Magnesium in PDB 7z4j: SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State

The binding sites of Magnesium atom in the SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State (pdb code 7z4j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State, PDB code: 7z4j:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:124.9 occ:1.00 O A:HOH303 1.9 95.0 1.0 O A:HOH306 1.9 113.9 1.0 OP1 A:U50 2.0 92.3 1.0 O A:HOH305 2.0 95.4 1.0 O A:HOH302 2.0 93.3 1.0 O A:HOH301 2.0 99.7 1.0 O A:HOH304 2.1 95.4 1.0 P A:U50 3.3 92.9 1.0 OP2 A:U50 3.8 91.0 1.0 O6 A:G62 4.1 90.7 1.0 O5' A:U50 4.2 82.8 1.0 O3' A:A49 4.3 84.1 1.0 OP1 A:A51 4.4 74.5 1.0 OP1 A:A52 4.5 74.0 1.0 C5' A:U50 4.6 77.3 1.0 O6 A:G53 4.8 95.1 1.0 NZ B:LYS1123 4.9 91.4 1.0

Magnesium binding site 2 out of 4 in the SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1401 b:62.4 occ:1.00 OP1 D:DT-3 1.9 101.7 1.0 OD2 B:ASP10 2.0 115.6 1.0 ND1 B:HIS983 2.0 101.0 1.0 CE1 B:HIS983 2.8 108.0 1.0 CG B:ASP10 2.9 121.2 1.0 CG B:HIS983 3.2 104.0 1.0 P D:DT-3 3.2 109.0 1.0 OD1 B:ASP10 3.2 120.3 1.0 MG B:MG1402 3.7 83.4 1.0 CB B:HIS983 3.7 100.0 1.0 CA B:HIS983 3.7 98.1 1.0 OP2 D:DT-3 3.8 97.5 1.0 NE2 B:HIS983 4.0 110.3 1.0 O5' D:DT-3 4.0 91.9 1.0 CB B:ASP10 4.1 116.9 1.0 OD2 B:ASP986 4.1 113.0 1.0 CD2 B:HIS983 4.2 101.4 1.0 O3' D:DA-4 4.3 110.0 1.0 O B:ASP10 4.4 118.9 1.0 C5' D:DT-3 4.4 97.2 1.0 CD2 B:HIS982 4.5 108.6 1.0 N B:HIS983 4.6 103.6 1.0 CB B:ASP986 4.7 94.5 1.0 O B:HIS983 4.8 107.0 1.0 C B:HIS983 4.8 96.7 1.0 NE2 B:HIS982 4.8 112.2 1.0 OG B:SER15 4.8 119.2 1.0 C B:ASP10 4.8 116.5 1.0 CG B:ASP986 4.9 109.3 1.0

Magnesium binding site 3 out of 4 in the SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1402 b:83.4 occ:1.00 O3' D:DA-4 2.1 110.0 1.0 OD1 B:ASP10 2.1 120.3 1.0 OP1 D:DT-3 2.3 101.7 1.0 OE1 B:GLU762 2.4 123.9 1.0 P D:DT-3 2.7 109.0 1.0 CG B:ASP10 3.1 121.2 1.0 OD2 B:ASP10 3.4 115.6 1.0 C5' D:DT-3 3.5 97.2 1.0 CD B:GLU762 3.5 129.2 1.0 O5' D:DT-3 3.6 91.9 1.0 MG B:MG1401 3.7 62.4 1.0 O B:ILE11 3.7 113.4 1.0 OP2 D:DT-3 4.0 97.5 1.0 OE2 B:GLU762 4.2 124.9 1.0 CB B:ASP10 4.4 116.9 1.0 OD2 B:ASP986 4.6 113.0 1.0 CG B:GLU762 4.6 128.5 1.0 C B:ILE11 4.8 99.6 1.0 C B:ASP10 4.8 116.5 1.0 CA B:ASP10 4.8 113.1 1.0 N B:ILE11 4.8 106.6 1.0 C4' D:DT-3 4.8 92.2 1.0 CB B:GLU762 4.9 118.1 1.0

Magnesium binding site 4 out of 4 in the SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SPCAS9 Bound to 18-Nucleotide Complementary Dna Substrate in the Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1403 b:56.4 occ:1.00 OP2 C:DT4 1.9 104.6 1.0 O B:HOH1501 1.9 88.1 1.0 O C:HOH101 2.0 86.0 1.0 OD1 B:ASN863 2.0 109.4 1.0 OD1 B:ASP839 2.1 116.5 1.0 O3' c:DG3 2.3 91.1 1.0 P C:DT4 3.0 115.9 1.0 CG B:ASP839 3.0 119.9 1.0 CG B:ASN863 3.0 112.0 1.0 CB B:ASP839 3.2 114.6 1.0 O5' C:DT4 3.3 106.8 1.0 ND2 B:ASN863 3.3 110.7 1.0 CA B:ASP839 3.4 113.7 1.0 O3' C:DG3 3.5 101.9 1.0 C3' c:DG3 3.6 85.8 1.0 N B:HIS840 3.8 110.9 1.0 NZ B:LYS866 3.9 97.5 1.0 C B:ASP839 4.1 117.3 1.0 C4' c:DG3 4.1 86.9 1.0 OD2 B:ASP839 4.2 117.1 1.0 O B:ASN863 4.3 116.8 1.0 OP1 C:DT4 4.3 105.9 1.0 C5' c:DG3 4.3 85.5 1.0 CB B:ASN863 4.4 110.2 1.0 O B:HIS840 4.5 120.4 1.0 N B:ASP839 4.6 114.0 1.0 C5' C:DT4 4.6 101.0 1.0 C2' c:DG3 4.7 84.1 1.0 C B:ASN863 4.8 112.0 1.0 CA B:ASN863 4.9 107.6 1.0 CA B:HIS840 5.0 108.3 1.0

M.Pacesa, L.Loeff, I.Querques, L.M.Muckenfuss, M.Sawicka, M.Jinek. R-Loop Formation and Conformational Activation Mechanisms of CAS9. Nature V. 609 191 2022.
ISSN: ESSN 1476-4687
PubMed: 36002571
DOI: 10.1038/S41586-022-05114-0