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Manganese in PDB 4lvs: Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min

Enzymatic activity of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min

All present enzymatic activity of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min, PDB code: 4lvs was solved by B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.67 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.982, 78.506, 55.138, 90.00, 113.24, 90.00
R / Rfree (%) 21.6 / 28.1

Other elements in 4lvs:

The structure of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min (pdb code 4lvs). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min, PDB code: 4lvs:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4lvs

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Manganese binding site 1 out of 6 in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:23.1
occ:1.00
 OD1 A:ASP192 2.1 19.3 1.0
OD2 A:ASP190 2.2 26.0 1.0
OD2 A:ASP256 2.2 33.6 1.0
O1A A:DTP401 2.3 21.9 1.0
O P:HOH205 2.4 26.7 1.0
O A:HOH524 2.4 25.4 1.0
CG A:ASP190 3.1 21.6 1.0
CG A:ASP192 3.2 27.6 1.0
CG A:ASP256 3.4 27.1 1.0
OD1 A:ASP190 3.4 17.0 1.0
PA A:DTP401 3.4 28.7 1.0
OD2 A:ASP192 3.6 24.4 1.0
O2A A:DTP401 3.7 31.8 1.0
MN A:MN403 3.7 23.8 1.0
O5' A:DTP401 3.9 34.5 1.0
CB A:ASP256 4.0 22.8 1.0
C5' A:DTP401 4.3 34.9 1.0
OD1 A:ASP256 4.4 26.6 1.0
O P:HOH207 4.5 35.8 1.0
CB A:ASP192 4.5 21.8 1.0
OP1 P:DC10 4.5 30.1 0.9
CB A:ASP190 4.5 15.8 1.0
O2G A:DTP401 4.6 28.4 1.0
C3' P:DC10 4.6 52.0 0.9
O3' P:DC10 4.8 57.8 0.9
O3A A:DTP401 4.9 24.3 1.0
C5' P:DC10 4.9 38.9 0.9
O1B A:DTP401 5.0 22.9 1.0

Manganese binding site 2 out of 6 in 4lvs

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Manganese binding site 2 out of 6 in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:23.8
occ:1.00
 O2G A:DTP401 2.0 28.4 1.0
OD1 A:ASP190 2.0 17.0 1.0
OD2 A:ASP192 2.1 24.4 1.0
O1B A:DTP401 2.2 22.9 1.0
O1A A:DTP401 2.3 21.9 1.0
O A:HOH503 2.3 25.9 1.0
PB A:DTP401 3.1 25.8 1.0
CG A:ASP190 3.2 21.6 1.0
CG A:ASP192 3.2 27.6 1.0
PG A:DTP401 3.2 25.9 1.0
PA A:DTP401 3.3 28.7 1.0
O3A A:DTP401 3.5 24.3 1.0
OD1 A:ASP192 3.6 19.3 1.0
O3B A:DTP401 3.6 27.6 1.0
OD2 A:ASP190 3.6 26.0 1.0
MN A:MN402 3.7 23.1 1.0
O3G A:DTP401 3.8 32.3 1.0
O A:ASP190 4.1 22.5 1.0
C5' A:DTP401 4.1 34.9 1.0
N A:ASP190 4.2 22.6 1.0
OG A:SER180 4.2 30.5 1.0
O A:HOH506 4.3 23.0 1.0
C A:ASP190 4.3 21.6 1.0
O5' A:DTP401 4.3 34.5 1.0
CB A:ASP190 4.4 15.8 1.0
O1G A:DTP401 4.4 29.4 1.0
CB A:ASP192 4.5 21.8 1.0
O2A A:DTP401 4.5 31.8 1.0
CA A:ASP190 4.5 19.3 1.0
N A:SER180 4.5 31.2 1.0
O2B A:DTP401 4.6 26.6 1.0
CA A:GLY179 4.6 25.3 1.0
O A:HOH524 4.8 25.4 1.0
N A:ASP192 4.8 17.0 1.0
N A:MET191 5.0 27.2 1.0

Manganese binding site 3 out of 6 in 4lvs

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Manganese binding site 3 out of 6 in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:30.0
occ:1.00
 O A:HOH621 2.1 30.0 1.0
O A:HOH620 2.2 30.0 1.0
O A:HOH622 2.2 30.0 1.0
O A:HOH619 2.3 30.0 1.0
OD1 A:ASP124 2.5 45.1 1.0
OD2 A:ASP124 3.1 37.8 1.0
CG A:ASP124 3.2 41.8 1.0
OG1 A:THR121 4.0 34.9 1.0
CB A:ASP124 4.7 35.5 1.0

Manganese binding site 4 out of 6 in 4lvs

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Manganese binding site 4 out of 6 in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:70.3
occ:1.00
 O P:HOH211 2.5 51.8 1.0
N7 P:DG4 2.8 31.2 1.0
C8 P:DG4 3.7 39.1 1.0
C5 P:DG4 3.9 34.2 1.0
O6 P:DG4 3.9 31.0 1.0
N6 P:DA5 4.0 20.0 1.0
C6 P:DG4 4.3 26.5 1.0
C2' P:DT3 4.3 20.0 1.0
OP2 P:DG4 4.6 43.3 1.0
N9 P:DG4 4.9 40.7 1.0
O4 T:DT12 5.0 23.2 1.0

Manganese binding site 5 out of 6 in 4lvs

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Manganese binding site 5 out of 6 in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:75.7
occ:1.00
 O P:HOH210 2.9 47.4 1.0
N7 T:DG15 3.9 37.4 1.0
O6 T:DG15 4.2 32.2 1.0
N7 T:DA14 4.2 34.1 1.0
C8 T:DA14 4.5 32.1 1.0
N4 T:DC16 4.6 25.2 1.0
C5 T:DG15 4.7 31.4 1.0
O6 P:DG1 4.9 21.5 1.0
C8 T:DG15 4.9 35.3 1.0
C6 T:DG15 4.9 32.8 1.0

Manganese binding site 6 out of 6 in 4lvs

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Manganese binding site 6 out of 6 in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn102

b:78.1
occ:1.00
 O T:HOH220 1.9 51.6 1.0
O D:HOH106 2.8 33.3 1.0
O T:HOH224 3.2 49.1 1.0
N7 T:DG3 4.5 44.6 1.0
O6 T:DG3 4.7 30.7 1.0

Reference:

B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson. Observing A Dna Polymerase Choose Right From Wrong. Cell(Cambridge,Mass.) V. 154 157 2013.
ISSN: ISSN 0092-8674
PubMed: 23827680
DOI: 10.1016/J.CELL.2013.05.048
Page generated: Sat Oct 5 20:17:15 2024

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