Magnesium 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
Potassium	(K)	11 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp, PDB code: 7sr6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 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 Magnesium with other atoms in the Mg 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:Mg601 b:62.0 occ:1.00 O3B A:DCP602 2.1 85.8 1.0 O A:LEU122 2.1 100.3 1.0 O1A A:DCP602 2.2 56.9 1.0 OD1 A:ASP121 2.6 102.5 1.0 O2G A:DCP602 2.7 75.9 1.0 OD2 A:ASP196 2.7 89.3 1.0 PG A:DCP602 3.0 80.7 1.0 O1B A:DCP602 3.0 75.5 1.0 PB A:DCP602 3.1 86.2 1.0 C A:LEU122 3.3 100.4 1.0 PA A:DCP602 3.4 68.9 1.0 O3A A:DCP602 3.6 73.0 1.0 CG A:ASP121 3.7 99.4 1.0 CG A:ASP196 3.8 95.1 1.0 O1G A:DCP602 4.0 79.9 1.0 O3G A:DCP602 4.1 57.5 1.0 CA A:LYS123 4.1 104.3 1.0 N A:LYS123 4.1 106.6 1.0 OD2 A:ASP121 4.2 91.6 1.0 N A:ASP124 4.2 94.1 1.0 OD1 A:ASP196 4.2 97.4 1.0 C5' A:DCP602 4.3 56.6 1.0 O A:HOH736 4.3 68.3 1.0 N A:LEU122 4.3 89.9 1.0 CA A:LEU122 4.4 87.9 1.0 O5' A:DCP602 4.4 58.2 1.0 C A:ASP121 4.4 83.2 1.0 O2B A:DCP602 4.4 100.4 1.0 C A:LYS123 4.5 102.3 1.0 O2A A:DCP602 4.5 61.5 1.0 O A:ASP121 4.6 109.4 1.0 NZ A:LYS230 4.6 108.3 1.0 N A:CYS125 4.7 91.7 1.0 CB A:ASP121 4.9 88.2 1.0 CA A:ASP124 5.0 92.2 1.0

Magnesium binding site 2 out of 5 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 Magnesium with other atoms in the Mg 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:Mg612 b:45.3 occ:0.50 N A:ASP516 2.5 57.9 1.0 O A:THR467 2.6 59.4 1.0 OE1 A:GLU496 2.8 60.6 1.0 OD1 A:ASP516 3.1 74.2 1.0 CB A:ASP516 3.2 76.1 1.0 CG A:ASP516 3.3 84.2 1.0 C A:SER515 3.4 58.4 1.0 CA A:ASP516 3.4 65.3 1.0 CA A:SER515 3.4 57.9 1.0 OD1 A:ASP468 3.4 53.4 1.0 O A:HOH738 3.5 38.2 1.0 OG A:SER515 3.6 61.4 1.0 CD A:GLU496 3.6 56.0 1.0 C A:THR467 3.6 65.7 1.0 CG A:ASP468 3.7 66.8 1.0 CA A:ASP468 3.8 61.7 1.0 CB A:ASP468 3.8 59.4 1.0 OD1 A:ASN577 3.8 61.7 1.0 OE2 A:GLU496 3.9 60.4 1.0 CB A:SER515 4.0 58.1 1.0 OD2 A:ASP516 4.1 101.3 1.0 N A:ASP468 4.2 64.5 1.0 N A:SER517 4.3 55.6 1.0 C A:ASP516 4.3 56.9 1.0 OD2 A:ASP468 4.6 69.0 1.0 O A:SER515 4.6 56.3 1.0 OG1 A:THR467 4.6 62.2 1.0 N A:SER515 4.7 57.0 1.0 CG A:GLU496 4.7 46.3 1.0 O A:ILE514 4.8 49.2 1.0 CA A:THR467 4.8 66.8 1.0 N A:THR467 5.0 57.3 1.0 CG A:ASN577 5.0 58.9 1.0

