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Zinc in PDB 4ndg: Human Aprataxin (Aptx) Bound to Rna-Dna and Zn - Adenosine Vanadate Transition State Mimic Complex

Protein crystallography data

The structure of Human Aprataxin (Aptx) Bound to Rna-Dna and Zn - Adenosine Vanadate Transition State Mimic Complex, PDB code: 4ndg 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) 39.06 / 2.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.276, 114.580, 124.658, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 26

Other elements in 4ndg:

The structure of Human Aprataxin (Aptx) Bound to Rna-Dna and Zn - Adenosine Vanadate Transition State Mimic Complex also contains other interesting chemical elements:

Vanadium (V) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Aprataxin (Aptx) Bound to Rna-Dna and Zn - Adenosine Vanadate Transition State Mimic Complex (pdb code 4ndg). 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 and Zn - Adenosine Vanadate Transition State Mimic Complex, PDB code: 4ndg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4ndg

Go back to Zinc Binding Sites List in 4ndg
Zinc binding site 1 out of 2 in the Human Aprataxin (Aptx) Bound to Rna-Dna and Zn - Adenosine Vanadate Transition State Mimic 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 and Zn - Adenosine Vanadate Transition State Mimic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:97.5
occ:1.00
NE2 A:HIS335 2.0 86.9 1.0
NE2 A:HIS339 2.1 0.0 1.0
SG A:CYS322 2.1 0.7 1.0
SG A:CYS319 2.4 96.9 1.0
CD2 A:HIS339 2.9 0.5 1.0
CE1 A:HIS335 3.0 99.0 1.0
CB A:CYS322 3.0 97.3 1.0
CD2 A:HIS335 3.0 82.7 1.0
CE1 A:HIS339 3.2 90.4 1.0
N A:CYS322 3.2 98.3 1.0
CB A:CYS319 3.3 84.0 1.0
CA A:CYS322 3.6 99.3 1.0
CB A:GLU321 4.0 0.5 1.0
ND1 A:HIS335 4.1 90.8 1.0
CG A:HIS339 4.1 0.4 1.0
CG A:HIS335 4.1 0.4 1.0
ND1 A:HIS339 4.2 0.9 1.0
C A:GLU321 4.2 0.9 1.0
C A:CYS322 4.5 0.1 1.0
CA A:GLU321 4.5 0.3 1.0
N A:GLU321 4.7 0.9 1.0
CA A:CYS319 4.7 86.0 1.0
N A:GLN323 4.7 0.5 1.0

Zinc binding site 2 out of 2 in 4ndg

Go back to Zinc Binding Sites List in 4ndg
Zinc binding site 2 out of 2 in the Human Aprataxin (Aptx) Bound to Rna-Dna and Zn - Adenosine Vanadate Transition State Mimic 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 and Zn - Adenosine Vanadate Transition State Mimic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:0.7
occ:1.00
SG B:CYS322 1.9 0.5 1.0
NE2 B:HIS335 1.9 0.7 1.0
NE2 B:HIS339 2.1 0.2 1.0
SG B:CYS319 2.2 0.5 1.0
CD2 B:HIS335 2.8 0.0 1.0
CE1 B:HIS339 3.0 94.3 1.0
CB B:CYS322 3.0 0.3 1.0
CE1 B:HIS335 3.0 0.6 1.0
CB B:CYS319 3.1 98.1 1.0
CD2 B:HIS339 3.2 0.8 1.0
N B:CYS322 3.3 0.9 1.0
CA B:CYS322 3.7 0.8 1.0
CG B:HIS335 4.0 99.9 1.0
ND1 B:HIS335 4.1 0.0 1.0
ND1 B:HIS339 4.2 93.9 1.0
CG B:HIS339 4.3 0.0 1.0
C B:CYS322 4.4 0.8 1.0
CB B:GLU321 4.4 0.8 1.0
N B:GLN323 4.5 0.1 1.0
C B:GLU321 4.5 0.3 1.0
CA B:CYS319 4.6 89.0 1.0
N B:GLU321 4.8 0.1 1.0
CA B:GLU321 4.8 0.5 1.0
O B:HIS335 4.9 0.1 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 05:36:55 2020

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