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Zinc 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:

Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8ak4

Go back to Zinc Binding Sites List in 8ak4
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn803

b:59.1
occ:1.00
 OD2 A:ASP191 2.0 93.6 1.0
OD1 A:ASP191 2.0 98.7 1.0
ND1 A:HIS230 2.0 93.5 1.0
CG A:ASP191 2.3 102.4 1.0
CG A:HIS230 2.9 101.6 1.0
CE1 A:HIS230 3.1 98.5 1.0
CB A:HIS230 3.2 94.3 1.0
NZ A:LYS232 3.8 90.1 1.0
CB A:ASP191 3.8 91.8 1.0
CD2 A:HIS230 4.1 109.8 1.0
NE2 A:HIS230 4.2 114.1 1.0
CA A:HIS230 4.7 95.8 1.0
CA A:ASP191 4.7 93.9 1.0
O A:ARG229 4.9 99.5 1.0
CE A:LYS232 5.0 99.8 1.0

Zinc binding site 2 out of 4 in 8ak4

Go back to Zinc Binding Sites List in 8ak4
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn804

b:48.6
occ:1.00
 SG A:CYS421 2.2 76.2 1.0
SG A:CYS418 2.3 68.0 1.0
SG A:CYS441 2.3 98.7 1.0
SG A:CYS436 2.4 69.2 1.0
CB A:CYS441 2.6 85.2 1.0
CB A:CYS421 2.9 70.3 1.0
CB A:CYS418 3.3 84.9 1.0
CA A:CYS441 3.6 96.7 1.0
N A:CYS421 4.0 78.2 1.0
CB A:CYS436 4.0 87.8 1.0
CA A:CYS421 4.1 93.7 1.0
N A:CYS441 4.2 101.5 1.0
CG2 A:VAL420 4.2 67.4 1.0
CG1 A:VAL341 4.7 79.9 1.0
CA A:CYS418 4.8 74.0 1.0
C A:CYS441 4.8 89.2 1.0
C A:VAL420 4.9 77.5 1.0
C A:CYS421 4.9 100.2 1.0

Zinc binding site 3 out of 4 in 8ak4

Go back to Zinc Binding Sites List in 8ak4
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn binding site number 3 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:Zn805

b:30.9
occ:0.50
 NE2 A:HIS423 2.0 70.5 1.0
CE1 A:HIS423 2.7 74.0 1.0
CD2 A:HIS423 3.2 70.2 1.0
CB A:ALA440 3.6 104.1 1.0
ND1 A:HIS423 3.9 96.6 1.0
CG A:HIS423 4.1 81.2 1.0
CB A:ALA577 4.8 88.5 1.0
O A:CYS421 4.8 89.3 1.0

Zinc binding site 4 out of 4 in 8ak4

Go back to Zinc Binding Sites List in 8ak4
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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:Zn806

b:67.5
occ:1.00
 OD2 A:ASP99 2.0 115.0 1.0
OD2 A:ASP97 2.0 109.9 1.0
OD1 A:ASP99 2.0 119.3 1.0
OD1 A:ASP97 2.0 127.8 1.0
CG A:ASP97 2.2 113.7 1.0
CG A:ASP99 2.3 116.0 1.0
CB A:ASP97 3.7 102.9 1.0
CB A:ASP99 3.8 121.5 1.0
OE2 A:GLU100 4.0 129.1 1.0
CG A:GLU100 4.1 126.2 1.0
CD A:GLU100 4.4 128.9 1.0
N A:GLU100 4.4 106.3 1.0
N A:ASP99 4.5 109.3 1.0
CA A:ASP99 4.6 109.6 1.0
CA A:ASP97 4.7 86.2 1.0
C A:ASP99 4.8 113.0 1.0
C A:ASP97 4.9 92.8 1.0
CB A:GLU100 5.0 101.9 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: Wed Oct 30 17:51:50 2024

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