Magnesium binding site 3 out of 5 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 Magnesium with other atoms in the Mg 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 D:Mg103 b:67.3 occ:1.00 CD1 F:LEU333 2.8 110.8 1.0 N3 D:DA24 3.4 106.5 1.0 NZ F:LYS113 3.5 112.9 1.0 C2 D:DA24 3.5 106.9 1.0 CA F:GLY331 3.7 71.2 1.0 CB F:ALA334 3.7 76.1 1.0 C4 D:DA24 3.9 113.8 1.0 CG F:LEU333 4.0 112.2 1.0 OE1 F:GLN353 4.0 76.4 1.0 N F:GLY331 4.1 78.9 1.0 N1 D:DA24 4.1 98.1 1.0 N F:ALA334 4.4 90.5 1.0 CD F:GLN353 4.4 81.8 1.0 C5 D:DA24 4.4 104.2 1.0 C6 D:DA24 4.5 92.2 1.0 C F:GLY331 4.5 69.5 1.0 N9 D:DA24 4.6 112.0 1.0 C2' D:DA24 4.6 135.0 1.0 CD2 F:LEU333 4.7 120.3 1.0 CA F:ALA334 4.7 79.2 1.0 O F:GLY331 4.7 82.9 1.0 ND2 F:ASN354 4.8 111.0 1.0 CE F:LYS113 4.8 98.6 1.0 CG F:GLN353 4.8 72.7 1.0 NE2 F:GLN353 4.9 83.0 1.0 C1' D:DA24 5.0 125.2 1.0

Magnesium binding site 4 out of 5 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 Magnesium with other atoms in the Mg 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 F:Mg602 b:60.8 occ:1.00 OD1 F:ASP121 1.9 87.6 1.0 O2B F:TTP605 2.0 48.7 1.0 O1G F:TTP605 2.1 75.9 1.0 O1A F:TTP605 2.2 69.2 1.0 OD2 F:ASP196 2.2 82.3 1.0 O F:LEU122 2.2 76.5 1.0 CG F:ASP121 2.6 81.2 1.0 OD2 F:ASP121 2.6 84.0 1.0 CG F:ASP196 3.2 86.1 1.0 PB F:TTP605 3.3 71.2 1.0 C F:LEU122 3.4 78.7 1.0 PA F:TTP605 3.4 87.4 1.0 PG F:TTP605 3.5 89.2 1.0 O3A F:TTP605 3.6 73.4 1.0 N F:LEU122 3.8 71.0 1.0 OD1 F:ASP196 3.8 75.3 1.0 C5' F:TTP605 3.8 69.0 1.0 O3B F:TTP605 3.8 66.2 1.0 O5' F:TTP605 4.0 70.3 1.0 NZ F:LYS230 4.0 66.8 1.0 CB F:ASP121 4.0 81.1 1.0 CA F:LEU122 4.1 70.0 1.0 O2G F:TTP605 4.3 80.4 1.0 CB F:ASP196 4.4 74.7 1.0 C F:ASP121 4.4 81.8 1.0 N F:LYS123 4.4 77.0 1.0 O1B F:TTP605 4.6 64.0 1.0 CB F:CYS125 4.6 82.6 1.0 O3G F:TTP605 4.6 74.6 1.0 CA F:ASP121 4.6 80.2 1.0 O2A F:TTP605 4.7 72.0 1.0 CA F:LYS123 4.7 82.0 1.0 CB F:LEU122 4.7 71.9 1.0 N F:CYS125 4.8 84.0 1.0 N F:ASP124 4.9 81.0 1.0

Magnesium binding site 5 out of 5 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 Magnesium with other atoms in the Mg 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 G:Mg611 b:69.8 occ:1.00 O G:VAL427 2.1 70.8 1.0 O G:GLY428 2.8 74.5 1.0 O G:ARG89 3.0 65.1 1.0 C G:VAL427 3.0 73.4 1.0 C G:GLY428 3.1 63.4 1.0 CA G:ARG89 3.4 53.4 1.0 CA G:GLY428 3.5 68.0 1.0 C G:ARG89 3.6 52.4 1.0 N G:GLY428 3.6 79.2 1.0 CB G:ARG89 3.7 57.7 1.0 N G:ILE429 3.8 57.0 1.0 ND2 G:ASN92 3.9 58.7 1.0 CG G:ARG89 3.9 53.3 1.0 CA G:VAL427 4.2 67.5 1.0 CB G:ALA93 4.3 55.4 1.0 N G:ALA93 4.3 60.7 1.0 CA G:ILE429 4.5 56.6 1.0 CB G:ASN92 4.5 64.1 1.0 CG G:ASN92 4.6 58.0 1.0 CA G:ALA93 4.6 57.1 1.0 N G:ARG89 4.7 54.4 1.0 CD G:ARG89 4.8 52.0 1.0 N G:ALA90 4.8 44.9 1.0 CG1 G:ILE429 4.8 60.7 1.0 C G:ASN92 4.9 58.1 1.0 CB G:VAL427 4.9 69.2 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