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Vanadium in PDB 1nop: Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase (TDP1) in Complex with Vanadate, Dna and A Human Topoisomerase I-Derived Peptide

Protein crystallography data

The structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase (TDP1) in Complex with Vanadate, Dna and A Human Topoisomerase I-Derived Peptide, PDB code: 1nop was solved by D.R.Davies, H.Interthal, J.J.Champoux, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.35 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.803, 104.719, 193.924, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 25.2

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase (TDP1) in Complex with Vanadate, Dna and A Human Topoisomerase I-Derived Peptide (pdb code 1nop). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase (TDP1) in Complex with Vanadate, Dna and A Human Topoisomerase I-Derived Peptide, PDB code: 1nop:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 1nop

Go back to Vanadium Binding Sites List in 1nop
Vanadium binding site 1 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase (TDP1) in Complex with Vanadate, Dna and A Human Topoisomerase I-Derived Peptide


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase (TDP1) in Complex with Vanadate, Dna and A Human Topoisomerase I-Derived Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V699

b:27.2
occ:1.00
V A:VO4699 0.0 27.2 1.0
O1 A:VO4699 1.6 26.1 1.0
O3 A:VO4699 1.7 27.2 1.0
O3' D:DT806 1.8 24.8 1.0
OH C:TYR723 2.0 22.6 1.0
NE2 A:HIS263 2.0 25.6 1.0
C3' D:DT806 2.9 27.3 1.0
CE1 A:HIS263 3.0 24.4 1.0
CZ C:TYR723 3.1 22.9 1.0
CD2 A:HIS263 3.1 24.8 1.0
NE2 A:HIS493 3.4 16.2 1.0
CE2 C:TYR723 3.6 24.0 1.0
CE1 A:HIS493 3.7 16.4 1.0
O A:HOH728 3.7 15.0 1.0
C2' D:DT806 3.9 27.4 1.0
ND2 A:ASN516 4.0 24.0 1.0
C4' D:DT806 4.1 27.9 1.0
ND1 A:HIS263 4.1 25.6 1.0
CE1 C:TYR723 4.1 23.1 1.0
CG A:HIS263 4.2 25.1 1.0
NZ A:LYS265 4.2 17.4 1.0
ND2 A:ASN283 4.3 22.2 1.0
NZ A:LYS495 4.3 18.2 1.0
CE A:LYS265 4.3 17.3 1.0
CD2 A:TYR204 4.4 25.4 1.0
CE A:LYS495 4.6 19.0 1.0
CD2 A:HIS493 4.6 15.2 1.0
C1' D:DT806 4.7 27.8 1.0
CE2 A:TYR204 4.8 26.1 1.0
ND1 A:HIS493 4.9 16.9 1.0
O4' D:DT806 5.0 28.4 1.0
CD2 C:TYR723 5.0 24.4 1.0

Vanadium binding site 2 out of 2 in 1nop

Go back to Vanadium Binding Sites List in 1nop
Vanadium binding site 2 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase (TDP1) in Complex with Vanadate, Dna and A Human Topoisomerase I-Derived Peptide


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase (TDP1) in Complex with Vanadate, Dna and A Human Topoisomerase I-Derived Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V699

b:33.9
occ:1.00
V B:VO4699 0.0 33.9 1.0
O1 B:VO4699 1.5 33.7 1.0
O3 B:VO4699 1.7 33.6 1.0
O3' F:DT806 1.8 55.7 1.0
NE2 B:HIS263 2.2 22.1 1.0
C3' F:DT806 2.8 57.2 1.0
CE1 B:HIS263 3.0 20.7 1.0
CD2 B:HIS263 3.3 20.6 1.0
NE2 B:HIS493 3.5 21.0 1.0
C2' F:DT806 3.7 57.4 1.0
CE1 B:HIS493 3.9 21.2 1.0
C4' F:DT806 4.0 58.0 1.0
ND2 B:ASN516 4.1 19.7 1.0
NZ B:LYS265 4.1 17.5 1.0
ND1 B:HIS263 4.2 21.6 1.0
NZ B:LYS495 4.3 18.1 1.0
CE B:LYS265 4.3 17.7 1.0
ND2 B:ASN283 4.3 16.2 1.0
CG B:HIS263 4.3 21.5 1.0
CD2 B:TYR204 4.4 26.7 1.0
C1' F:DT806 4.6 57.9 1.0
CE B:LYS495 4.6 17.8 1.0
CD2 B:HIS493 4.7 19.4 1.0
O4' F:DT806 4.8 58.3 1.0
CE2 B:TYR204 5.0 29.4 1.0

Reference:

D.R.Davies, H.Interthal, J.J.Champoux, W.G.J.Hol. Crystal Structure of A Transition State Mimic For TDP1 Assembled From Vanadate, Dna, and A Topoisomerase I-Derived Peptide Chem.Biol. V. 10 139 2003.
ISSN: ISSN 1074-5521
PubMed: 12618186
DOI: 10.1016/S1074-5521(03)00021-8
Page generated: Wed Dec 16 02:30:10 2020

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