Magnesium in PDB 9nvu: Engineered Orufiscb-Omegarna-Target Dna Complex

The structure of Engineered Orufiscb-Omegarna-Target Dna Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Engineered Orufiscb-Omegarna-Target Dna Complex (pdb code 9nvu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Engineered Orufiscb-Omegarna-Target Dna Complex, PDB code: 9nvu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Engineered Orufiscb-Omegarna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Engineered Orufiscb-Omegarna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg701 b:30.0 occ:1.00 OP2 N:DT-5 1.9 20.0 1.0 OD2 P:ASP60 2.0 92.1 1.0 NE2 P:HIS445 2.2 85.4 1.0 CD2 P:HIS445 2.5 85.4 1.0 HD2 P:HIS445 2.5 85.4 1.0 P N:DT-5 2.8 20.0 1.0 O5' N:DT-5 3.1 20.0 1.0 CG P:ASP60 3.1 92.1 1.0 OP1 N:DT-5 3.2 20.0 1.0 CE1 P:HIS445 3.3 85.4 1.0 HA P:HIS445 3.5 85.4 1.0 CG P:HIS445 3.5 85.4 1.0 OD1 P:ASP60 3.6 92.1 1.0 HE1 P:HIS445 3.9 85.4 1.0 ND1 P:HIS445 3.9 85.4 1.0 MG P:MG702 4.1 30.0 1.0 OD2 P:ASP448 4.1 89.6 1.0 H3' N:DT-5 4.2 20.0 1.0 O3' N:DC-6 4.3 20.0 1.0 CA P:HIS445 4.3 85.4 1.0 CB P:HIS445 4.4 85.4 1.0 CB P:ASP60 4.4 92.1 1.0 C5' N:DT-5 4.5 20.0 1.0 HB3 P:ASP60 4.5 92.1 1.0 O P:PRO61 4.5 89.7 1.0 HB3 P:HIS445 4.6 85.4 1.0 HB2 P:ASP448 4.6 89.6 1.0 HD1 P:HIS445 4.7 85.4 1.0 H5'' N:DT-5 4.7 20.0 1.0 N P:HIS445 4.8 85.4 1.0 HB2 P:ASN65 4.8 91.7 1.0 H P:HIS445 4.9 85.4 1.0 O P:ASN65 5.0 91.7 1.0 O3' N:DT-5 5.0 20.0 1.0 C3' N:DT-5 5.0 20.0 1.0 HB2 P:ASP60 5.0 92.1 1.0 HE2 P:LYS443 5.0 85.6 1.0

Magnesium binding site 2 out of 4 in the Engineered Orufiscb-Omegarna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Engineered Orufiscb-Omegarna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg702 b:30.0 occ:1.00 OP1 N:DT-5 1.8 20.0 1.0 OD1 P:ASP60 1.8 92.1 1.0 OE1 P:GLU295 1.8 85.4 1.0 H4' N:DC-6 2.6 20.0 1.0 CD P:GLU295 2.8 85.4 1.0 HD22 P:ASN297 2.9 59.1 1.0 CG P:ASP60 3.0 92.1 1.0 OE2 P:GLU295 3.2 85.4 1.0 P N:DT-5 3.3 20.0 1.0 OD2 P:ASP60 3.5 92.1 1.0 C4' N:DC-6 3.7 20.0 1.0 HD2 P:PRO61 3.7 89.7 1.0 HA P:ASP60 3.8 92.1 1.0 ND2 P:ASN297 3.9 59.1 1.0 H5'' N:DC-6 3.9 20.0 1.0 HB3 P:GLU295 4.0 85.4 1.0 OP2 N:DT-5 4.0 20.0 1.0 HD11 P:ILE452 4.0 90.2 1.0 OD1 P:ASN297 4.0 59.1 1.0 MG P:MG701 4.1 30.0 1.0 CG P:GLU295 4.1 85.4 1.0 O3' N:DC-6 4.2 20.0 1.0 O5' N:DT-5 4.2 20.0 1.0 O P:PRO61 4.2 89.7 1.0 CB P:ASP60 4.2 92.1 1.0 C5' N:DC-6 4.3 20.0 1.0 C3' N:DC-6 4.4 20.0 1.0 HG2 P:GLU295 4.4 85.4 1.0 CG P:ASN297 4.4 59.1 1.0 CA P:ASP60 4.4 92.1 1.0 HB3 P:ASP448 4.4 89.6 1.0 O4' N:DC-6 4.5 20.0 1.0 OD2 P:ASP448 4.5 89.6 1.0 H5' N:DC-6 4.5 20.0 1.0 CB P:GLU295 4.5 85.4 1.0 CD P:PRO61 4.5 89.7 1.0 HB2 P:ASP60 4.5 92.1 1.0 HD21 P:ASN297 4.6 59.1 1.0 H5' N:DT-5 4.6 20.0 1.0 N P:PRO61 4.6 89.7 1.0 C P:ASP60 4.7 92.1 1.0 HG21 P:THR432 4.8 83.1 1.0 HG1 P:THR432 4.8 83.1 1.0 HB2 P:GLU295 4.8 85.4 1.0 H1' N:DC-6 4.8 20.0 1.0 C5' N:DT-5 4.9 20.0 1.0 HD3 P:PRO61 4.9 89.7 1.0 H3' N:DC-6 4.9 20.0 1.0 HD12 P:ILE452 4.9 90.2 1.0 CD1 P:ILE452 4.9 90.2 1.0 HG3 P:GLU295 5.0 85.4 1.0 H5'' N:DT-5 5.0 20.0 1.0

