Magnesium in PDB 8sqh: Spry-CAS9:Grna Complex Targeting Ttc Pam Dna

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Spry-CAS9:Grna Complex Targeting Ttc Pam Dna (pdb code 8sqh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Spry-CAS9:Grna Complex Targeting Ttc Pam Dna, PDB code: 8sqh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8sqh

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Magnesium binding site 1 out of 4 in the Spry-CAS9:Grna Complex Targeting Ttc Pam Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Spry-CAS9:Grna Complex Targeting Ttc Pam Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1401

b:192.3
occ:1.00
 OP1 D:DC34 2.0 204.3 1.0
OE1 A:GLU762 2.0 178.5 1.0
OD1 A:ASP10 2.1 178.4 1.0
CD A:GLU762 2.9 178.5 1.0
P D:DC34 3.0 204.3 1.0
CG A:ASP10 3.1 178.4 1.0
OE2 A:GLU762 3.1 178.5 1.0
O5' D:DC34 3.4 204.3 1.0
OD2 A:ASP10 3.4 178.4 1.0
OP2 D:DC34 3.6 204.3 1.0
CG A:GLU762 4.3 178.5 1.0
CB A:ASP10 4.3 178.4 1.0
MG A:MG1402 4.4 184.8 1.0
CB A:GLU762 4.7 178.5 1.0
C5' D:DC34 4.7 204.3 1.0
CA A:ASP10 4.8 178.4 1.0
N A:ILE11 4.8 181.9 1.0
OG A:SER960 5.0 176.6 1.0
C A:ASP10 5.0 178.4 1.0
OD2 A:ASP986 5.0 172.3 1.0

Magnesium binding site 2 out of 4 in 8sqh

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Magnesium binding site 2 out of 4 in the Spry-CAS9:Grna Complex Targeting Ttc Pam Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Spry-CAS9:Grna Complex Targeting Ttc Pam Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1402

b:184.8
occ:1.00
 OD2 A:ASP10 2.0 178.4 1.0
ND1 A:HIS983 2.0 170.7 1.0
OP2 D:DC34 2.1 204.3 1.0
CG A:ASP10 2.8 178.4 1.0
CG A:HIS983 2.9 170.7 1.0
CE1 A:HIS983 3.1 170.7 1.0
CB A:HIS983 3.2 170.7 1.0
CA A:HIS983 3.3 170.7 1.0
OD1 A:ASP10 3.4 178.4 1.0
P D:DC34 3.5 204.3 1.0
OG A:SER15 3.8 190.8 1.0
CB A:ASP10 3.8 178.4 1.0
CD2 A:HIS983 4.1 170.7 1.0
OP1 D:DC34 4.1 204.3 1.0
NE2 A:HIS983 4.1 170.7 1.0
O A:ASP10 4.2 178.4 1.0
C A:HIS983 4.3 170.7 1.0
O A:HIS983 4.3 170.7 1.0
N A:HIS983 4.3 170.7 1.0
O5' D:DC34 4.4 204.3 1.0
MG A:MG1401 4.4 192.3 1.0
C A:ASP10 4.5 178.4 1.0
N A:GLY12 4.6 199.7 1.0
CB A:SER15 4.7 190.8 1.0
N A:GLY17 4.7 168.8 1.0
C5' D:DC34 4.8 204.3 1.0
OD2 A:ASP986 4.8 172.3 1.0
CA A:ASP10 4.8 178.4 1.0
CB A:ASP986 5.0 172.3 1.0

Magnesium binding site 3 out of 4 in 8sqh

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Magnesium binding site 3 out of 4 in the Spry-CAS9:Grna Complex Targeting Ttc Pam Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Spry-CAS9:Grna Complex Targeting Ttc Pam Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1403

b:196.4
occ:1.00
 OD1 A:ASP839 2.2 197.0 1.0
OP1 c:DT0 2.2 189.2 1.0
NZ A:LYS866 2.2 199.8 1.0
OD1 A:ASN863 2.2 201.4 1.0
O A:HIS840 3.1 200.7 1.0
CG A:ASP839 3.1 197.0 1.0
CG A:ASN863 3.4 201.4 1.0
P c:DT0 3.6 189.2 1.0
CE A:LYS866 3.7 199.8 1.0
N A:HIS840 3.8 200.7 1.0
O A:LYS866 3.9 199.8 1.0
CB A:ASP839 3.9 197.0 1.0
ND2 A:ASN863 3.9 201.4 1.0
OD2 A:ASP839 4.0 197.0 1.0
C A:HIS840 4.1 200.7 1.0
CA A:ASP839 4.1 197.0 1.0
OP2 c:DT0 4.1 189.2 1.0
C A:ASP839 4.3 197.0 1.0
CD A:LYS866 4.3 199.8 1.0
CA A:HIS840 4.4 200.7 1.0
O5' c:DT0 4.4 189.2 1.0
C3' C:DG22 4.5 199.8 1.0
O A:ASN863 4.5 201.4 1.0
O3' C:DG22 4.6 199.8 1.0
CB A:ASN863 4.6 201.4 1.0
CG A:LYS866 4.7 199.8 1.0
CB A:LYS866 4.8 199.8 1.0
CA A:ASN863 4.9 201.4 1.0
CB A:HIS840 5.0 200.7 1.0

Magnesium binding site 4 out of 4 in 8sqh

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Magnesium binding site 4 out of 4 in the Spry-CAS9:Grna Complex Targeting Ttc Pam Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Spry-CAS9:Grna Complex Targeting Ttc Pam Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:201.9
occ:1.00
 OP2 B:A65 2.1 195.9 1.0
OP1 B:A65 2.2 195.9 1.0
P B:A65 2.5 195.9 1.0
OE2 A:GLU57 3.5 206.7 1.0
O5' B:A65 3.6 195.9 1.0
C5' B:A65 3.7 195.9 1.0
O3' B:U64 3.7 195.3 1.0
OG1 A:THR1102 4.0 174.8 1.0
CD A:GLU57 4.2 206.7 1.0
CG A:GLU57 4.3 206.7 1.0
C3' B:U64 4.6 195.3 1.0
O5' B:U64 4.7 195.3 1.0
N A:GLU57 4.8 206.7 1.0
CG2 A:THR1102 4.9 174.8 1.0
CB A:GLU57 4.9 206.7 1.0

Reference:

G.N.Hibshman, J.P.K.Bravo, D.W.Taylor. Unraveling the Mechanisms of Pamless Dna Interrogation By Spry-CAS9 Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-47830-3
Page generated: Fri Oct 4 19:58:22 2024

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