Atomistry » Manganese » PDB 4ee3-4fo6 » 4f3o
Atomistry »
  Manganese »
    PDB 4ee3-4fo6 »
      4f3o »

Manganese in PDB 4f3o: Dna Polymerase I Large Fragment Complex 5

Enzymatic activity of Dna Polymerase I Large Fragment Complex 5

All present enzymatic activity of Dna Polymerase I Large Fragment Complex 5:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase I Large Fragment Complex 5, PDB code: 4f3o was solved by W.Wang, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.56 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.830, 109.330, 150.110, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase I Large Fragment Complex 5 (pdb code 4f3o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Dna Polymerase I Large Fragment Complex 5, PDB code: 4f3o:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4f3o

Go back to Manganese Binding Sites List in 4f3o
Manganese binding site 1 out of 2 in the Dna Polymerase I Large Fragment Complex 5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase I Large Fragment Complex 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn904

b:16.5
occ:0.33
O A:TYR654 1.8 40.4 1.0
C A:TYR654 3.0 41.9 1.0
OD2 A:ASP830 3.2 43.9 1.0
HA A:SER655 3.3 55.6 1.0
HB2 A:ASP653 3.4 46.1 1.0
CG A:ASP830 3.5 41.7 1.0
OD1 A:ASP653 3.6 56.4 1.0
O A:HOH1025 3.7 30.1 1.0
H A:GLN656 3.7 57.6 1.0
HB2 A:TYR654 3.7 48.0 1.0
OD1 A:ASP830 3.8 34.2 1.0
HB2 A:ASP830 3.8 41.5 1.0
N A:TYR654 3.9 40.0 1.0
CA A:TYR654 3.9 41.3 1.0
N A:SER655 3.9 44.1 1.0
H A:ILE657 3.9 48.9 1.0
CA A:SER655 4.0 46.3 1.0
H A:TYR654 4.0 48.0 1.0
N A:GLN656 4.2 48.0 1.0
CB A:ASP653 4.2 38.4 1.0
C A:ASP653 4.2 40.8 1.0
CB A:ASP830 4.3 34.6 1.0
CB A:TYR654 4.3 40.0 1.0
HG22 A:ILE657 4.3 43.6 1.0
CG A:ASP653 4.4 47.9 1.0
C A:SER655 4.4 44.6 1.0
HB3 A:TYR654 4.4 48.0 1.0
O A:ASP830 4.5 35.2 1.0
HB A:ILE657 4.6 46.7 1.0
O A:ASP653 4.7 42.9 1.0
H A:SER655 4.8 53.0 1.0
N A:ILE657 4.8 40.7 1.0
CA A:ASP653 4.8 39.2 1.0
HA A:TYR654 4.8 49.6 1.0
HB3 A:ASP830 4.8 41.5 1.0
HA A:ASP653 4.9 47.1 1.0
HB3 A:ASP653 5.0 46.1 1.0

Manganese binding site 2 out of 2 in 4f3o

Go back to Manganese Binding Sites List in 4f3o
Manganese binding site 2 out of 2 in the Dna Polymerase I Large Fragment Complex 5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase I Large Fragment Complex 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn904

b:8.9
occ:0.20
O D:TYR654 2.1 16.3 1.0
O D:HOH1034 2.3 15.8 1.0
O2B D:D3T901 2.4 17.0 0.8
OD2 D:ASP830 2.8 24.0 1.0
HA D:SER655 3.3 12.3 1.0
C D:TYR654 3.3 12.9 1.0
H D:GLN656 3.4 17.6 1.0
O2A D:D3T901 3.4 21.6 0.8
CG D:ASP830 3.4 13.1 1.0
O D:HOH1486 3.6 25.6 1.0
PB D:D3T901 3.7 15.1 0.8
C5' D:D3T901 3.8 13.9 0.8
HB2 D:ASP653 3.8 19.8 1.0
OD1 D:ASP830 3.9 13.4 1.0
OD2 D:ASP653 3.9 26.7 1.0
HB2 D:ASP830 4.0 15.6 1.0
N D:GLN656 4.0 14.7 1.0
CA D:SER655 4.0 10.3 1.0
N D:SER655 4.1 13.0 1.0
H D:ILE657 4.2 14.0 1.0
O3A D:D3T901 4.2 15.7 0.8
PA D:D3T901 4.2 19.6 0.8
HB2 D:TYR654 4.3 13.1 1.0
CB D:ASP830 4.3 13.0 1.0
HG22 D:ILE657 4.4 20.1 1.0
O1G D:D3T901 4.4 20.2 0.8
CA D:TYR654 4.4 9.4 1.0
C D:SER655 4.4 13.7 1.0
N D:TYR654 4.5 11.4 1.0
H D:TYR654 4.6 13.6 1.0
O5' D:D3T901 4.6 16.2 0.8
O D:HOH1309 4.7 29.3 1.0
CB D:ASP653 4.7 16.5 1.0
O1B D:D3T901 4.7 20.8 0.8
O3B D:D3T901 4.7 21.9 0.8
HA D:GLN656 4.8 17.6 1.0
CB D:TYR654 4.8 10.9 1.0
HB3 D:ASP830 4.8 15.6 1.0
CG D:ASP653 4.8 19.2 1.0
C4' D:D3T901 4.8 14.1 0.8
O D:HOH1065 4.9 15.3 1.0
HB3 D:TYR654 4.9 13.1 1.0
O D:ASP830 4.9 13.3 1.0
C D:ASP653 4.9 11.0 1.0
H D:SER655 5.0 15.6 1.0
CA D:GLN656 5.0 14.7 1.0

Reference:

W.Wang, H.W.Hellinga, L.S.Beese. Structures of A High-Fidelity Dna Polymerase To Be Published.
Page generated: Tue Dec 15 04:20:25 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy