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Magnesium in PDB 3spy: RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da

Enzymatic activity of RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da

All present enzymatic activity of RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da, PDB code: 3spy was solved by S.Xia, W.H.Konigsberg, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.67 / 2.14
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.336, 120.598, 130.812, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (pdb code 3spy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da, PDB code: 3spy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3spy

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Magnesium binding site 1 out of 5 in the RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da


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(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:26.6
occ:1.00
 OD1 A:ASP411 1.9 30.8 1.0
O2B A:UPC902 2.0 24.9 1.0
O1G A:UPC902 2.0 28.0 1.0
OD1 A:ASP623 2.1 26.2 1.0
O A:LEU412 2.2 24.3 1.0
O2A A:UPC902 2.3 26.1 1.0
CG A:ASP411 3.0 34.6 1.0
PB A:UPC902 3.1 23.6 1.0
CG A:ASP623 3.2 25.6 1.0
PG A:UPC902 3.3 26.1 1.0
C A:LEU412 3.4 25.4 1.0
PA A:UPC902 3.4 30.5 1.0
O3B A:UPC902 3.5 26.8 1.0
OD2 A:ASP411 3.5 38.2 1.0
C3A A:UPC902 3.6 26.8 1.0
OD2 A:ASP623 3.6 28.0 1.0
MG A:MG904 3.6 39.2 1.0
O A:HOH1014 3.8 44.6 1.0
O A:HOH1199 3.8 34.4 1.0
N A:LEU412 3.9 26.6 1.0
C5' A:UPC902 4.0 20.9 1.0
O2G A:UPC902 4.1 29.5 1.0
CA A:LEU412 4.1 26.5 1.0
O5' A:UPC902 4.2 26.7 1.0
CB A:ASP411 4.3 28.0 1.0
C A:ASP411 4.3 28.2 1.0
N A:ALA415 4.4 22.7 1.0
N A:THR413 4.4 25.3 1.0
N A:SER414 4.4 22.8 1.0
O1B A:UPC902 4.5 23.3 1.0
CB A:ASP623 4.5 24.5 1.0
CB A:LEU412 4.5 24.8 1.0
CB A:ALA415 4.6 21.5 1.0
CA A:THR413 4.7 24.6 1.0
O1A A:UPC902 4.7 33.6 1.0
O3G A:UPC902 4.7 31.4 1.0
C A:THR413 4.8 24.1 1.0
CA A:ASP411 4.8 29.8 1.0
O A:ASP411 4.8 29.3 1.0
O A:HOH1267 4.9 39.5 1.0

Magnesium binding site 2 out of 5 in 3spy

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Magnesium binding site 2 out of 5 in the RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:39.2
occ:1.00
 O P:HOH493 1.9 35.1 1.0
OD2 A:ASP623 2.0 28.0 1.0
O2A A:UPC902 2.2 26.1 1.0
O3' P:DC115 2.3 24.5 1.0
OD2 A:ASP411 2.3 38.2 1.0
O A:HOH1267 2.5 39.5 1.0
CG A:ASP623 3.0 25.6 1.0
PA A:UPC902 3.2 30.5 1.0
CG A:ASP411 3.3 34.6 1.0
C3' P:DC115 3.3 20.4 1.0
OD1 A:ASP623 3.4 26.2 1.0
OD1 A:ASP411 3.5 30.8 1.0
O1A A:UPC902 3.6 33.6 1.0
MG A:MG903 3.6 26.6 1.0
O5' A:UPC902 3.8 26.7 1.0
C5' A:UPC902 3.8 20.9 1.0
O A:HOH1199 4.1 34.4 1.0
O A:ASP621 4.2 25.4 1.0
C2' P:DC115 4.3 25.2 1.0
CB A:ASP623 4.3 24.5 1.0
CB A:SER624 4.4 28.3 1.0
C4' P:DC115 4.4 23.8 1.0
C A:ASP623 4.4 25.2 1.0
N A:ASP623 4.5 24.4 1.0
O A:HOH1033 4.5 17.4 1.0
N A:SER624 4.6 26.3 1.0
CA A:ASP623 4.6 25.2 1.0
CB A:ASP411 4.6 28.0 1.0
O A:ASP623 4.7 25.8 1.0
O2B A:UPC902 4.7 24.9 1.0
C3A A:UPC902 4.8 26.8 1.0
C5' P:DC115 4.8 23.6 1.0
O1G A:UPC902 4.8 28.0 1.0
OG A:SER624 4.8 27.6 1.0
O5' P:DC115 4.9 25.0 1.0

Magnesium binding site 3 out of 5 in 3spy

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Magnesium binding site 3 out of 5 in the RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:92.6
occ:1.00
 O A:LYS531 2.7 57.3 1.0
O A:ASN505 2.9 61.5 1.0
C A:LYS531 3.2 55.6 1.0
O A:LEU533 3.6 47.4 1.0
O A:ALA502 3.6 49.7 1.0
CA A:PRO506 3.6 61.0 1.0
CA A:LYS531 3.6 55.1 1.0
O A:ILE530 3.6 48.4 1.0
N A:ASN507 3.8 63.1 1.0
C A:ASN505 3.8 61.5 1.0
N A:LYS532 4.1 54.7 1.0
C A:PRO506 4.1 62.2 1.0
CD1 A:LEU538 4.1 37.9 1.0
N A:LEU533 4.1 51.6 1.0
N A:PRO506 4.2 60.6 1.0
CB A:ALA502 4.3 43.7 1.0
C A:ALA502 4.4 47.7 1.0
OD1 A:ASN507 4.4 71.8 1.0
C A:ILE530 4.5 48.8 1.0
N A:LYS531 4.5 51.8 1.0
C A:LEU533 4.6 48.3 1.0
CA A:LYS532 4.6 54.3 1.0
CA A:ALA502 4.6 44.9 1.0
C A:LYS532 4.6 53.2 1.0
CB A:LYS531 4.7 56.4 1.0
CB A:PRO506 4.7 60.9 1.0
CA A:LEU533 4.9 49.6 1.0
CA A:ASN507 4.9 64.7 1.0
CB A:ASN507 4.9 65.4 1.0

Magnesium binding site 4 out of 5 in 3spy

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Magnesium binding site 4 out of 5 in the RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg906

b:43.5
occ:1.00
 O A:HOH1228 1.9 30.4 1.0
O A:HOH1014 2.3 44.6 1.0
O A:HOH973 2.4 33.5 1.0
O A:HOH936 2.4 30.3 1.0
O A:HOH1180 2.5 31.3 1.0
NZ A:LYS486 3.4 37.5 1.0
OE1 A:GLU716 3.8 40.9 1.0
OE2 A:GLU716 3.9 43.2 1.0
O2G A:UPC902 4.1 29.5 1.0
CD A:GLU716 4.1 42.8 1.0
CB A:ASP684 4.2 36.8 1.0
OE1 A:GLU686 4.2 51.5 1.0
OD2 A:ASP684 4.3 43.6 1.0
O A:ASP411 4.3 29.3 1.0
O A:HOH1099 4.5 33.5 1.0
O1G A:UPC902 4.5 28.0 1.0
OG1 A:THR413 4.6 30.6 1.0
PG A:UPC902 4.7 26.1 1.0
CE A:LYS486 4.7 33.3 1.0
CG A:ASP684 4.7 43.6 1.0
CG A:GLU686 4.8 47.5 1.0
OD1 A:ASP411 4.9 30.8 1.0
CB A:ASP411 4.9 28.0 1.0
CD A:GLU686 5.0 49.5 1.0
O3G A:UPC902 5.0 31.4 1.0
O A:HOH1155 5.0 38.0 1.0

Magnesium binding site 5 out of 5 in 3spy

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Magnesium binding site 5 out of 5 in the RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of RB69 Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg907

b:55.8
occ:1.00
 OE2 A:GLU116 2.5 41.9 1.0
O A:HOH1222 2.5 42.7 1.0
OD2 A:ASP114 2.8 44.4 1.0
CD A:GLU116 3.4 37.1 1.0
OE1 A:GLU116 3.7 41.0 1.0
CG A:ASP114 3.7 35.0 1.0
OD1 A:ASP114 3.9 31.3 1.0
CB A:ALA327 4.0 24.7 1.0
O A:ILE115 4.5 26.2 1.0
ND2 A:ASN324 4.7 31.0 1.0
CG A:GLU116 4.8 32.7 1.0
CA A:ASN324 4.9 26.4 1.0
O A:TYR323 5.0 30.5 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 11:07:01 2024

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