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Vanadium in PDB 1mu9: Crystal Structure of A Human Tyrosyl-Dna Phosphodiesterase (TDP1)- Vanadate Complex

Protein crystallography data

The structure of Crystal Structure of A Human Tyrosyl-Dna Phosphodiesterase (TDP1)- Vanadate Complex, PDB code: 1mu9 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) 19.97 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.028, 104.980, 194.297, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 21.4

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of A Human Tyrosyl-Dna Phosphodiesterase (TDP1)- Vanadate Complex (pdb code 1mu9). 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 A Human Tyrosyl-Dna Phosphodiesterase (TDP1)- Vanadate Complex, PDB code: 1mu9:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 1mu9

Go back to Vanadium Binding Sites List in 1mu9
Vanadium binding site 1 out of 2 in the Crystal Structure of A Human Tyrosyl-Dna Phosphodiesterase (TDP1)- Vanadate Complex


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 A Human Tyrosyl-Dna Phosphodiesterase (TDP1)- Vanadate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V609

b:27.9
occ:1.00
V A:VO4609 0.0 27.9 1.0
O4 A:VO4609 1.7 29.6 1.0
O3 A:VO4609 1.8 29.0 1.0
O2 A:GOL610 1.9 29.9 1.0
O1 A:GOL610 2.0 27.2 1.0
NE2 A:HIS263 2.1 24.8 1.0
C2 A:GOL610 2.8 31.9 1.0
C1 A:GOL610 2.9 31.0 1.0
CE1 A:HIS263 3.0 24.0 1.0
CD2 A:HIS263 3.1 24.1 1.0
NE2 A:HIS493 3.6 20.6 1.0
O A:HOH703 3.9 25.3 1.0
CE1 A:HIS493 3.9 19.9 1.0
ND1 A:HIS263 4.1 24.4 1.0
C3 A:GOL610 4.1 34.5 1.0
NZ A:LYS265 4.2 24.6 1.0
CG A:HIS263 4.2 25.2 1.0
ND2 A:ASN516 4.3 25.1 1.0
ND2 A:ASN283 4.3 24.1 1.0
O A:HOH912 4.3 41.3 1.0
NZ A:LYS495 4.5 21.4 1.0
CD2 A:TYR204 4.5 32.5 1.0
CE A:LYS265 4.5 25.8 1.0
CD2 A:HIS493 4.7 20.4 1.0
CE A:LYS495 4.8 20.4 1.0
CE2 A:TYR204 4.9 33.2 1.0

Vanadium binding site 2 out of 2 in 1mu9

Go back to Vanadium Binding Sites List in 1mu9
Vanadium binding site 2 out of 2 in the Crystal Structure of A Human Tyrosyl-Dna Phosphodiesterase (TDP1)- Vanadate Complex


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 A Human Tyrosyl-Dna Phosphodiesterase (TDP1)- Vanadate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V609

b:21.5
occ:1.00
V B:VO4609 0.0 21.5 1.0
O4 B:VO4609 1.6 23.7 1.0
O3 B:VO4609 1.7 23.4 1.0
O1 B:GOL610 2.0 20.8 1.0
O2 B:GOL610 2.0 24.0 1.0
NE2 B:HIS263 2.1 17.6 1.0
C2 B:GOL610 2.9 26.7 1.0
C1 B:GOL610 2.9 24.6 1.0
CE1 B:HIS263 2.9 16.2 1.0
CD2 B:HIS263 3.1 15.4 1.0
NE2 B:HIS493 3.5 18.3 1.0
CE1 B:HIS493 3.8 18.4 1.0
O B:HOH989 4.0 20.6 1.0
NZ B:LYS265 4.1 20.5 1.0
O B:HOH896 4.1 37.4 1.0
ND1 B:HIS263 4.1 16.8 1.0
ND2 B:ASN516 4.1 18.8 1.0
CG B:HIS263 4.2 16.3 1.0
NZ B:LYS495 4.3 19.5 1.0
C3 B:GOL610 4.3 30.4 1.0
CE B:LYS265 4.3 21.6 1.0
ND2 B:ASN283 4.3 16.3 1.0
CD2 B:TYR204 4.5 26.0 1.0
CE B:LYS495 4.7 20.3 1.0
CD2 B:HIS493 4.7 16.6 1.0
CE2 B:TYR204 5.0 27.3 1.0

Reference:

D.R.Davies, H.Interthal, J.J.Champoux, W.G.J.Hol. Insights Into Substrate Binding and Catalytic Mechanism of Human Tyrosyl-Dna Phosphodiesterase (TDP1) From Vanadate- and Tungstate-Inhibited Structures J.Mol.Biol. V. 324 917 2002.
ISSN: ISSN 0022-2836
PubMed: 12470949
DOI: 10.1016/S0022-2836(02)01154-3
Page generated: Thu Oct 29 07:04:17 2020

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