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Magnesium in PDB 8j12: Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex

Other elements in 8j12:

The structure of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex (pdb code 8j12). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex, PDB code: 8j12:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8j12

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Magnesium binding site 1 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:60.7
occ:1.00
OD2 A:ASP141 2.5 83.6 1.0
OD1 A:ASP141 2.8 85.8 1.0
CG A:ASP141 3.0 83.8 1.0
OP1 C:C-88 4.1 63.8 1.0
OP1 C:C-87 4.4 75.2 1.0
CB A:ASP141 4.5 76.2 1.0
OP2 C:C-87 4.8 72.2 1.0

Magnesium binding site 2 out of 7 in 8j12

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Magnesium binding site 2 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:75.2
occ:1.00
NH2 B:ARG214 3.7 88.3 1.0
OE1 B:GLU316 4.3 82.8 1.0
OE2 B:GLU316 4.5 83.4 1.0
C5 C:U16 4.6 68.7 1.0
CZ B:ARG214 4.6 89.1 1.0
NH1 B:ARG214 4.6 90.1 1.0
O4 C:U16 4.7 80.9 1.0
CD B:GLU316 4.8 82.7 1.0
C4 C:U16 4.9 73.5 1.0
O6 C:G17 5.0 78.5 1.0
OP2 C:U16 5.0 74.1 1.0

Magnesium binding site 3 out of 7 in 8j12

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Magnesium binding site 3 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:34.6
occ:1.00
N6 C:A-182 4.4 68.0 1.0
O6 C:G-187 4.6 74.0 1.0
N7 C:A-182 4.9 68.7 1.0

Magnesium binding site 4 out of 7 in 8j12

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Magnesium binding site 4 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:26.7
occ:1.00
O4 C:U-5 3.9 69.6 1.0
O6 C:G-4 4.1 70.4 1.0
O4 C:U-185 4.3 77.6 1.0
N6 C:A-3 4.3 66.5 1.0
C4 C:U-5 4.4 64.7 1.0
C5 C:U-5 4.8 63.8 1.0
N7 C:G-4 4.9 61.3 1.0
O6 C:G-186 4.9 69.5 1.0
O4 C:U-184 4.9 77.6 1.0

Magnesium binding site 5 out of 7 in 8j12

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Magnesium binding site 5 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:54.5
occ:1.00
O6 C:G-122 4.2 74.8 1.0
N7 C:G-122 4.2 58.8 1.0
O2' C:C-188 4.7 71.5 1.0
C4' C:C-188 4.8 63.9 1.0
OP1 C:A-89 4.8 76.6 1.0
OP2 C:A-89 4.8 76.4 1.0
C6 C:G-122 5.0 71.5 1.0
C5 C:G-122 5.0 62.2 1.0

Magnesium binding site 6 out of 7 in 8j12

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Magnesium binding site 6 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg104

b:65.8
occ:1.00
N7 C:G-82 4.3 86.8 1.0
N7 C:G-81 4.4 85.6 1.0
O6 C:G-81 4.5 97.1 1.0
O6 C:G-82 4.6 86.9 1.0
C5 C:G-82 5.0 79.8 1.0

Magnesium binding site 7 out of 7 in 8j12

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Magnesium binding site 7 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg105

b:30.0
occ:1.00
OP2 C:A-106 2.9 65.6 1.0
P C:A-106 4.2 78.3 1.0
N7 C:A-105 4.2 63.1 1.0
N6 C:A-105 4.2 72.0 1.0
O2' C:G-107 4.3 82.9 1.0
O5' C:A-106 4.4 75.8 1.0
OP2 C:A-105 4.5 72.9 1.0
C8 C:A-106 4.8 71.6 1.0
O3' C:G-107 4.8 77.5 1.0
N7 C:A-106 4.9 70.5 1.0
C5 C:A-105 5.0 57.4 1.0

Reference:

T.Hino, N.S.Omura, R.Nakagawa, T.Togashi, N.S.Takeda, T.Hiramoto, S.Tasaka, H.Hirano, T.Tokuyama, H.Uosaki, H.Ishiguro, H.Yamano, Y.Ozaki, D.Motooka, H.Mori, Y.Kirita, Y.Kise, Y.Itoh, S.Matoba, H.Aburatani, N.Yachie, V.Siksnys, T.Ohmori, A.Hoshino, O.Nureki. Minimal and Most Efficient Genome Editing Cas Enzyme To Be Published.
Page generated: Fri Oct 4 11:27:59 2024

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