Magnesium in PDB 8ppu: Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches

The structure of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Magnesium atom in the Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches (pdb code 8ppu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches, PDB code: 8ppu:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:19.4 occ:1.00 OD1 A:ASN450 1.9 31.9 1.0 OD2 A:ASP404 2.0 23.2 1.0 NE2 A:HIS497 2.5 17.0 1.0 CG A:ASP404 2.8 19.2 1.0 CD2 A:HIS560 2.9 31.4 1.0 OD1 A:ASP404 3.0 32.0 1.0 CG A:ASN450 3.2 28.4 1.0 MG A:MG702 3.2 37.0 1.0 CE1 A:HIS497 3.3 21.8 1.0 CD2 A:HIS497 3.6 25.1 1.0 SP P:PST21 3.8 86.0 1.0 CG A:HIS560 3.8 27.3 1.0 NE2 A:HIS560 3.9 32.3 1.0 ND2 A:ASN450 4.1 24.7 1.0 CB A:ASN450 4.1 15.7 1.0 N A:ASN450 4.1 9.1 1.0 CB A:HIS560 4.1 28.3 1.0 CB A:ASP404 4.1 11.3 1.0 OD2 A:ASP360 4.2 26.0 1.0 CA A:HIS560 4.3 22.0 1.0 ND1 A:HIS497 4.5 17.6 1.0 OP1 P:PST21 4.5 80.3 1.0 CA A:ASN450 4.6 15.6 1.0 P P:PST21 4.6 91.6 1.0 CG A:HIS497 4.7 17.4 1.0 N A:ALA451 4.8 37.2 1.0 C A:ASN450 4.9 17.5 1.0 ND1 A:HIS560 5.0 24.4 1.0

Magnesium binding site 2 out of 3 in the Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:37.0 occ:1.00 OD2 A:ASP360 2.0 26.0 1.0 OD2 A:ASP404 2.2 23.2 1.0 OP1 P:PST21 2.6 80.3 1.0 NE2 A:HIS362 2.8 14.9 1.0 NE2 A:HIS562 3.0 40.1 1.0 MG A:MG701 3.2 19.4 1.0 CG A:ASP360 3.3 20.2 1.0 CG A:ASP404 3.3 19.2 1.0 P P:PST21 3.6 91.6 1.0 CD2 A:HIS362 3.7 21.7 1.0 CE1 A:HIS362 3.8 21.1 1.0 CB A:ASP404 3.8 11.3 1.0 SP P:PST21 3.9 86.0 1.0 CD2 A:HIS562 3.9 34.8 1.0 CE1 A:HIS562 3.9 38.3 1.0 CB A:ASP360 4.1 23.9 1.0 OD1 A:ASP360 4.1 20.3 1.0 O5' P:PST21 4.2 85.3 1.0 OD1 A:ASP404 4.4 32.0 1.0 CA A:HIS560 4.5 22.0 1.0 O A:HIS560 4.6 42.6 1.0 CD2 A:HIS560 4.7 31.4 1.0 OD1 A:ASN450 4.7 31.9 1.0 C5' P:PST21 4.7 83.8 1.0 O3' P:PST21 4.8 80.0 1.0 CA A:ASP360 4.9 21.0 1.0 C A:HIS560 4.9 32.6 1.0 NE2 A:HIS497 4.9 17.0 1.0 CE1 A:HIS497 4.9 21.8 1.0 ND1 A:HIS362 4.9 14.1 1.0 CG A:HIS362 4.9 16.7 1.0 O3' P:PST20 5.0 95.7 1.0

Magnesium binding site 3 out of 3 in the Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1304 b:12.3 occ:1.00 OD1 B:ASP958 2.5 29.9 1.0 OD1 B:ASP956 2.6 26.1 1.0 CB B:ASN954 3.0 19.5 1.0 OD2 B:ASP958 3.1 17.3 1.0 CG B:ASP958 3.2 20.9 1.0 ND2 B:ASN954 3.3 33.5 1.0 CG B:ASN954 3.7 29.6 1.0 CG B:ASP956 3.7 18.4 1.0 CA B:ASN954 4.1 12.9 1.0 OD2 B:ASP956 4.1 19.9 1.0 N B:ASN954 4.2 22.1 1.0 C B:ASN954 4.5 10.0 1.0 N B:ASP956 4.6 24.8 1.0 N B:CYS955 4.6 22.1 1.0 CB B:ASP958 4.6 13.3 1.0 OD1 B:ASN954 4.9 25.4 1.0 CB B:ASP956 5.0 8.4 1.0

L.Betancurt-Anzola, K.M.Zatopek, M.Martinez-Carranza, A.F.Gardner, L.Sauguet. Molecular Basis For Proof-Reading By Family-D Dna Polymerases To Be Published.