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Manganese in PDB 4klt: Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min

Enzymatic activity of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min

All present enzymatic activity of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min, PDB code: 4klt 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) 25.76 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.082, 78.596, 54.980, 90.00, 112.43, 90.00
R / Rfree (%) 22.9 / 29.3

Other elements in 4klt:

The structure of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min (pdb code 4klt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min, PDB code: 4klt:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4klt

Go back to Manganese Binding Sites List in 4klt
Manganese binding site 1 out of 4 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 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 Product Complex with MN2+, 30 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:65.7
occ:1.00
OD1 A:ASP124 2.5 39.7 1.0
CG A:ASP124 3.3 36.4 1.0
OD2 A:ASP124 3.4 31.5 1.0
O A:HOH567 4.1 39.1 1.0
NZ A:LYS127 4.3 46.1 1.0
OG1 A:THR121 4.5 33.2 1.0
CB A:ASP124 4.8 29.2 1.0

Manganese binding site 2 out of 4 in 4klt

Go back to Manganese Binding Sites List in 4klt
Manganese binding site 2 out of 4 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 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 Product Complex with MN2+, 30 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:52.4
occ:0.60
OD2 A:ASP192 2.3 27.5 1.0
O22 A:PPV406 2.3 33.6 0.6
OD1 A:ASP190 2.4 33.8 1.0
O21 A:PPV406 2.4 25.8 0.6
O A:HOH627 2.4 38.0 1.0
P2 A:PPV406 3.2 44.0 0.6
MN A:MN405 3.3 33.0 0.4
O32 A:PPV406 3.3 26.6 0.6
CG A:ASP190 3.4 40.7 1.0
CG A:ASP192 3.5 32.7 1.0
P1 A:PPV406 3.5 34.7 0.6
O A:HOH686 3.6 47.3 1.0
OPP A:PPV406 3.8 52.6 0.6
O A:ASP190 3.9 32.0 1.0
OD2 A:ASP190 4.0 31.7 1.0
O31 A:PPV406 4.1 38.9 0.6
OG A:SER180 4.1 30.1 1.0
OD1 A:ASP192 4.1 26.1 1.0
CA A:GLY179 4.2 33.8 1.0
N A:SER180 4.3 31.9 1.0
C A:ASP190 4.3 28.0 1.0
N A:ASP190 4.3 30.7 1.0
O A:HOH504 4.4 22.3 1.0
O A:HOH634 4.5 37.3 1.0
CB A:ASP192 4.6 23.6 1.0
O12 A:PPV406 4.6 38.7 0.6
CB A:ASP190 4.6 28.0 1.0
CA A:ASP190 4.7 27.6 1.0
MN A:MN405 4.7 29.5 0.4
C5' P:DA11 4.7 44.7 1.0
O11 A:PPV406 4.8 43.6 0.6
O5' P:DA11 4.8 47.4 1.0
C A:GLY179 4.9 35.9 1.0
N A:ASP192 4.9 29.0 1.0

Manganese binding site 3 out of 4 in 4klt

Go back to Manganese Binding Sites List in 4klt
Manganese binding site 3 out of 4 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 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 Product Complex with MN2+, 30 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:33.0
occ:0.40
MN A:MN405 0.0 33.0 0.4
MN A:MN405 1.8 29.5 0.4
O A:HOH634 2.4 37.3 1.0
OD1 A:ASP192 2.5 26.1 1.0
O A:HOH686 2.6 47.3 1.0
O5' P:DA11 2.6 47.4 1.0
OD2 A:ASP192 2.7 27.5 1.0
OD2 A:ASP190 2.7 31.7 1.0
CG A:ASP192 2.9 32.7 1.0
O P:HOH128 3.0 24.8 1.0
OD1 A:ASP190 3.2 33.8 1.0
MN A:MN404 3.3 52.4 0.6
CG A:ASP190 3.4 40.7 1.0
C5' P:DA11 3.4 44.7 1.0
O3' P:DC10 3.5 47.5 1.0
P P:DA11 3.8 48.0 1.0
C3' P:DC10 4.0 38.2 1.0
O32 A:PPV406 4.1 26.6 0.6
OD2 A:ASP256 4.3 34.0 1.0
CB A:ASP192 4.4 23.6 1.0
OP2 P:DA11 4.5 46.4 1.0
O21 A:PPV406 4.5 25.8 0.6
C4' P:DA11 4.7 52.5 1.0
O P:HOH118 4.7 35.6 1.0
OP1 P:DA11 4.8 51.9 1.0
CB A:ASP190 4.9 28.0 1.0
C4' P:DC10 4.9 37.2 1.0
O22 A:PPV406 5.0 33.6 0.6

Manganese binding site 4 out of 4 in 4klt

Go back to Manganese Binding Sites List in 4klt
Manganese binding site 4 out of 4 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 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 Product Complex with MN2+, 30 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:29.5
occ:0.40
MN A:MN405 0.0 29.5 0.4
MN A:MN405 1.8 33.0 0.4
O P:HOH128 2.1 24.8 1.0
OD1 A:ASP192 2.2 26.1 1.0
OD2 A:ASP190 2.5 31.7 1.0
OD2 A:ASP256 2.6 34.0 1.0
O A:HOH634 3.0 37.3 1.0
CG A:ASP192 3.3 32.7 1.0
CG A:ASP256 3.3 32.0 1.0
O3' P:DC10 3.4 47.5 1.0
CG A:ASP190 3.4 40.7 1.0
OD2 A:ASP192 3.6 27.5 1.0
O5' P:DA11 3.7 47.4 1.0
OD1 A:ASP190 3.7 33.8 1.0
C3' P:DC10 3.8 38.2 1.0
CB A:ASP256 4.0 17.5 1.0
O P:HOH118 4.0 35.6 1.0
C5' P:DC10 4.0 37.2 1.0
OD1 A:ASP256 4.0 28.6 1.0
C4' P:DC10 4.2 37.2 1.0
P P:DA11 4.2 48.0 1.0
O A:HOH686 4.3 47.3 1.0
CB A:ASP192 4.6 23.6 1.0
CB A:ASP190 4.7 28.0 1.0
O A:MET191 4.7 25.1 1.0
MN A:MN404 4.7 52.4 0.6
OP2 P:DA11 4.7 46.4 1.0
OP1 P:DC10 4.7 26.6 1.0
O5' P:DC10 4.8 31.2 1.0
NH2 A:ARG254 4.8 24.4 1.0
C5' P:DA11 4.8 44.7 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: Tue Dec 15 04:23:29 2020

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