Magnesium binding site 3 out of 4 in the Engineered Orufiscb-Omegarna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Engineered Orufiscb-Omegarna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg101 b:30.0 occ:1.00 OP1 T:DA4 1.8 11.9 1.0 NE2 P:HIS375 2.0 92.6 1.0 O3' T:DG3 2.1 6.3 1.0 P T:DA4 2.6 15.7 1.0 H5' T:DA4 2.8 4.5 1.0 CE1 P:HIS375 2.8 92.6 1.0 HD1 P:HIS351 2.8 87.7 1.0 HE2 P:HIS379 2.8 86.6 1.0 HE1 P:HIS375 2.9 92.6 1.0 HA P:HIS351 3.0 87.7 1.0 ND1 P:HIS351 3.1 87.7 1.0 CD2 P:HIS375 3.3 92.6 1.0 NE2 P:HIS379 3.3 86.6 1.0 C5' T:DA4 3.4 4.5 1.0 H P:HIS352 3.5 86.8 1.0 O5' T:DA4 3.5 12.8 1.0 C3' T:DG3 3.5 2.5 1.0 H4' T:DG3 3.6 3.6 1.0 H5'' T:DA4 3.6 4.5 1.0 HD2 P:HIS375 3.7 92.6 1.0 OP2 T:DA4 3.8 8.1 1.0 H2'' T:DG3 3.8 1.7 1.0 CG P:HIS351 3.9 87.7 1.0 CE1 P:HIS351 3.9 87.7 1.0 CA P:HIS351 3.9 87.7 1.0 C4' T:DG3 4.0 3.6 1.0 ND1 P:HIS375 4.0 92.6 1.0 CD2 P:HIS379 4.1 86.6 1.0 H5'' T:DG3 4.1 7.1 1.0 HE1 P:HIS351 4.1 87.7 1.0 N P:HIS352 4.2 86.8 1.0 CE1 P:HIS379 4.2 86.6 1.0 H3' T:DG3 4.2 2.5 1.0 C2' T:DG3 4.2 1.7 1.0 CB P:HIS351 4.3 87.7 1.0 CG P:HIS375 4.3 92.6 1.0 HD2 P:HIS379 4.3 86.6 1.0 HB2 P:HIS351 4.3 87.7 1.0 HE1 P:HIS379 4.4 86.6 1.0 C P:HIS351 4.6 87.7 1.0 HB2 P:HIS352 4.6 86.8 1.0 O P:HIS352 4.7 86.8 1.0 C5' T:DG3 4.7 7.1 1.0 H2' T:DG3 4.8 1.7 1.0 CD2 P:HIS351 4.8 87.7 1.0 NE2 P:HIS351 4.8 87.7 1.0 C4' T:DA4 4.8 7.4 1.0 HD1 P:HIS375 4.9 92.6 1.0 N P:HIS351 5.0 87.7 1.0

Magnesium binding site 4 out of 4 in the Engineered Orufiscb-Omegarna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Engineered Orufiscb-Omegarna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ W:Mg301 b:7.4 occ:1.00 OP1 W:A67 1.9 9.0 1.0 P W:A67 3.3 5.6 1.0 H5'' W:A67 3.5 5.5 1.0 O5' W:A67 4.1 5.7 1.0 OP2 W:A67 4.2 4.8 1.0 C5' W:A67 4.3 5.5 1.0 O3' W:G66 4.3 11.5 1.0 OP1 W:A134 4.4 5.2 1.0 HB1 P:ALA111 4.6 70.0 1.0 OP2 W:A134 4.6 5.2 1.0 H5' W:A67 4.6 5.5 1.0 OP2 W:G68 4.6 5.3 1.0 H5' W:A134 4.9 2.5 1.0 P W:A134 5.0 10.7 1.0

S.Kannan, H.Altae-Tran, S.Zhu, P.Xu, D.Strebinger, R.Oshiro, G.Faure, L.Moeller, J.Pham, K.S.Mears, H.M.Ni, R.K.Macrae, F.Zhang. Evolution-Guided Protein Design of Iscb For Persistent Epigenome Editing in Vivo. Nat.Biotechnol. 2025.
ISSN: ISSN 1087-0156
PubMed: 40335752
DOI: 10.1038/S41587-025-02655-3