Manganese in PDB 5hrh: The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex

The structure of The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex, PDB code: 5hrh was solved by Y.Q.Chen, J.Zhang, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.99 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.500, 70.030, 86.010, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 27.3

The binding sites of Manganese atom in the The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex (pdb code 5hrh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex, PDB code: 5hrh:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:66.0 occ:1.00 O3G A:DGT201 1.9 80.6 1.0 OD1 A:ASP49 2.0 87.2 1.0 O A:HOH301 2.1 60.0 1.0 O1B A:DGT201 2.2 95.5 1.0 OD2 A:ASP51 2.4 59.5 1.0 O1A A:DGT201 2.5 71.6 1.0 CG A:ASP51 3.1 65.2 1.0 CG A:ASP49 3.2 80.4 1.0 PG A:DGT201 3.2 78.4 1.0 PB A:DGT201 3.3 76.0 1.0 PA A:DGT201 3.4 73.5 1.0 O A:ASP49 3.5 82.1 1.0 O3A A:DGT201 3.5 82.2 1.0 OD1 A:ASP51 3.5 73.1 1.0 O3B A:DGT201 3.7 71.7 1.0 OD2 A:ASP49 3.7 55.0 1.0 OG A:SER39 3.7 82.9 1.0 O5' A:DGT201 3.8 56.1 1.0 O2G A:DGT201 3.9 93.3 1.0 MN A:MN203 3.9 71.0 1.0 C A:ASP49 4.0 88.1 1.0 N A:SER39 4.2 56.0 1.0 CB A:ASP51 4.2 64.4 1.0 O1G A:DGT201 4.4 73.0 1.0 N A:ASP49 4.4 89.8 1.0 CB A:ASP49 4.4 93.8 1.0 CA A:ASP49 4.5 92.8 1.0 N A:ASP51 4.5 66.8 1.0 CA A:GLY38 4.6 55.7 1.0 O2B A:DGT201 4.7 46.0 1.0 CB A:SER39 4.7 67.8 1.0 O A:HOH302 4.8 68.6 1.0 N A:VAL50 4.8 82.5 1.0 C A:VAL50 4.8 77.7 1.0 O2A A:DGT201 4.8 54.2 1.0 C5' A:DGT201 4.9 62.7 1.0 C A:GLY38 5.0 61.6 1.0 CA A:VAL50 5.0 76.3 1.0 CA A:ASP51 5.0 64.8 1.0

Manganese binding site 2 out of 4 in the The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:71.0 occ:1.00 O A:HOH302 2.1 68.6 1.0 OD2 A:ASP100 2.3 76.2 1.0 OD2 A:ASP49 2.4 55.0 1.0 OD1 A:ASP51 2.4 73.1 1.0 O1A A:DGT201 2.4 71.6 1.0 CG A:ASP51 3.1 65.2 1.0 OD2 A:ASP51 3.2 59.5 1.0 CG A:ASP100 3.3 70.7 1.0 CG A:ASP49 3.3 80.4 1.0 PA A:DGT201 3.4 73.5 1.0 OD1 A:ASP49 3.6 87.2 1.0 CB A:ASP100 3.7 61.3 1.0 C5' A:DGT201 3.8 62.7 1.0 O5' A:DGT201 3.8 56.1 1.0 O2A A:DGT201 3.8 54.2 1.0 MN A:MN202 3.9 66.0 1.0 C3' D:DA9 4.3 0.9 1.0 OD1 A:ASP100 4.4 74.9 1.0 CB A:ASP51 4.5 64.4 1.0 OP1 D:DA9 4.6 1.0 1.0 NE2 A:GLN98 4.7 78.6 1.0 CB A:ASP49 4.7 93.8 1.0 O3G A:DGT201 4.7 80.6 1.0 O3A A:DGT201 4.8 82.2 1.0 CZ A:PHE102 4.9 84.5 1.0 CE1 A:PHE102 4.9 76.2 1.0 C4' D:DA9 4.9 0.9 1.0

Manganese binding site 3 out of 4 in the The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:73.0 occ:1.00 OD1 B:ASP49 2.0 89.4 1.0 O3G B:DGT201 2.2 75.2 1.0 O1B B:DGT201 2.2 86.2 1.0 OD2 B:ASP51 2.3 76.6 1.0 O1A B:DGT201 2.5 85.1 1.0 CG B:ASP51 3.0 67.8 1.0 CG B:ASP49 3.2 80.0 1.0 OD1 B:ASP51 3.3 63.5 1.0 PB B:DGT201 3.3 76.6 1.0 PA B:DGT201 3.4 71.6 1.0 PG B:DGT201 3.5 70.2 1.0 O B:ASP49 3.5 77.1 1.0 O3A B:DGT201 3.5 76.3 1.0 OG B:SER39 3.6 73.4 1.0 OD2 B:ASP49 3.7 70.2 1.0 O5' B:DGT201 3.7 47.7 1.0 O3B B:DGT201 3.8 71.4 1.0 MN B:MN203 4.0 68.1 1.0 N B:SER39 4.0 50.0 1.0 C B:ASP49 4.0 72.3 1.0 O2G B:DGT201 4.2 73.3 1.0 CB B:ASP51 4.2 56.5 1.0 CB B:ASP49 4.4 74.8 1.0 N B:ASP49 4.4 70.9 1.0 CA B:GLY38 4.4 55.5 1.0 CA B:ASP49 4.5 70.8 1.0 N B:ASP51 4.5 56.4 1.0 CB B:SER39 4.5 63.9 1.0 O1G B:DGT201 4.6 49.9 1.0 O2B B:DGT201 4.6 68.3 1.0 N B:VAL50 4.7 64.8 1.0 C B:VAL50 4.7 65.6 1.0 C B:GLY38 4.8 61.1 1.0 O2A B:DGT201 4.8 44.9 1.0 C5' B:DGT201 4.8 55.7 1.0 CA B:SER39 4.9 54.7 1.0 CA B:VAL50 4.9 65.5 1.0 CA B:ASP51 4.9 52.9 1.0

Manganese binding site 4 out of 4 in the The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of Asfvpolx(H115F/R127A Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn203 b:68.1 occ:1.00 OD2 B:ASP100 1.9 82.6 1.0 OD2 B:ASP49 2.1 70.2 1.0 O1A B:DGT201 2.3 85.1 1.0 OD1 B:ASP51 2.4 63.5 1.0 CG B:ASP100 3.0 83.2 1.0 CG B:ASP49 3.1 80.0 1.0 CG B:ASP51 3.3 67.8 1.0 PA B:DGT201 3.4 71.6 1.0 OD1 B:ASP49 3.5 89.4 1.0 OD2 B:ASP51 3.5 76.6 1.0 CB B:ASP100 3.6 44.4 1.0 O2A B:DGT201 3.7 44.9 1.0 OP1 G:DA9 3.7 0.3 1.0 OD1 B:ASP100 3.9 73.6 1.0 O5' B:DGT201 4.0 47.7 1.0 MN B:MN202 4.0 73.0 1.0 C5' B:DGT201 4.0 55.7 1.0 NE2 B:GLN98 4.2 70.6 1.0 CB B:ASP49 4.5 74.8 1.0 CB B:ASP51 4.7 56.5 1.0 O3G B:DGT201 4.8 75.2 1.0 O3A B:DGT201 4.8 76.3 1.0 CA B:ASP100 5.0 44.6 1.0

Y.Q.Chen, J.Zhang, J.H.Gan. The Crystal Structure of Se-Asfvpolx(L52/163M Mutant) in Complex with 1NT-Gap DNA1 To Be Published.