Atomistry » Manganese » PDB 4k3v-4lt5 » 4klt
Atomistry »
  Manganese »
    PDB 4k3v-4lt5 »
      4klt »

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: Sat Oct 5 20:03:47 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy