Calcium in PDB 6pqx: Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)

The binding sites of Calcium atom in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc) (pdb code 6pqx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc), PDB code: 6pqx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:0.9 occ:1.00 O A:GLY126 2.3 75.6 1.0 OP2 D:DA17 2.3 0.3 1.0 OE2 A:GLU435 2.3 75.8 1.0 OD2 A:ASP125 2.4 74.2 1.0 OD1 A:ASP125 2.4 74.2 1.0 CG A:ASP125 2.7 74.2 1.0 O3' D:DG16 2.7 82.8 1.0 P D:DA17 3.1 0.3 1.0 C A:GLY126 3.3 75.6 1.0 CD A:GLU435 3.5 75.8 1.0 N A:ALA127 4.0 76.8 1.0 CA A:ALA127 4.0 76.8 1.0 C3' D:DG16 4.1 82.8 1.0 O5' D:DA17 4.1 0.3 1.0 N A:GLY126 4.2 75.6 1.0 OP1 D:DA17 4.2 0.3 1.0 C5' D:DA17 4.2 0.3 1.0 CB A:ASP125 4.2 74.2 1.0 OE1 A:GLU435 4.3 75.8 1.0 CG A:GLU435 4.3 75.8 1.0 CB A:ALA127 4.3 76.8 1.0 CA A:GLY126 4.4 75.6 1.0 C4' D:DG16 4.4 82.8 1.0 ND2 A:ASN438 4.5 63.3 1.0 OP1 D:DG16 4.6 82.8 1.0 CA A:CA602 4.7 66.0 1.0 C A:ASP125 4.9 74.2 1.0 C2' D:DG16 4.9 82.8 1.0 CA A:ASP125 5.0 74.2 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:66.0 occ:1.00 OD2 A:ASP224 2.5 84.2 1.0 OP1 D:DA17 2.6 0.3 1.0 OP2 D:DA17 2.7 0.3 1.0 O3' B:DT16 2.8 0.7 1.0 P D:DA17 3.1 0.3 1.0 CG A:ASP224 3.7 84.2 1.0 C3' B:DT16 3.9 0.7 1.0 O5' D:DA17 4.0 0.3 1.0 NE2 A:HIS274 4.1 82.8 1.0 CB A:LYS226 4.1 86.3 1.0 CG A:LYS226 4.2 86.3 1.0 CE1 A:HIS274 4.2 82.8 1.0 C4' B:DT16 4.4 0.7 1.0 O3' D:DG16 4.5 82.8 1.0 CB A:ASP224 4.5 84.2 1.0 OD1 A:ASP224 4.6 84.2 1.0 CA A:CA601 4.7 0.9 1.0 C5' D:DA17 4.8 0.3 1.0 OE2 A:GLU185 4.9 98.6 1.0 OD2 A:ASP125 4.9 74.2 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca601 b:96.1 occ:1.00 O E:GLY126 2.3 72.0 1.0 OE2 E:GLU435 2.3 72.7 1.0 OD2 E:ASP125 2.4 68.8 1.0 OD1 E:ASP125 2.4 68.8 1.0 OP2 H:DA17 2.5 0.2 1.0 CG E:ASP125 2.8 68.8 1.0 O3' H:DG16 3.0 82.9 1.0 P H:DA17 3.3 0.2 1.0 C E:GLY126 3.3 72.0 1.0 CD E:GLU435 3.5 72.7 1.0 OP1 H:DA17 4.0 0.2 1.0 N E:ALA127 4.0 69.8 1.0 CA E:ALA127 4.1 69.8 1.0 CA E:CA602 4.2 61.9 1.0 N E:GLY126 4.2 72.0 1.0 OE1 E:GLU435 4.3 72.7 1.0 C3' H:DG16 4.3 82.9 1.0 CB E:ASP125 4.3 68.8 1.0 CG E:GLU435 4.3 72.7 1.0 CB E:ALA127 4.4 69.8 1.0 CA E:GLY126 4.4 72.0 1.0 ND2 E:ASN438 4.6 63.0 1.0 O5' H:DA17 4.6 0.2 1.0 C4' H:DG16 4.7 82.9 1.0 C2' H:DG16 4.7 82.9 1.0 C E:ASP125 4.9 68.8 1.0 C5' H:DA17 5.0 0.2 1.0 CA E:ASP125 5.0 68.8 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca602 b:61.9 occ:1.00 OD2 E:ASP224 2.5 78.8 1.0 OP1 H:DA17 2.9 0.2 1.0 OP2 H:DA17 3.3 0.2 1.0 P H:DA17 3.6 0.2 1.0 O3' F:DT16 3.6 0.8 1.0 CG E:ASP224 3.7 78.8 1.0 NE2 E:HIS274 4.2 79.6 1.0 CA E:CA601 4.2 96.1 1.0 C3' F:DT16 4.3 0.8 1.0 CE1 E:HIS274 4.4 79.6 1.0 CB E:LYS226 4.5 84.0 1.0 CB E:ASP224 4.5 78.8 1.0 C4' F:DT16 4.5 0.8 1.0 OD2 E:ASP125 4.5 68.8 1.0 CG E:LYS226 4.5 84.0 1.0 OD1 E:ASP224 4.6 78.8 1.0 O3' H:DG16 4.7 82.9 1.0 O5' H:DA17 4.7 0.2 1.0 OE2 E:GLU185 4.9 88.9 1.0 OE2 E:GLU435 4.9 72.7 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