Potassium in PDB 7sr6: Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp

The structure of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp, PDB code: 7sr6 was solved by E.T.Baldwin, C.Nichols, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.85 / 2.62
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	177.697, 177.697, 117.414, 90, 90, 120
R / Rfree (%)	16.8 / 21.8

The structure of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Potassium atom in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp (pdb code 7sr6). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 11 binding sites of Potassium where determined in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp, PDB code: 7sr6:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 11 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range: probe atom residue distance (Å) B Occ A:K609 b:92.2 occ:1.00 CE1 A:TYR519 3.8 71.2 1.0 CD1 A:TYR519 4.2 60.7 1.0 C5' E:DT11 4.3 65.9 1.0 CB A:THR370 4.3 49.7 1.0 CZ A:TYR519 4.3 73.8 1.0 CG2 A:THR370 4.5 48.8 1.0 OG1 A:THR370 4.5 48.2 1.0 OP1 E:DT11 4.6 62.2 1.0 OH A:TYR519 4.6 75.9 1.0 O E:HOH101 4.6 64.5 1.0 CD2 A:PHE371 4.7 53.7 1.0 C3' E:DT11 4.8 63.9 1.0 CE2 A:PHE371 4.8 55.5 1.0 C4' E:DT11 4.8 63.5 1.0 OP1 E:DT12 4.9 60.2 1.0 O3' E:DT11 5.0 62.8 1.0

Potassium binding site 2 out of 11 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range: probe atom residue distance (Å) B Occ A:K610 b:71.8 occ:1.00 CA A:GLY176 3.9 70.7 1.0 C A:GLY176 4.0 66.5 1.0 N A:ARG177 4.1 65.7 1.0 O A:THR173 4.2 82.0 1.0 CB B:PRO151 4.4 54.5 1.0 CA A:THR173 4.5 59.9 1.0 O A:GLN172 4.6 68.7 1.0 O A:GLY176 4.6 68.6 1.0 O B:PRO151 4.7 83.0 1.0 OE1 A:GLN180 4.8 71.1 1.0 N A:GLY176 4.8 64.3 1.0 C A:THR173 4.8 68.3 1.0 CG B:PRO151 4.8 56.0 1.0 CD B:PRO151 4.9 63.5 1.0

Potassium binding site 3 out of 11 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range: probe atom residue distance (Å) B Occ A:K611 b:101.3 occ:1.00 O A:HIS365 3.3 71.8 1.0 O A:HOH749 3.7 54.8 1.0 O A:ILE532 3.9 78.2 1.0 C A:HIS365 4.3 63.0 1.0 NE2 A:HIS345 4.3 68.9 1.0 CA A:SER366 4.3 73.0 1.0 N A:TYR534 4.4 79.1 1.0 NH2 A:ARG296 4.4 90.4 1.0 CD1 A:LEU531 4.5 65.8 1.0 CE1 A:HIS365 4.6 53.2 1.0 CB A:TYR534 4.7 85.0 1.0 NE2 A:HIS365 4.7 55.4 1.0 N A:SER366 4.7 68.7 1.0 CA A:LYS533 4.8 72.6 1.0 OG1 A:THR367 4.8 62.4 1.0 ND1 A:HIS365 4.9 56.0 1.0 CG A:LEU531 4.9 61.8 1.0 C A:ILE532 4.9 67.0 1.0 C A:LYS533 4.9 67.1 1.0 CD2 A:HIS365 5.0 51.9 1.0 N A:THR367 5.0 69.6 1.0

Potassium binding site 4 out of 11 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range: probe atom residue distance (Å) B Occ B:K614 b:92.8 occ:1.00 CB B:TRP34 3.6 64.9 1.0 O D:HOH203 3.8 39.9 1.0 CG B:TRP34 3.9 63.7 1.0 CD1 B:TRP34 4.3 65.6 1.0 CD2 B:TRP34 4.4 63.8 1.0 CE3 B:TRP34 4.9 64.5 1.0

Potassium binding site 5 out of 11 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range: probe atom residue distance (Å) B Occ B:K615 b:84.8 occ:1.00 SG B:CYS171 4.1 101.7 1.0 CB B:LEU122 4.5 83.8 1.0 CB B:ASP196 4.5 95.4 1.0 O B:GLY394 4.9 82.9 1.0

