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Magnesium in PDB 8bd5: CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex

Other elements in 8bd5:

The structure of CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex (pdb code 8bd5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex, PDB code: 8bd5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8bd5

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Magnesium binding site 1 out of 7 in the CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:138.7
occ:1.00
 OG1 E:THR67 2.1 132.1 1.0
O1B E:ATP301 2.1 136.9 1.0
O2A E:ATP301 2.2 136.9 1.0
O1G E:ATP301 2.2 136.9 1.0
PG E:ATP301 2.6 136.9 1.0
PB E:ATP301 2.7 136.9 1.0
O3B E:ATP301 2.7 136.9 1.0
CB E:THR67 2.8 132.1 1.0
O2G E:ATP301 2.8 136.9 1.0
PA E:ATP301 3.0 136.9 1.0
O3A E:ATP301 3.0 136.9 1.0
O1A E:ATP301 3.5 136.9 1.0
N E:THR67 3.5 132.1 1.0
CA E:THR67 3.7 132.1 1.0
OE2 E:GLU145 3.8 120.6 1.0
CG2 E:THR67 4.0 132.1 1.0
NZ E:LYS66 4.1 136.0 1.0
O3G E:ATP301 4.1 136.9 1.0
O2B E:ATP301 4.2 136.9 1.0
O5' E:ATP301 4.4 136.9 1.0
OE2 F:GLU162 4.6 112.6 1.0
N E:LYS66 4.7 136.0 1.0
C E:LYS66 4.7 136.0 1.0
OD2 E:ASP144 4.8 123.0 1.0
NH2 E:ARG63 4.8 133.4 1.0
NH2 F:ARG189 4.9 121.0 1.0
OD1 E:ASP144 4.9 123.0 1.0
C E:THR67 4.9 132.1 1.0

Magnesium binding site 2 out of 7 in 8bd5

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Magnesium binding site 2 out of 7 in the CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:128.1
occ:1.00
 O1B F:ATP301 2.2 133.1 1.0
O3B F:ATP301 2.3 133.1 1.0
O1G F:ATP301 2.4 133.1 1.0
PG F:ATP301 2.6 133.1 1.0
PB F:ATP301 2.7 133.1 1.0
O2G F:ATP301 2.8 133.1 1.0
OE2 F:GLU145 3.0 111.3 1.0
CG2 F:THR67 3.0 120.5 1.0
CD F:GLU145 3.8 111.3 1.0
NH2 G:ARG189 3.8 151.5 1.0
O3A F:ATP301 3.8 133.1 1.0
O2B F:ATP301 3.9 133.1 1.0
OG1 F:THR67 3.9 120.5 1.0
O3G F:ATP301 4.1 133.1 1.0
CB F:THR67 4.1 120.5 1.0
O2A F:ATP301 4.2 133.1 1.0
OE1 F:GLU145 4.3 111.3 1.0
OD1 F:ASP144 4.3 107.5 1.0
O F:GLY65 4.4 125.4 1.0
OD2 F:ASP144 4.4 107.5 1.0
PA F:ATP301 4.7 133.1 1.0
CG F:GLU145 4.8 111.3 1.0
CG F:ASP144 4.8 107.5 1.0
N F:THR67 5.0 120.5 1.0

Magnesium binding site 3 out of 7 in 8bd5

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Magnesium binding site 3 out of 7 in the CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:234.2
occ:1.00
 O1B G:ATP301 2.1 236.8 1.0
OG1 G:THR67 2.2 220.2 1.0
O3B G:ATP301 2.2 236.8 1.0
O2A G:ATP301 2.3 236.8 1.0
PB G:ATP301 2.4 236.8 1.0
O1G G:ATP301 2.5 236.8 1.0
PG G:ATP301 2.8 236.8 1.0
O3A G:ATP301 2.9 236.8 1.0
PA G:ATP301 3.1 236.8 1.0
CB G:THR67 3.2 220.2 1.0
O2G G:ATP301 3.5 236.8 1.0
N G:THR67 3.8 220.2 1.0
O2B G:ATP301 3.9 236.8 1.0
O1A G:ATP301 3.9 236.8 1.0
OE2 H:GLU162 4.0 240.1 1.0
CA G:THR67 4.1 220.2 1.0
O3G G:ATP301 4.1 236.8 1.0
CG2 G:THR67 4.3 220.2 1.0
NH2 G:ARG63 4.4 241.0 1.0
O5' G:ATP301 4.4 236.8 1.0
NH2 H:ARG189 4.5 252.3 1.0
C5' G:ATP301 4.7 236.8 1.0
CD H:GLU162 4.7 240.1 1.0
N G:LYS66 4.9 219.0 1.0
NE G:ARG63 5.0 241.0 1.0
C G:LYS66 5.0 219.0 1.0

