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

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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 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 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 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 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 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

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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

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.
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