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Magnesium in PDB 3si6: RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MG2+

Enzymatic activity of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MG2+

All present enzymatic activity of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MG2+:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MG2+, PDB code: 3si6 was solved by M.Wang, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.31 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.458, 120.195, 131.205, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MG2+ (pdb code 3si6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MG2+, PDB code: 3si6:

Magnesium binding site 1 out of 1 in 3si6

Go back to Magnesium Binding Sites List in 3si6
Magnesium binding site 1 out of 1 in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:25.1
occ:1.00
 O A:LEU412 1.9 15.6 1.0
O1G A:DUP904 2.0 20.7 1.0
O2B A:DUP904 2.0 19.0 1.0
OD1 A:ASP623 2.1 26.6 1.0
O A:HOH1485 2.1 26.4 1.0
OD2 A:ASP411 2.3 29.2 1.0
PB A:DUP904 3.1 19.5 1.0
C A:LEU412 3.1 15.1 1.0
CG A:ASP623 3.2 22.9 1.0
PG A:DUP904 3.2 18.2 1.0
N3A A:DUP904 3.3 21.7 1.0
CG A:ASP411 3.5 27.6 1.0
O3B A:DUP904 3.5 19.2 1.0
OD2 A:ASP623 3.7 24.1 1.0
N A:LEU412 3.7 16.2 1.0
O2G A:DUP904 3.9 16.5 1.0
CA A:LEU412 3.9 15.6 1.0
CB A:ASP411 4.0 21.9 1.0
N A:SER414 4.1 14.1 1.0
N A:THR413 4.1 15.6 1.0
C A:ASP411 4.2 18.9 1.0
CA A:THR413 4.3 16.7 1.0
C A:THR413 4.4 15.4 1.0
CB A:ASP623 4.4 20.1 1.0
O3G A:DUP904 4.4 20.2 1.0
O1B A:DUP904 4.5 19.3 1.0
OD1 A:ASP411 4.5 30.5 1.0
CB A:LEU412 4.6 15.3 1.0
O A:HOH1182 4.6 48.2 1.0
N A:LEU415 4.6 11.1 1.0
CA A:ASP411 4.7 19.9 1.0
O A:ASP411 4.8 20.7 1.0
CA A:SER414 4.8 14.3 1.0
PA A:DUP904 4.9 26.4 1.0
O A:ASP623 4.9 17.1 1.0
C5' A:DUP904 5.0 15.6 1.0
O A:HOH1756 5.0 30.4 1.0

Reference:

S.Xia, M.Wang, G.Blaha, W.H.Konigsberg, J.Wang. Structural Insights Into Complete Metal Ion Coordination From Ternary Complexes of B Family RB69 Dna Polymerase. Biochemistry V. 50 9114 2011.
ISSN: ISSN 0006-2960
PubMed: 21923197
DOI: 10.1021/BI201260H
Page generated: Thu Aug 15 11:00:00 2024

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