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

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

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

Zinc

(Zn)

2 atoms

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

Vanadium 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 Vanadium with other atoms in the V 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:V401 b:61.8 occ:1.00 V A:V5A401 0.0 61.8 1.0 OV1 A:V5A401 1.6 38.5 1.0 OV2 A:V5A401 1.6 37.6 1.0 O5' A:V5A401 1.7 54.2 1.0 OP3 D:G1 2.0 79.8 1.0 NE2 A:HIS260 2.1 56.6 1.0 C5' A:V5A401 2.6 44.3 1.0 CD2 A:HIS260 3.1 54.3 1.0 CE1 A:HIS260 3.1 48.4 1.0 P D:G1 3.3 59.2 1.0 NE2 A:HIS262 3.6 38.8 1.0 O5' D:G1 3.6 48.5 1.0 OP2 D:G1 3.8 73.5 1.0 ND1 A:HIS251 3.8 57.8 1.0 C4' A:V5A401 3.9 48.2 1.0 O A:HOH501 4.1 51.5 1.0 CE1 A:HIS262 4.2 62.9 1.0 ND1 A:HIS260 4.2 53.6 1.0 CG A:HIS260 4.3 57.9 1.0 OP1 D:G1 4.4 71.2 1.0 CE1 A:HIS251 4.5 52.8 1.0 CB A:PRO254 4.5 73.8 1.0 N A:SER255 4.6 71.7 1.0 CA A:PRO254 4.6 72.9 1.0 CG A:HIS251 4.7 55.5 1.0 CD2 A:HIS262 4.7 41.2 1.0 N A:MET256 4.8 59.5 1.0 CG A:MET256 4.8 53.7 1.0 C3' A:V5A401 4.8 48.6 1.0 CB A:HIS251 4.8 46.5 1.0 CB A:MET256 4.9 53.4 1.0 O4' A:V5A401 4.9 47.6 1.0

Vanadium 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 Vanadium with other atoms in the V 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:V401 b:71.0 occ:1.00 V B:V5A401 0.0 71.0 1.0 OV1 B:V5A401 1.6 71.1 1.0 OV2 B:V5A401 1.6 53.8 1.0 O5' B:V5A401 1.7 52.4 1.0 OP3 G:G1 2.0 77.0 1.0 NE2 B:HIS260 2.1 0.1 1.0 C5' B:V5A401 2.6 50.2 1.0 CE1 B:HIS260 3.0 0.9 1.0 CD2 B:HIS260 3.1 96.8 1.0 P G:G1 3.3 63.3 1.0 O5' G:G1 3.6 68.5 1.0 NE2 B:HIS262 3.7 61.9 1.0 C4' B:V5A401 3.9 49.8 1.0 ND1 B:HIS251 4.1 63.9 1.0 OP2 G:G1 4.1 65.0 1.0 ND1 B:HIS260 4.1 0.9 1.0 CG B:HIS260 4.2 99.3 1.0 OP1 G:G1 4.2 70.9 1.0 CE1 B:HIS262 4.4 60.5 1.0 N B:SER255 4.4 92.8 1.0 CB B:PRO254 4.5 0.7 1.0 CA B:PRO254 4.5 97.9 1.0 C3' B:V5A401 4.7 54.1 1.0 N B:MET256 4.7 82.2 1.0 CG B:MET256 4.7 72.3 1.0 CE1 B:HIS251 4.8 59.4 1.0 CB B:MET256 4.8 81.4 1.0 CD2 B:HIS262 4.8 63.4 1.0 CG B:HIS251 4.9 53.3 1.0 O4' B:V5A401 4.9 57.8 1.0 C5' G:G1 5.0 64.9 1.0 CB B:HIS251 5.0 68.8 1.0

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