Atomistry » Vanadium » PDB 3omx-4zg4 » 4ndg
Atomistry »
  Vanadium »
    PDB 3omx-4zg4 »
      4ndg »

Vanadium 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:

Zinc (Zn) 2 atoms

Vanadium Binding Sites:

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 4ndg

Go back to Vanadium Binding Sites List in 4ndg
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 4ndg

Go back to Vanadium Binding Sites List in 4ndg
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

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: Thu Oct 29 07:05:32 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy