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

Enzymatic activity of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing A Mismatch

Other elements in 8ppt:

Magnesium Binding Sites:

Magnesium binding site 1 out of 3 in 8ppt

Magnesium Binding Sites List in 8ppt

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 A Mismatch


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 A Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:11.7 occ:1.00 OD1 A:ASN450 2.0 16.0 1.0 OD2 A:ASP404 2.1 17.8 1.0 ND1 A:HIS560 2.2 26.7 1.0 NE2 A:HIS497 2.4 11.7 1.0 MG A:MG702 2.6 20.4 1.0 CE1 A:HIS560 3.0 23.8 1.0 CG A:ASN450 3.2 23.0 1.0 CG A:ASP404 3.2 15.1 1.0 CG A:HIS560 3.3 25.3 1.0 CD2 A:HIS497 3.3 10.9 1.0 CE1 A:HIS497 3.4 12.3 1.0 OD1 A:ASP404 3.7 22.3 1.0 CB A:HIS560 3.7 25.0 1.0 CA A:HIS560 3.9 18.0 1.0 CB A:ASN450 4.0 19.7 1.0 ND2 A:ASN450 4.1 13.8 1.0 NE2 A:HIS560 4.2 18.9 1.0 OP1 P:DC18 4.2 72.7 1.0 OD2 A:ASP360 4.3 21.2 1.0 OP2 P:DC18 4.3 76.2 1.0 CD2 A:HIS560 4.3 20.2 1.0 N A:ASN450 4.4 5.8 1.0 CB A:ASP404 4.5 10.2 1.0 CG A:HIS497 4.5 4.2 1.0 ND1 A:HIS497 4.5 11.4 1.0 O A:HIS560 4.7 27.2 1.0 CA A:ASN450 4.8 10.4 1.0 P P:DC18 4.8 78.8 1.0 C A:HIS560 4.9 22.7 1.0 N A:HIS560 4.9 11.1 1.0

Magnesium binding site 2 out of 3 in 8ppt

Magnesium Binding Sites List in 8ppt

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 A Mismatch


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 A Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:20.4 occ:1.00 OD2 A:ASP404 2.4 17.8 1.0 OP1 P:DC18 2.5 72.7 1.0 OD2 A:ASP360 2.6 21.2 1.0 MG A:MG701 2.6 11.7 1.0 NE2 A:HIS362 3.3 15.9 1.0 NE2 A:HIS562 3.4 31.2 1.0 CG A:ASP404 3.4 15.1 1.0 P P:DC18 3.6 78.8 1.0 CG A:ASP360 3.8 14.5 1.0 ND1 A:HIS560 3.8 26.7 1.0 OD1 A:ASN450 3.8 16.0 1.0 CE1 A:HIS362 3.9 22.5 1.0 C5' P:DC18 4.0 71.8 1.0 OP2 P:DC18 4.0 76.2 1.0 CD2 A:HIS562 4.1 23.0 1.0 OD1 A:ASP404 4.2 22.3 1.0 CB A:ASP404 4.2 10.2 1.0 O5' P:DC18 4.2 81.2 1.0 CA A:HIS560 4.3 18.0 1.0 CE1 A:HIS562 4.3 27.8 1.0 NE2 A:HIS497 4.4 11.7 1.0 O A:HIS560 4.4 27.2 1.0 CD2 A:HIS362 4.4 21.8 1.0 CE1 A:HIS560 4.5 23.8 1.0 OD1 A:ASP360 4.5 14.5 1.0 CG A:HIS560 4.7 25.3 1.0 C A:HIS560 4.7 22.7 1.0 CE1 A:HIS497 4.8 12.3 1.0 CB A:ASP360 4.9 19.1 1.0 CB A:HIS560 4.9 25.0 1.0 CG A:ASN450 5.0 23.0 1.0 O3' P:DG17 5.0 103.5 1.0

Magnesium binding site 3 out of 3 in 8ppt

Magnesium Binding Sites List in 8ppt

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 A Mismatch


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 A Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1304 b:30.6 occ:1.00 OD1 B:ASP956 2.6 22.3 1.0 OD1 B:ASP958 2.7 23.3 1.0 CB B:ASN954 3.3 20.9 1.0 OD2 B:ASP958 3.3 18.1 1.0 CG B:ASP958 3.4 19.6 1.0 OD1 B:ASN954 3.5 31.3 1.0 CG B:ASP956 3.6 20.1 1.0 CG B:ASN954 3.8 26.1 1.0 OD2 B:ASP956 3.9 23.2 1.0 CA B:ASN954 4.5 18.1 1.0 N B:ASN954 4.6 24.3 1.0 N B:ASP956 4.9 22.7 1.0 CB B:ASP958 4.9 7.8 1.0 CB B:ASP956 4.9 9.3 1.0 C B:ASN954 4.9 13.5 1.0 N B:CYS955 5.0 18.9 1.0

Reference: