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Magnesium in PDB 7s4x: CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation

Magnesium Binding Sites:

The binding sites of Magnesium atom in the CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation (pdb code 7s4x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation, PDB code: 7s4x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7s4x

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Magnesium binding site 1 out of 5 in the CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1401

b:42.7
occ:1.00
OE1 A:GLU762 1.9 35.0 1.0
OD1 A:ASP10 2.0 30.0 1.0
CG A:ASP10 3.1 30.0 1.0
CD A:GLU762 3.1 35.0 1.0
P D:DC34 3.3 44.5 1.0
OD2 A:ASP10 3.6 30.0 1.0
OP1 D:DC34 3.8 44.5 1.0
OE2 A:GLU762 3.8 35.0 1.0
O5' D:DC34 4.0 44.5 1.0
C5' D:DC34 4.0 44.5 1.0
O A:ILE11 4.1 29.9 1.0
CG A:GLU762 4.1 35.0 1.0
MG A:MG1402 4.2 32.8 1.0
CB A:ASP10 4.3 30.0 1.0
OP2 D:DC34 4.3 44.5 1.0
CB A:GLU762 4.4 35.0 1.0
CA A:ASP10 4.5 30.0 1.0
C A:ASP10 4.6 30.0 1.0
N A:ILE11 4.6 29.9 1.0
C A:ILE11 4.9 29.9 1.0
OD2 A:ASP986 4.9 29.2 1.0
OG A:SER960 4.9 38.6 1.0

Magnesium binding site 2 out of 5 in 7s4x

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Magnesium binding site 2 out of 5 in the CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1402

b:32.8
occ:1.00
OP1 D:DC34 1.9 44.5 1.0
OD2 A:ASP10 2.0 30.0 1.0
ND1 A:HIS983 2.1 30.4 1.0
CE1 A:HIS983 2.8 30.4 1.0
CG A:ASP10 3.1 30.0 1.0
CG A:HIS983 3.2 30.4 1.0
P D:DC34 3.2 44.5 1.0
OG A:SER15 3.6 33.2 1.0
OD1 A:ASP10 3.6 30.0 1.0
CB A:HIS983 3.7 30.4 1.0
CA A:HIS983 3.9 30.4 1.0
NE2 A:HIS983 4.0 30.4 1.0
O A:ASP10 4.1 30.0 1.0
C5' D:DC34 4.1 44.5 1.0
O5' D:DC34 4.1 44.5 1.0
MG A:MG1401 4.2 42.7 1.0
CD2 A:HIS983 4.2 30.4 1.0
CB A:ASP10 4.3 30.0 1.0
OP2 D:DC34 4.3 44.5 1.0
OP1 D:DG35 4.6 55.5 1.0
C A:ASP10 4.7 30.0 1.0
N A:HIS983 4.7 30.4 1.0
CD2 A:HIS982 4.7 30.8 1.0
OD2 A:ASP986 4.7 29.2 1.0
CB A:SER15 4.8 33.2 1.0
OP2 D:DG35 4.8 55.5 1.0
NE2 A:HIS982 4.9 30.8 1.0
C A:HIS983 5.0 30.4 1.0

Magnesium binding site 3 out of 5 in 7s4x

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Magnesium binding site 3 out of 5 in the CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1403

b:49.6
occ:1.00
OD1 A:ASP839 2.4 54.6 1.0
OP2 c:DT23 2.5 51.7 1.0
OD1 A:ASN863 3.1 58.8 1.0
CG A:ASP839 3.6 54.6 1.0
O A:HIS840 3.9 51.3 1.0
P c:DT23 3.9 51.7 1.0
NZ A:LYS866 3.9 64.0 1.0
C3' C:DG22 4.0 49.8 1.0
N A:HIS840 4.0 51.3 1.0
CG A:ASN863 4.1 58.8 1.0
O A:LYS866 4.1 64.0 1.0
O3' C:DG22 4.3 49.8 1.0
ND2 A:ASN863 4.4 58.8 1.0
CB A:ASP839 4.4 54.6 1.0
CA A:ASP839 4.4 54.6 1.0
OP3 c:DT23 4.4 51.7 1.0
OD2 A:ASP839 4.5 54.6 1.0
CD A:LYS866 4.5 64.0 1.0
OP1 C:DG22 4.7 49.8 1.0
C A:ASP839 4.7 54.6 1.0
C A:HIS840 4.7 51.3 1.0
C5' C:DG22 4.7 49.8 1.0
O5' C:DG22 4.7 49.8 1.0
O5' c:DT23 4.7 51.7 1.0
CA A:HIS840 4.8 51.3 1.0
CE A:LYS866 4.8 64.0 1.0
C4' C:DG22 4.9 49.8 1.0
C2' C:DG22 4.9 49.8 1.0
OP1 c:DT23 4.9 51.7 1.0
O A:ASN863 4.9 58.8 1.0
CB A:HIS840 5.0 51.3 1.0

Magnesium binding site 4 out of 5 in 7s4x

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Magnesium binding site 4 out of 5 in the CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1404

b:45.9
occ:1.00
OG1 A:THR1102 2.7 34.5 1.0
OP2 B:A65 2.8 46.2 1.0
OP1 B:U64 3.6 40.1 1.0
CB A:THR1102 4.0 34.5 1.0
O A:THR1102 4.1 34.5 1.0
P B:A65 4.1 46.2 1.0
OE1 A:GLU57 4.1 46.2 1.0
N A:THR1102 4.2 34.5 1.0
OP1 B:A65 4.4 46.2 1.0
CA A:THR1102 4.5 34.5 1.0
C A:THR1102 4.5 34.5 1.0
CG2 A:THR1102 4.6 34.5 1.0
P B:U64 4.6 40.1 1.0
OE2 A:GLU57 4.8 46.2 1.0
OP2 B:U64 4.8 40.1 1.0
O A:VAL1100 4.8 35.0 1.0
CD A:GLU57 4.9 46.2 1.0
N4 B:C67 4.9 53.2 1.0

Magnesium binding site 5 out of 5 in 7s4x

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Magnesium binding site 5 out of 5 in the CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of CAS9:Grna in Complex with 18-20MM Dna, 1 Minute Time-Point, Kinked Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:42.1
occ:1.00
O6 B:G4 4.2 45.6 1.0
OP2 B:A2 4.2 78.9 1.0
O4 c:DT34 4.2 41.9 1.0
O6 c:DG35 4.5 44.0 1.0
C7 c:DT34 4.5 41.9 1.0
N4 B:C5 4.6 38.8 1.0
OP2 B:C3 4.8 51.8 1.0
O5' B:A2 4.8 78.9 1.0
P B:A2 4.9 78.9 1.0
N4 c:DC36 4.9 46.9 1.0

Reference:

J.P.K.Bravo, M.S.Liu, G.N.Hibshman, T.L.Dangerfield, K.Jung, R.S.Mccool, K.A.Johnson, D.W.Taylor. Structural Basis For Mismatch Surveillance By Crispr-CAS9. Nature V. 603 343 2022.
ISSN: ESSN 1476-4687
PubMed: 35236982
DOI: 10.1038/S41586-022-04470-1
Page generated: Thu Oct 3 08:10:39 2024

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