Magnesium binding site 4 out of 7 in 8bd5

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Magnesium binding site 4 out of 7 in the CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:305.9
occ:1.00
 OG1 H:THR67 2.1 294.0 1.0
O1G H:ATP301 2.2 311.1 1.0
O1B H:ATP301 2.2 311.1 1.0
O2A H:ATP301 2.2 311.1 1.0
PB H:ATP301 2.6 311.1 1.0
O3B H:ATP301 2.6 311.1 1.0
PG H:ATP301 2.7 311.1 1.0
PA H:ATP301 2.7 311.1 1.0
O3A H:ATP301 2.7 311.1 1.0
CB H:THR67 2.9 294.0 1.0
O1A H:ATP301 3.0 311.1 1.0
O2G H:ATP301 3.2 311.1 1.0
N H:THR67 3.5 294.0 1.0
CA H:THR67 3.8 294.0 1.0
CG2 H:THR67 4.1 294.0 1.0
O2B H:ATP301 4.1 311.1 1.0
O3G H:ATP301 4.1 311.1 1.0
O5' H:ATP301 4.2 311.1 1.0
N H:LYS66 4.7 295.6 1.0
NH2 I:ARG189 4.7 287.2 1.0
C H:LYS66 4.7 295.6 1.0
OE2 I:GLU162 4.8 281.2 1.0

Magnesium binding site 5 out of 7 in 8bd5

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Magnesium binding site 5 out of 7 in the CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:329.5
occ:1.00
 O1B I:ATP301 2.1 329.6 1.0
O3B I:ATP301 2.2 329.6 1.0
O2A I:ATP301 2.2 329.6 1.0
O2G I:ATP301 2.4 329.6 1.0
PB I:ATP301 2.4 329.6 1.0
PG I:ATP301 2.5 329.6 1.0
OG1 I:THR67 2.7 312.3 1.0
O1G I:ATP301 2.9 329.6 1.0
O3A I:ATP301 2.9 329.6 1.0
PA I:ATP301 3.1 329.6 1.0
CB I:THR67 3.5 312.3 1.0
NH2 I:ARG63 3.8 327.6 1.0
O2B I:ATP301 3.9 329.6 1.0
N I:THR67 4.0 312.3 1.0
O3G I:ATP301 4.0 329.6 1.0
O1A I:ATP301 4.1 329.6 1.0
O5' I:ATP301 4.2 329.6 1.0
CA I:THR67 4.4 312.3 1.0
CG2 I:THR67 4.6 312.3 1.0
CZ I:ARG63 4.9 327.6 1.0
CB I:LYS66 5.0 311.1 1.0

Magnesium binding site 6 out of 7 in 8bd5

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Magnesium binding site 6 out of 7 in the CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg302

b:335.9
occ:1.00
 O1B J:ATP301 2.0 336.2 1.0
OG1 J:THR67 2.0 329.3 1.0
O2A J:ATP301 2.4 336.2 1.0
PB J:ATP301 2.5 336.2 1.0
O3A J:ATP301 2.6 336.2 1.0
PA J:ATP301 2.6 336.2 1.0
O3B J:ATP301 2.8 336.2 1.0
O1A J:ATP301 2.8 336.2 1.0
CB J:THR67 3.0 329.3 1.0
N J:THR67 3.5 329.3 1.0
CA J:THR67 3.8 329.3 1.0
PG J:ATP301 3.8 336.2 1.0
O2G J:ATP301 3.9 336.2 1.0
O2B J:ATP301 4.0 336.2 1.0
O5' J:ATP301 4.2 336.2 1.0
O1G J:ATP301 4.2 336.2 1.0
CG2 J:THR67 4.2 329.3 1.0
NH2 J:ARG63 4.4 335.6 1.0
OD1 J:ASP144 4.5 308.8 1.0
C J:LYS66 4.6 332.3 1.0
N J:LYS66 4.6 332.3 1.0
CB J:LYS66 4.7 332.3 1.0
OD2 J:ASP144 4.8 308.8 1.0
CA J:LYS66 4.9 332.3 1.0

Magnesium binding site 7 out of 7 in 8bd5

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Magnesium binding site 7 out of 7 in the CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of CAS12K-Sgrna-Dsdna-S15-Tniq-Tnsc Transposon Recruitment Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:312.1
occ:1.00
 O1B K:ATP301 2.0 314.2 1.0
O1G K:ATP301 2.0 314.2 1.0
PG K:ATP301 2.4 314.2 1.0
O3B K:ATP301 2.5 314.2 1.0
OG1 K:THR67 2.6 300.4 1.0
O2G K:ATP301 2.6 314.2 1.0
PB K:ATP301 2.6 314.2 1.0
O3A K:ATP301 3.3 314.2 1.0
CB K:THR67 3.5 300.4 1.0
O2A K:ATP301 3.6 314.2 1.0
O3G K:ATP301 3.9 314.2 1.0
O2B K:ATP301 4.0 314.2 1.0
PA K:ATP301 4.0 314.2 1.0
N K:THR67 4.3 300.4 1.0
CA K:THR67 4.5 300.4 1.0
CG2 K:THR67 4.6 300.4 1.0
O1A K:ATP301 4.6 314.2 1.0
OD1 K:ASP144 4.6 268.8 1.0

Reference:

M.Schmitz, I.Querques, S.Oberli, C.Chanez, M.Jinek. Structural Basis For the Assembly of the Type V Crispr-Associated Transposon Complex. Cell V. 185 4999 2022.
ISSN: ISSN 1097-4172
PubMed: 36435179
DOI: 10.1016/J.CELL.2022.11.009
Page generated: Thu Oct 3 19:15:50 2024

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