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Manganese in PDB 2pyj: PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex)

Enzymatic activity of PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex)

All present enzymatic activity of PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex):
2.7.7.7;

Protein crystallography data

The structure of PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex), PDB code: 2pyj was solved by A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lazaro, M.De Vega, L.Blanco, M.Salas, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.07 / 2.03
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.835, 114.667, 104.761, 90.00, 94.07, 90.00
R / Rfree (%) 18.9 / 23.4

Other elements in 2pyj:

The structure of PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex) (pdb code 2pyj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex), PDB code: 2pyj:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2pyj

Go back to Manganese Binding Sites List in 2pyj
Manganese binding site 1 out of 2 in the PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn9003

b:5.1
occ:1.00
O2B A:DGT1588 1.9 3.3 1.0
OD1 A:ASP458 1.9 17.5 1.0
OD2 A:ASP249 2.0 11.2 1.0
O3G A:DGT1588 2.0 5.0 1.0
O2A A:DGT1588 2.0 6.8 1.0
O A:VAL250 2.1 9.1 1.0
CG A:ASP458 3.1 15.3 1.0
PB A:DGT1588 3.1 4.3 1.0
CG A:ASP249 3.2 14.6 1.0
PA A:DGT1588 3.3 5.8 1.0
C A:VAL250 3.3 12.3 1.0
PG A:DGT1588 3.3 6.6 1.0
MG A:MG9004 3.4 16.2 1.0
O3A A:DGT1588 3.6 5.8 1.0
O3B A:DGT1588 3.6 5.4 1.0
OD2 A:ASP458 3.6 15.2 1.0
OD1 A:ASP249 3.8 17.6 1.0
O A:HOH9435 3.8 8.5 1.0
O A:HOH9090 3.9 8.6 1.0
N A:VAL250 4.0 11.1 1.0
CA A:VAL250 4.1 12.3 1.0
C5' A:DGT1588 4.1 4.7 1.0
O5' A:DGT1588 4.2 5.1 1.0
O2G A:DGT1588 4.2 6.9 1.0
N A:SER252 4.2 14.2 1.0
C A:ASP249 4.3 10.3 1.0
N A:ASN251 4.3 10.8 1.0
CB A:ASP458 4.4 15.7 1.0
CB A:ASP249 4.4 12.8 1.0
O1G A:DGT1588 4.5 8.7 1.0
O1B A:DGT1588 4.5 2.7 1.0
O1A A:DGT1588 4.6 5.7 1.0
CA A:ASN251 4.6 12.3 1.0
N A:LEU253 4.7 12.2 1.0
CB A:VAL250 4.7 12.1 1.0
O A:ASP249 4.7 11.9 1.0
C A:ASN251 4.8 12.4 1.0
CA A:ASP249 4.8 12.2 1.0
O A:HOH9326 4.9 17.3 1.0
O A:ASP458 4.9 12.8 1.0
CA A:SER252 5.0 12.8 1.0

Manganese binding site 2 out of 2 in 2pyj

Go back to Manganese Binding Sites List in 2pyj
Manganese binding site 2 out of 2 in the PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn9001

b:2.0
occ:1.00
OD2 B:ASP458 1.6 13.8 1.0
O3G B:DGT1589 1.9 2.1 1.0
O2A B:DGT1589 2.0 2.8 1.0
OD1 B:ASP249 2.0 14.3 1.0
O2B B:DGT1589 2.0 2.0 1.0
O B:VAL250 2.1 14.0 1.0
CG B:ASP458 2.9 12.5 1.0
CG B:ASP249 3.1 15.2 1.0
PB B:DGT1589 3.2 2.1 1.0
PA B:DGT1589 3.3 2.4 1.0
C B:VAL250 3.3 11.1 1.0
PG B:DGT1589 3.3 2.5 1.0
OD2 B:ASP249 3.4 18.1 1.0
OD1 B:ASP458 3.4 16.3 1.0
O3A B:DGT1589 3.5 2.5 1.0
MG B:MG9002 3.6 6.5 1.0
O3B B:DGT1589 3.6 2.0 1.0
O B:HOH9017 3.8 2.0 1.0
N B:VAL250 3.9 15.1 1.0
O B:HOH9150 4.0 2.4 1.0
O2G B:DGT1589 4.0 2.0 1.0
CA B:VAL250 4.0 11.7 1.0
CB B:ASP458 4.1 12.2 1.0
C5' B:DGT1589 4.1 2.7 1.0
O5' B:DGT1589 4.2 2.6 1.0
C B:ASP249 4.2 11.2 1.0
N B:SER252 4.3 13.6 1.0
N B:ASN251 4.4 11.6 1.0
CB B:ASP249 4.4 12.4 1.0
O1G B:DGT1589 4.5 2.3 1.0
O1A B:DGT1589 4.5 2.9 1.0
CB B:VAL250 4.5 12.6 1.0
O1B B:DGT1589 4.6 2.9 1.0
O B:ASP249 4.6 13.2 1.0
N B:LEU253 4.7 12.5 1.0
O B:HOH9130 4.7 6.2 1.0
O B:ASP458 4.7 12.0 1.0
CA B:ASN251 4.8 11.6 1.0
CA B:ASP249 4.8 14.1 1.0
C B:ASN251 5.0 13.0 1.0

Reference:

A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lazaro, M.De Vega, L.Blanco, M.Salas, T.A.Steitz. Structures of PHI29 Dna Polymerase Complexed with Substrate: the Mechanism of Translocation in B-Family Polymerases Embo J. V. 26 3494 2007.
ISSN: ISSN 0261-4189
PubMed: 17611604
DOI: 10.1038/SJ.EMBOJ.7601780
Page generated: Sat Oct 5 14:57:47 2024

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