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Zinc in PDB 4ndf: Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex

Protein crystallography data

The structure of Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex, PDB code: 4ndf was solved by M.J.Schellenberg, P.S.Tumbale, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.41 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.429, 116.211, 117.141, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.5

Other elements in 4ndf:

The structure of Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex also contains other interesting chemical elements:

Potassium (K) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex (pdb code 4ndf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex, PDB code: 4ndf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4ndf

Go back to Zinc Binding Sites List in 4ndf
Zinc binding site 1 out of 2 in the Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:32.9
occ:1.00
NE2 A:HIS335 2.0 33.0 1.0
NE2 A:HIS339 2.1 40.6 1.0
SG A:CYS322 2.3 43.3 1.0
SG A:CYS319 2.4 34.8 1.0
CD2 A:HIS339 3.0 38.8 1.0
CD2 A:HIS335 3.0 31.4 1.0
CE1 A:HIS335 3.0 37.3 1.0
CE1 A:HIS339 3.1 42.9 1.0
CB A:CYS319 3.2 32.7 1.0
CB A:CYS322 3.4 46.7 1.0
N A:CYS322 3.7 48.9 1.0
CA A:CYS322 4.1 45.4 1.0
ND1 A:HIS335 4.1 36.7 1.0
CG A:HIS339 4.1 41.0 1.0
CG A:HIS335 4.1 34.4 1.0
CB A:GLU321 4.2 56.8 1.0
ND1 A:HIS339 4.2 44.2 1.0
C A:GLU321 4.6 50.0 1.0
CA A:CYS319 4.7 30.2 1.0
C A:CYS322 4.7 44.1 1.0
CA A:GLU321 4.7 50.2 1.0
N A:GLU321 4.8 42.8 1.0
N A:GLN323 4.9 40.8 1.0
CB A:GLN324 4.9 48.1 1.0

Zinc binding site 2 out of 2 in 4ndf

Go back to Zinc Binding Sites List in 4ndf
Zinc binding site 2 out of 2 in the Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:37.3
occ:1.00
NE2 B:HIS335 2.1 42.4 1.0
NE2 B:HIS339 2.1 46.9 1.0
SG B:CYS322 2.3 49.3 1.0
SG B:CYS319 2.4 36.9 1.0
CE1 B:HIS339 3.0 52.5 1.0
CE1 B:HIS335 3.0 45.6 1.0
CD2 B:HIS335 3.1 39.7 1.0
CD2 B:HIS339 3.1 47.4 1.0
CB B:CYS319 3.2 34.9 1.0
CB B:CYS322 3.3 52.6 1.0
N B:CYS322 3.6 46.1 1.0
CA B:CYS322 4.0 50.1 1.0
ND1 B:HIS339 4.1 53.8 1.0
ND1 B:HIS335 4.1 44.3 1.0
CG B:HIS335 4.2 42.0 1.0
CG B:HIS339 4.2 50.4 1.0
CB B:GLU321 4.5 51.7 1.0
C B:CYS322 4.6 48.8 1.0
C B:GLU321 4.6 50.3 1.0
CB B:GLN324 4.6 46.8 1.0
CA B:CYS319 4.7 33.3 1.0
N B:GLN323 4.8 44.3 1.0
CA B:GLU321 4.9 48.1 1.0
N B:GLU321 4.9 43.9 1.0
N B:GLN324 4.9 44.7 1.0

Reference:

P.Tumbale, J.S.Williams, M.J.Schellenberg, T.A.Kunkel, R.S.Williams. Aprataxin Resolves Adenylated Rna-Dna Junctions to Maintain Genome Integrity. Nature V. 506 111 2013.
ISSN: ISSN 0028-0836
PubMed: 24362567
DOI: 10.1038/NATURE12824
Page generated: Wed Dec 16 05:36:47 2020

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