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Manganese in PDB 8ak4: Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans

Enzymatic activity of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans

All present enzymatic activity of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans:
6.5.1.2;

Protein crystallography data

The structure of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans, PDB code: 8ak4 was solved by A.Fernandes, A.K.Williamson, P.M.Matias, E.Moe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.97 / 3.36
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 70.844, 73.434, 149.942, 90, 90, 90
R / Rfree (%) 21.5 / 27.5

Other elements in 8ak4:

The structure of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans (pdb code 8ak4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans, PDB code: 8ak4:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8ak4

Go back to Manganese Binding Sites List in 8ak4
Manganese binding site 1 out of 2 in the Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:59.0
occ:1.00
 OD1 A:ASP295 2.1 63.8 1.0
OD1 A:ASP293 2.2 77.1 1.0
NE2 A:HIS287 2.2 86.9 1.0
CE1 A:HIS287 2.9 73.4 1.0
CG A:ASP293 3.2 81.7 1.0
CD2 A:HIS287 3.3 85.9 1.0
CG A:ASP295 3.4 74.5 1.0
O A:ALA294 3.4 88.9 1.0
OD2 A:ASP293 3.6 83.5 1.0
C A:ALA294 3.9 88.1 1.0
ND1 A:HIS287 4.0 73.3 1.0
MN A:MN802 4.0 61.9 1.0
NH2 A:ARG189 4.1 85.5 1.0
CA A:ASP295 4.1 98.9 1.0
OD2 A:ASP295 4.2 71.5 1.0
N A:ASP295 4.2 89.6 1.0
CG A:HIS287 4.2 89.0 1.0
N A:ALA294 4.3 87.7 1.0
CB A:ASP295 4.3 98.9 1.0
CB A:ASP293 4.5 79.1 1.0
O A:GLY391 4.6 84.3 1.0
C A:GLY391 4.6 89.5 1.0
CA A:ALA294 4.8 80.1 1.0
CA A:ASP293 4.8 85.8 1.0
C A:ASP293 4.8 93.1 1.0
N A:GLY392 4.9 100.3 1.0

Manganese binding site 2 out of 2 in 8ak4

Go back to Manganese Binding Sites List in 8ak4
Manganese binding site 2 out of 2 in the Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn802

b:61.9
occ:1.00
 OD2 A:ASP293 2.1 83.5 1.0
OD2 A:ASP130 2.2 85.3 1.0
OD2 A:ASP295 2.2 71.5 1.0
CG A:ASP295 2.9 74.5 1.0
OD1 A:ASP295 3.0 63.8 1.0
CG A:ASP293 3.3 81.7 1.0
CG A:ASP130 3.4 83.4 1.0
CA A:GLY391 3.7 90.4 1.0
OD1 A:ASP293 3.7 77.1 1.0
MN A:MN801 4.0 59.0 1.0
N A:GLY391 4.1 92.2 1.0
CB A:ASP130 4.3 88.6 1.0
OD1 A:ASP130 4.3 76.7 1.0
CB A:ASP295 4.4 98.9 1.0
C A:GLY391 4.5 89.5 1.0
CB A:ASP293 4.5 79.1 1.0
CD A:PRO210 4.6 84.4 1.0
CG A:PRO210 4.7 80.5 1.0
O A:GLY391 4.9 84.3 1.0

Reference:

A.Fernandes, A.Williamson, P.M.Matias, E.Moe. Structure/Function Studies of the Nad + -Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans Reveal Importance of the Brct Domain For Dna Binding. Extremophiles V. 27 26 2023.
ISSN: ESSN 1433-4909
PubMed: 37712998
DOI: 10.1007/S00792-023-01309-Z
Page generated: Sun Oct 6 11:19:05 2024

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