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Manganese in PDB 3sq0: Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)

Enzymatic activity of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)

All present enzymatic activity of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+), PDB code: 3sq0 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) 88.24 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.146, 119.669, 130.639, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) (pdb code 3sq0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+), PDB code: 3sq0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 3sq0

Go back to Manganese Binding Sites List in 3sq0
Manganese binding site 1 out of 5 in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn905

b:30.4
occ:1.00
 OD1 A:ASP623 2.0 29.1 1.0
OD1 A:ASP411 2.1 30.0 1.0
O2B A:DUP904 2.1 27.8 1.0
O1G A:DUP904 2.1 31.4 1.0
O A:LEU412 2.2 31.8 1.0
O2A A:DUP904 2.3 30.6 1.0
CG A:ASP623 3.1 29.4 1.0
CG A:ASP411 3.2 31.9 1.0
PB A:DUP904 3.2 27.2 1.0
C A:LEU412 3.3 30.5 1.0
PG A:DUP904 3.4 30.6 1.0
MN A:MN906 3.4 32.4 1.0
PA A:DUP904 3.5 30.9 1.0
OD2 A:ASP623 3.6 28.6 1.0
N3A A:DUP904 3.6 30.6 1.0
O3B A:DUP904 3.7 30.8 1.0
OD2 A:ASP411 3.7 31.2 1.0
N A:LEU412 3.9 31.6 1.0
O A:HOH978 3.9 28.9 1.0
CA A:LEU412 4.1 29.7 1.0
C5' A:DUP904 4.1 27.4 1.0
O2G A:DUP904 4.1 30.2 1.0
N A:SER414 4.3 27.1 1.0
O5' A:DUP904 4.3 31.6 1.0
N A:THR413 4.4 29.7 1.0
CB A:ASP623 4.4 29.4 1.0
CB A:ASP411 4.4 28.8 1.0
N A:LEU415 4.5 27.9 1.0
C A:ASP411 4.5 30.7 1.0
CB A:LEU412 4.6 30.4 1.0
O A:HOH922 4.6 27.0 1.0
O1B A:DUP904 4.6 30.4 1.0
C A:THR413 4.6 29.0 1.0
CA A:THR413 4.6 31.1 1.0
O1A A:DUP904 4.7 30.9 1.0
CB A:LEU415 4.8 27.5 1.0
O3G A:DUP904 4.9 33.4 1.0
O A:ASP623 4.9 30.9 1.0
CA A:SER414 4.9 30.2 1.0
CA A:ASP411 5.0 30.3 1.0

Manganese binding site 2 out of 5 in 3sq0

Go back to Manganese Binding Sites List in 3sq0
Manganese binding site 2 out of 5 in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn906

b:32.4
occ:1.00
 OD2 A:ASP623 2.1 28.6 1.0
O2A A:DUP904 2.1 30.6 1.0
O A:HOH922 2.1 27.0 1.0
OD2 A:ASP411 2.1 31.2 1.0
O A:HOH1118 2.3 25.3 1.0
CG A:ASP411 3.0 31.9 1.0
CG A:ASP623 3.0 29.4 1.0
OD1 A:ASP411 3.1 30.0 1.0
OD1 A:ASP623 3.2 29.1 1.0
PA A:DUP904 3.3 30.9 1.0
MN A:MN905 3.4 30.4 1.0
O1A A:DUP904 3.7 30.9 1.0
C3' P:DOC115 3.9 35.2 1.0
O5' A:DUP904 3.9 31.6 1.0
O A:HOH1115 4.1 37.4 1.0
C5' A:DUP904 4.1 27.4 1.0
CB A:SER624 4.3 30.5 1.0
C A:ASP623 4.4 30.8 1.0
CB A:ASP623 4.4 29.4 1.0
O P:HOH226 4.4 27.9 1.0
O A:ASP621 4.4 32.3 1.0
CB A:ASP411 4.4 28.8 1.0
O1G A:DUP904 4.5 31.4 1.0
N A:SER624 4.5 28.2 1.0
O A:ASP623 4.5 30.9 1.0
N3A A:DUP904 4.7 30.6 1.0
N A:ASP623 4.7 28.8 1.0
OG A:SER624 4.7 29.9 1.0
CA A:ASP623 4.7 30.8 1.0
O2B A:DUP904 4.8 27.8 1.0
CA A:SER624 4.9 31.6 1.0
C5' P:DOC115 4.9 40.9 1.0
C4' P:DOC115 4.9 37.2 1.0
C2' P:DOC115 5.0 34.9 1.0

Manganese binding site 3 out of 5 in 3sq0

Go back to Manganese Binding Sites List in 3sq0
Manganese binding site 3 out of 5 in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn907

b:53.9
occ:1.00
 O A:HOH978 2.3 28.9 1.0
O A:HOH1070 2.3 45.8 1.0
OE1 A:GLU686 2.5 50.7 1.0
O A:HOH1073 2.7 36.2 1.0
OE1 A:GLU716 3.1 57.0 1.0
CD A:GLU686 3.5 49.9 1.0
O A:HOH1123 3.7 32.4 1.0
OE2 A:GLU686 3.8 55.6 1.0
CD A:GLU716 3.8 53.1 1.0
OD2 A:ASP684 4.1 51.2 1.0
OE2 A:GLU716 4.2 55.2 1.0
O A:HOH1089 4.2 39.6 1.0
CB A:ASP684 4.2 41.8 1.0
O A:ASP411 4.3 32.1 1.0
NZ A:LYS486 4.3 46.3 1.0
O2G A:DUP904 4.4 30.2 1.0
OG1 A:THR413 4.4 36.7 1.0
CG A:ASP684 4.5 50.0 1.0
O1G A:DUP904 4.6 31.4 1.0
CB A:ASP411 4.7 28.8 1.0
CG A:GLU686 4.7 43.2 1.0
OD1 A:ASP411 4.7 30.0 1.0
CE A:LYS486 4.8 38.6 1.0
CG A:GLU716 4.8 49.6 1.0
PG A:DUP904 4.8 30.6 1.0
CA A:THR413 4.9 31.1 1.0
C A:ASP411 5.0 30.7 1.0

Manganese binding site 4 out of 5 in 3sq0

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Manganese binding site 4 out of 5 in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn908

b:52.3
occ:1.00
 O A:HOH934 2.0 39.1 1.0
OE2 A:GLU116 2.1 43.9 1.0
O A:HOH1139 2.2 48.0 1.0
OD2 A:ASP114 2.4 48.1 1.0
CD A:GLU116 3.1 40.3 1.0
OE1 A:GLU116 3.3 43.4 1.0
CG A:ASP114 3.3 41.9 1.0
OD1 A:ASP114 3.5 46.2 1.0
ND2 A:ASN324 4.2 38.5 1.0
O A:ILE115 4.3 36.2 1.0
CB A:ALA327 4.3 32.0 1.0
CG A:GLU116 4.4 37.0 1.0
CA A:ASN324 4.7 36.0 1.0
CB A:ASP114 4.7 37.1 1.0
C A:ILE115 5.0 36.4 1.0

Manganese binding site 5 out of 5 in 3sq0

Go back to Manganese Binding Sites List in 3sq0
Manganese binding site 5 out of 5 in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn909

b:0.8
occ:1.00
 OE2 A:GLU160 3.9 70.1 1.0
CD1 A:LEU152 4.5 47.2 1.0
OD1 A:ASP192 4.6 66.5 1.0
OE2 A:GLU161 4.8 68.7 1.0
CD A:GLU160 4.9 69.5 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: Sat Oct 5 17:54:33 2024

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