Potassium binding site 6 out of 11 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range: probe atom residue distance (Å) B Occ D:K101 b:64.3 occ:1.00 O4' D:DC7 3.2 48.0 1.0 O A:GLN102 3.7 72.7 1.0 C4' D:DC7 3.8 55.5 1.0 C1' D:DC7 3.9 52.3 1.0 NE2 A:GLN172 4.0 76.1 1.0 OE1 A:GLN172 4.0 56.6 1.0 N A:GLN102 4.1 59.1 1.0 C2' D:DC6 4.3 45.3 1.0 CB A:GLN102 4.4 57.9 1.0 C A:GLN102 4.4 63.5 1.0 CD A:GLN172 4.4 74.8 1.0 C5' D:DC7 4.5 55.0 1.0 CA A:GLN102 4.5 66.2 1.0 N A:LEU101 4.6 61.2 1.0 O2 D:DC6 4.7 38.9 1.0 C2' D:DC7 4.8 57.2 1.0 CB A:PRO100 4.8 67.3 1.0 O5' D:DC7 5.0 47.7 1.0

Potassium binding site 7 out of 11 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range: probe atom residue distance (Å) B Occ D:K102 b:60.6 occ:1.00 O4' D:DA12 3.4 51.1 1.0 N3 D:DA11 3.9 48.3 1.0 NE2 A:GLN268 4.2 71.6 1.0 C1' D:DA12 4.2 60.7 1.0 C4' D:DA12 4.3 55.2 1.0 C2 D:DA11 4.5 51.0 1.0 CB A:LEU295 4.6 47.3 1.0 N9 D:DA12 4.6 62.3 1.0 C2' D:DA11 4.7 53.5 1.0 O A:LEU295 4.8 57.0 1.0 C1' D:DA11 4.8 48.6 1.0 CD1 A:LEU264 4.8 77.0 1.0 N3 D:DA12 4.8 52.7 1.0 O2 E:DT18 4.9 75.9 1.0 CD1 A:LEU295 4.9 48.5 1.0 CD2 A:LEU295 4.9 47.5 1.0 C4 D:DA12 5.0 57.1 1.0 C5' D:DA12 5.0 48.6 1.0

Potassium binding site 8 out of 11 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range: probe atom residue distance (Å) B Occ F:K621 b:95.1 occ:1.00 O F:GLN102 3.3 61.8 1.0 NE2 F:GLN172 3.4 72.0 1.0 O4' H:DT8 3.5 62.2 1.0 C4' H:DT8 3.8 59.8 1.0 N F:GLN102 4.0 62.6 1.0 C F:GLN102 4.0 60.3 1.0 CB F:GLN102 4.2 65.0 1.0 C1' H:DT8 4.2 64.0 1.0 CA F:GLN102 4.3 67.4 1.0 CD F:GLN172 4.3 59.5 1.0 OE1 F:GLN172 4.4 69.7 1.0 C5' H:DT8 4.4 56.0 1.0 N F:LEU101 4.6 62.8 1.0 C2' H:DC7 4.7 58.5 1.0 CB F:PRO100 4.8 70.5 1.0 C2' H:DT8 4.8 68.5 1.0 C3' H:DT8 5.0 56.0 1.0

Potassium binding site 9 out of 11 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range: probe atom residue distance (Å) B Occ F:K622 b:84.8 occ:1.00 CE2 F:PHE371 3.8 62.5 1.0 CD2 F:PHE371 4.1 61.0 1.0 CG F:GLN522 4.4 61.3 1.0 N F:ALA523 4.4 48.1 1.0 O F:TYR519 4.4 59.7 1.0 CB F:GLN522 4.5 48.7 1.0 CD2 F:TYR519 4.6 55.6 1.0 CA F:ALA523 4.6 42.7 1.0 CB F:ALA523 4.7 43.0 1.0 CG F:TYR519 4.7 52.6 1.0 CE2 F:TYR519 4.8 51.5 1.0 C F:GLN522 4.9 48.8 1.0 CZ F:PHE371 5.0 69.2 1.0

Potassium binding site 10 out of 11 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range: probe atom residue distance (Å) B Occ G:K609 b:81.3 occ:1.00 CG G:TRP34 3.7 50.6 1.0 CD1 G:TRP34 3.9 54.5 1.0 CB G:TRP34 4.0 60.6 1.0 CD2 G:TRP34 4.2 57.0 1.0 OP1 H:DT8 4.3 61.8 1.0 NE1 G:TRP34 4.4 49.9 1.0 CE2 G:TRP34 4.5 51.2 1.0 CD F:PRO100 4.7 72.7 1.0 CG F:PRO100 4.7 72.9 1.0 CE3 G:TRP34 4.8 50.7 1.0

E.T.Baldwin, M.Gotte, E.P.Tchesnokov, E.Arnold, M.Hagel, C.Nichols, P.Dossang, M.Lamers, P.Wan, S.Steinbacher, D.L.Romero. Human Endogenous Retrovirus-K (Herv-K) Reverse Transcriptase (Rt) Structure and Biochemistry Reveals Remarkable Similarities to Hiv-1 Rt and Opportunities For Herv-K-Specific Inhibition. Proc.Natl.Acad.Sci.Usa V. 119 60119 2022.
ISSN: ESSN 1091-6490
PubMed: 35771941
DOI: 10.1073/PNAS.2200260119