Magnesium in PDB 8ppv: Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches

Enzymatic activity of Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches

Other elements in 8ppv:

Magnesium Binding Sites:

Magnesium binding site 1 out of 3 in 8ppv

Magnesium Binding Sites List in 8ppv

Magnesium binding site 1 out of 3 in the Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) 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 Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:32.1 occ:1.00 OD2 A:ASP360 1.9 25.3 1.0 NE2 A:HIS562 2.5 39.6 1.0 OD2 A:ASP404 2.9 23.5 1.0 CG A:ASP360 2.9 23.1 1.0 NE2 A:HIS362 3.1 15.1 1.0 MG A:MG702 3.2 17.0 1.0 CD2 A:HIS562 3.3 41.2 1.0 OD1 A:ASP360 3.6 24.0 1.0 CE1 A:HIS562 3.6 38.8 1.0 CG A:ASP404 3.7 16.8 1.0 CD2 A:HIS362 3.9 23.3 1.0 CB A:ASP360 4.0 27.7 1.0 CA A:HIS560 4.0 30.7 1.0 CB A:ASP404 4.0 16.9 1.0 CE1 A:HIS362 4.1 17.6 1.0 O A:HIS560 4.3 40.2 1.0 C A:HIS560 4.4 35.3 1.0 CG A:HIS562 4.5 40.8 1.0 N A:HIS560 4.6 32.2 1.0 OD1 A:ASP404 4.6 22.1 1.0 ND1 A:HIS562 4.6 44.5 1.0 ND1 A:HIS560 4.7 33.4 1.0 CE1 A:HIS497 4.7 19.3 1.0 NE2 A:HIS497 4.7 18.4 1.0 CA A:ASP360 4.9 22.2 1.0 OD1 A:ASN450 4.9 25.0 1.0

Magnesium binding site 2 out of 3 in 8ppv

Magnesium Binding Sites List in 8ppv

Magnesium binding site 2 out of 3 in the Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) 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 Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:17.0 occ:1.00 OD1 A:ASN450 1.8 25.0 1.0 OD2 A:ASP404 1.9 23.5 1.0 ND1 A:HIS560 2.9 33.4 1.0 CG A:ASN450 2.9 34.5 1.0 CG A:ASP404 3.0 16.8 1.0 NE2 A:HIS497 3.1 18.4 1.0 MG A:MG701 3.2 32.1 1.0 CE1 A:HIS560 3.5 32.1 1.0 OD1 A:ASP404 3.5 22.1 1.0 ND2 A:ASN450 3.6 30.2 1.0 CE1 A:HIS497 3.9 19.3 1.0 CG A:HIS560 4.0 33.3 1.0 CD2 A:HIS497 4.1 24.8 1.0 CB A:ASN450 4.1 29.4 1.0 OD2 A:ASP360 4.2 25.3 1.0 CB A:ASP404 4.3 16.9 1.0 N A:ASN450 4.4 15.4 1.0 CA A:HIS560 4.5 30.7 1.0 CB A:HIS560 4.5 30.3 1.0 NE2 A:HIS560 4.7 31.3 1.0 CA A:ASN450 4.7 23.2 1.0 N A:ALA451 4.9 26.2 1.0 O A:HIS560 4.9 40.2 1.0 C A:ASN450 4.9 24.3 1.0 NE2 A:HIS362 5.0 15.1 1.0

Magnesium binding site 3 out of 3 in 8ppv

Magnesium Binding Sites List in 8ppv

Magnesium binding site 3 out of 3 in the Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) 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 Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1304 b:21.0 occ:1.00 OD1 B:ASP956 2.4 21.5 1.0 OD1 B:ASP958 2.7 33.5 1.0 OD2 B:ASP958 3.0 16.3 1.0 ND2 B:ASN954 3.2 29.0 1.0 CG B:ASP958 3.2 20.1 1.0 CB B:ASN954 3.3 18.9 1.0 CG B:ASP956 3.5 27.2 1.0 CG B:ASN954 3.7 25.8 1.0 OD2 B:ASP956 3.9 26.8 1.0 CA B:ASN954 4.3 13.8 1.0 N B:ASN954 4.4 21.7 1.0 N B:ASP956 4.5 23.9 1.0 C B:ASN954 4.6 16.2 1.0 CB B:ASP956 4.7 17.6 1.0 N B:CYS955 4.7 19.0 1.0 CB B:ASP958 4.7 12.3 1.0 C B:ASP956 4.9 17.7 1.0 CA B:ASP956 4.9 16.3 1.0 OD1 B:ASN954 5.0 30.7 1.0 O B:ASP956 5.0 6.5 1.0

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