|
3.2
|
165.4
|
1.0
|
OG1
|
G:THR239
|
3.2
|
163.6
|
1.0
|
CD
|
G:GLU265
|
3.4
|
136.3
|
1.0
|
OE2
|
G:GLU265
|
3.5
|
143.8
|
1.0
|
OE2
|
G:GLU261
|
3.9
|
147.3
|
1.0
|
CE
|
G:LYS238
|
4.0
|
160.0
|
1.0
|
O3B
|
G:ADP601
|
4.0
|
171.4
|
1.0
|
OE1
|
G:GLU261
|
4.1
|
142.8
|
1.0
|
OD2
|
G:ASP329
|
4.1
|
144.6
|
1.0
|
NZ
|
G:LYS238
|
4.2
|
185.7
|
1.0
|
CD
|
G:GLU261
|
4.2
|
141.4
|
1.0
|
OD1
|
G:ASP329
|
4.3
|
131.0
|
1.0
|
CB
|
G:THR239
|
4.5
|
165.2
|
1.0
|
O3A
|
G:ADP601
|
4.6
|
165.9
|
1.0
|
CG
|
G:ASP329
|
4.6
|
131.7
|
1.0
|
CA
|
G:GLY235
|
4.7
|
185.8
|
1.0
|
CG
|
G:GLU265
|
4.8
|
120.4
|
1.0
|
CG
|
G:LYS238
|
4.9
|
160.4
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 7cos
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Magnesium Binding Sites List in 7cos
Magnesium binding site 5 out
of 7 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,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 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg602
b:149.3
occ:1.00
|
O2B
|
H:ADP601
|
2.6
|
168.2
|
1.0
|
OG1
|
H:THR239
|
2.6
|
144.6
|
1.0
|
OE1
|
H:GLU265
|
2.6
|
163.9
|
1.0
|
OE2
|
H:GLU265
|
3.0
|
160.8
|
1.0
|
O1B
|
H:ADP601
|
3.1
|
158.7
|
1.0
|
CD
|
H:GLU265
|
3.2
|
164.9
|
1.0
|
PB
|
H:ADP601
|
3.3
|
167.7
|
1.0
|
OE1
|
H:GLU261
|
3.4
|
176.1
|
1.0
|
CB
|
H:THR239
|
3.8
|
152.0
|
1.0
|
O1A
|
H:ADP601
|
3.9
|
170.0
|
1.0
|
CD
|
H:GLU261
|
4.0
|
166.8
|
1.0
|
OE2
|
H:GLU261
|
4.1
|
185.7
|
1.0
|
O3B
|
H:ADP601
|
4.4
|
174.1
|
1.0
|
O3A
|
H:ADP601
|
4.5
|
155.9
|
1.0
|
CG2
|
H:THR239
|
4.5
|
158.7
|
1.0
|
NZ
|
H:LYS238
|
4.6
|
174.7
|
1.0
|
CE
|
H:LYS238
|
4.6
|
152.6
|
1.0
|
CG
|
H:GLU265
|
4.7
|
154.5
|
1.0
|
PA
|
H:ADP601
|
4.7
|
164.1
|
1.0
|
CA
|
H:THR239
|
5.0
|
155.2
|
1.0
|
N
|
H:THR239
|
5.0
|
154.7
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 7cos
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Magnesium Binding Sites List in 7cos
Magnesium binding site 6 out
of 7 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg602
b:66.8
occ:1.00
|
OG1
|
I:THR239
|
2.6
|
100.7
|
1.0
|
OE1
|
I:GLU265
|
2.7
|
129.7
|
1.0
|
O2B
|
I:ADP601
|
2.9
|
114.8
|
1.0
|
O3B
|
I:ADP601
|
2.9
|
128.5
|
1.0
|
PB
|
I:ADP601
|
3.4
|
123.8
|
1.0
|
OE2
|
I:GLU265
|
3.4
|
156.4
|
1.0
|
CD
|
I:GLU265
|
3.4
|
134.5
|
1.0
|
CB
|
I:THR239
|
3.8
|
105.5
|
1.0
|
OE1
|
I:GLU261
|
3.9
|
124.1
|
1.0
|
OD2
|
I:ASP329
|
4.0
|
91.2
|
1.0
|
O2A
|
I:ADP601
|
4.0
|
146.4
|
1.0
|
CD
|
I:GLU261
|
4.2
|
111.0
|
1.0
|
OD1
|
I:ASP329
|
4.3
|
93.5
|
1.0
|
OE2
|
I:GLU261
|
4.3
|
107.9
|
1.0
|
O1B
|
I:ADP601
|
4.4
|
118.7
|
1.0
|
CG2
|
I:THR239
|
4.5
|
109.1
|
1.0
|
O3A
|
I:ADP601
|
4.5
|
118.5
|
1.0
|
CG
|
I:ASP329
|
4.6
|
90.5
|
1.0
|
CE
|
I:LYS238
|
4.6
|
110.0
|
1.0
|
NZ
|
I:LYS238
|
4.7
|
120.7
|
1.0
|
PA
|
I:ADP601
|
4.8
|
122.0
|
1.0
|
CG
|
I:GLU265
|
4.9
|
119.7
|
1.0
|
N
|
I:THR239
|
4.9
|
109.0
|
1.0
|
CA
|
I:THR239
|
4.9
|
105.0
|
1.0
|
CG
|
I:LYS238
|
5.0
|
110.7
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 7cos
Go back to
Magnesium Binding Sites List in 7cos
Magnesium binding site 7 out
of 7 in the Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Hexameric Ring Complex of Engineered V1-Atpase Bound to 4 Adps: A3(De)3_(Adp)3CAT,1NON-Cat, Hexameric Ring Complex of Engineered V1- Atpase Bound to 5 Adps: A3(De)3_(Adp)3CAT,2NON-Cat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg602
b:101.2
occ:1.00
|
OG
|
J:SER158
|
2.0
|
112.8
|
1.0
|
O1A
|
J:ADP601
|
2.1
|
131.5
|
1.0
|
CB
|
J:SER158
|
2.7
|
123.6
|
1.0
|
O3B
|
J:ADP601
|
2.8
|
139.8
|
1.0
|
OE2
|
J:GLU248
|
3.1
|
122.8
|
1.0
|
OE1
|
J:GLU248
|
3.5
|
95.5
|
1.0
|
PA
|
J:ADP601
|
3.6
|
149.3
|
1.0
|
CD
|
J:GLU248
|
3.7
|
100.2
|
1.0
|
OE2
|
J:GLU190
|
3.7
|
131.1
|
1.0
|
CD
|
J:GLU190
|
3.7
|
115.7
|
1.0
|
CG
|
J:GLU190
|
3.9
|
109.8
|
1.0
|
PB
|
J:ADP601
|
4.0
|
149.7
|
1.0
|
CA
|
J:SER158
|
4.1
|
139.7
|
1.0
|
C5'
|
J:ADP601
|
4.2
|
145.7
|
1.0
|
O5'
|
J:ADP601
|
4.2
|
162.8
|
1.0
|
O3A
|
J:ADP601
|
4.2
|
140.5
|
1.0
|
OE1
|
J:GLU190
|
4.3
|
95.5
|
1.0
|
CB
|
J:GLU190
|
4.4
|
97.9
|
1.0
|
O1B
|
J:ADP601
|
4.5
|
135.9
|
1.0
|
C
|
J:SER158
|
4.6
|
123.2
|
1.0
|
O2A
|
J:ADP601
|
4.7
|
144.0
|
1.0
|
CZ
|
J:PHE194
|
4.7
|
92.3
|
1.0
|
CE2
|
J:PHE194
|
4.8
|
93.4
|
1.0
|
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Reference:
T.Kosugi,
T.Iida,
M.Tanabe,
R.Iino,
N.Koga.
De Novo Design of Allosteric Control Into Rotary Motor V1-Atpase By Restoring Lost Function To Be Published.
Page generated: Sat Aug 21 16:21:25 2021
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