Magnesium in PDB 6pr5: Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc)

The structure of Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc) (pdb code 6pr5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc), PDB code: 6pr5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:63.8 occ:1.00 OE2 A:GLU185 2.2 60.5 1.0 OD1 A:ASP125 2.2 58.1 1.0 OD2 A:ASP224 2.2 59.6 1.0 O3' B:DA18 2.4 66.2 1.0 CD A:GLU185 3.2 60.5 1.0 CG A:ASP125 3.3 58.1 1.0 CG A:ASP224 3.3 59.6 1.0 OE1 A:GLU185 3.5 60.5 1.0 C3' B:DA18 3.7 66.2 1.0 OP2 D:DC17 3.7 70.0 1.0 OD2 A:ASP125 3.9 58.1 1.0 N A:GLY126 4.0 52.8 1.0 C4' B:DA18 4.1 66.2 1.0 OD1 A:ASP224 4.1 59.6 1.0 C2' B:DA18 4.2 66.2 1.0 CB A:ASP224 4.3 59.6 1.0 MG A:MG602 4.3 60.5 1.0 CB A:ASP125 4.4 58.1 1.0 CG1 A:ILE227 4.5 60.7 1.0 CA A:ASP125 4.5 58.1 1.0 O A:GLY126 4.5 52.8 1.0 CG A:GLU185 4.6 60.5 1.0 CD1 A:ILE227 4.7 60.7 1.0 C A:ASP125 4.8 58.1 1.0 CA A:GLY126 4.9 52.8 1.0 P D:DC17 4.9 70.0 1.0 C5' B:DA18 5.0 66.2 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:60.5 occ:1.00 OP2 D:DC17 2.2 70.0 1.0 OD2 A:ASP125 2.2 58.1 1.0 OE1 A:GLU435 2.3 52.7 1.0 O3' D:DG16 2.3 54.3 1.0 OE2 A:GLU435 2.6 52.7 1.0 P D:DC17 2.6 70.0 1.0 CD A:GLU435 2.7 52.7 1.0 CG A:ASP125 3.2 58.1 1.0 OP1 D:DC17 3.4 70.0 1.0 OD1 A:ASP125 3.5 58.1 1.0 C3' D:DG16 3.7 54.3 1.0 O3' B:DA18 4.0 66.2 1.0 O A:GLY126 4.0 52.8 1.0 O5' D:DC17 4.1 70.0 1.0 CG A:GLU435 4.1 52.7 1.0 ND2 A:ASN438 4.2 47.8 1.0 C2' D:DG16 4.2 54.3 1.0 C4' D:DG16 4.3 54.3 1.0 MG A:MG601 4.3 63.8 1.0 CB A:ASP125 4.6 58.1 1.0 C5' D:DC17 4.6 70.0 1.0 OP1 D:DG16 4.7 54.3 1.0 NE2 A:HIS274 4.8 54.2 1.0 CE1 A:HIS274 4.9 54.2 1.0 C1' D:DG16 4.9 54.3 1.0 C3' B:DA18 5.0 66.2 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:64.9 occ:1.00 O3' F:DC9 2.0 70.3 1.0 OD1 E:ASP125 2.1 58.4 1.0 OD2 E:ASP224 2.1 62.2 1.0 OP2 H:DC17 2.7 72.8 1.0 CG E:ASP125 2.9 58.4 1.0 MG E:MG602 3.2 58.6 1.0 OD2 E:ASP125 3.2 58.4 1.0 CG E:ASP224 3.3 62.2 1.0 C3' F:DC9 3.4 70.3 1.0 P H:DC17 3.7 72.8 1.0 OP1 H:DC17 3.8 72.8 1.0 OE2 E:GLU185 4.0 64.1 1.0 OD1 E:ASP224 4.0 62.2 1.0 C4' F:DC9 4.1 70.3 1.0 OE2 E:GLU435 4.1 52.0 1.0 CB E:ASP125 4.2 58.4 1.0 C2' F:DC9 4.2 70.3 1.0 CB E:ASP224 4.5 62.2 1.0 N E:GLY126 4.5 54.7 1.0 C5' F:DC9 4.6 70.3 1.0 O3' H:DG16 4.6 56.1 1.0 O E:GLY126 4.7 54.7 1.0 CA E:ASP125 4.7 58.4 1.0 OE1 E:GLU185 4.8 64.1 1.0 CD E:GLU185 4.8 64.1 1.0 CE1 E:HIS274 4.9 55.0 1.0 NE2 E:HIS274 4.9 55.0 1.0 O5' H:DC17 5.0 72.8 1.0 CD E:GLU435 5.0 52.0 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Hztransib Strand Transfer Complex (Stc) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:58.6 occ:1.00 OD2 E:ASP125 2.1 58.4 1.0 OE1 E:GLU435 2.1 52.0 1.0 O3' H:DG16 2.4 56.1 1.0 OP2 H:DC17 2.4 72.8 1.0 OE2 E:GLU435 2.7 52.0 1.0 CD E:GLU435 2.8 52.0 1.0 P H:DC17 2.8 72.8 1.0 CG E:ASP125 3.1 58.4 1.0 MG E:MG601 3.2 64.9 1.0 OD1 E:ASP125 3.4 58.4 1.0 OP1 H:DC17 3.4 72.8 1.0 C3' H:DG16 3.6 56.1 1.0 ND2 E:ASN438 4.1 48.2 1.0 C2' H:DG16 4.1 56.1 1.0 O E:GLY126 4.2 54.7 1.0 C4' H:DG16 4.2 56.1 1.0 O3' F:DC9 4.2 70.3 1.0 CG E:GLU435 4.2 52.0 1.0 O5' H:DC17 4.3 72.8 1.0 CB E:ASP125 4.5 58.4 1.0 OD2 E:ASP224 4.7 62.2 1.0 C5' H:DC17 4.8 72.8 1.0 C1' H:DG16 4.8 56.1 1.0 OP1 H:DG16 4.8 56.1 1.0 CB E:GLU435 4.9 52.0 1.0

C.Liu, Y.Yang, D.G.Schatz. Structures of A Rag-Like Transposase During Cut-and-Paste Transposition. Nature V. 575 540 2019.
ISSN: ESSN 1476-4687
PubMed: 31723264
DOI: 10.1038/S41586-019-1753-7