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Arsenic in PDB 2c7v: Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate

Enzymatic activity of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate

All present enzymatic activity of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate:
1.5.1.33;

Protein crystallography data

The structure of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate, PDB code: 2c7v was solved by A.Dawson, F.Gibellini, N.Sienkiewicz, P.K.Fyfe, K.Mcluskey, A.H.Fairlamb, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.54 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.655, 90.244, 82.841, 90.00, 115.76, 90.00
R / Rfree (%) 15.3 / 22.3

Other elements in 2c7v:

The structure of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate (pdb code 2c7v). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 8 binding sites of Arsenic where determined in the Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate, PDB code: 2c7v:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Arsenic binding site 1 out of 8 in 2c7v

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Arsenic binding site 1 out of 8 in the Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As59

b:46.8
occ:1.00
 AS A:CAF59 0.0 46.8 1.0
O1 A:CAF59 1.5 43.3 1.0
CE1 A:CAF59 1.8 44.9 1.0
CE2 A:CAF59 1.9 44.2 1.0
SG A:CAF59 2.2 36.2 1.0
CB A:CAF59 3.2 30.4 1.0
CA A:CAF59 3.6 29.7 1.0
N A:GLN60 3.9 28.7 1.0
C A:CAF59 4.0 29.2 1.0
O A:GLN60 4.1 26.0 1.0
O A:HOH2059 4.4 24.3 1.0
CB A:SER79 4.5 22.6 1.0
OG A:SER79 4.6 23.1 1.0
C A:GLN60 4.7 26.7 1.0
CG A:GLU75 4.8 25.5 1.0
O A:CAF59 4.9 29.3 1.0
O A:HOH2060 4.9 33.0 1.0
CA A:GLN60 4.9 28.1 1.0

Arsenic binding site 2 out of 8 in 2c7v

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Arsenic binding site 2 out of 8 in the Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As168

b:36.9
occ:0.50
 AS A:CAF168 0.0 36.9 0.5
O1 A:CAF168 1.5 38.5 0.5
CE1 A:CAF168 1.8 36.3 0.5
CE2 A:CAF168 1.8 37.2 0.5
SG A:CAF168 2.1 35.3 1.0
CB A:CAF168 3.1 27.5 1.0
O A:HOH2202 3.6 34.0 1.0
O A:HOH2119 4.0 33.0 1.0
C13 A:MTX1272 4.1 25.4 1.0
CA A:CAF168 4.2 26.9 1.0
N A:CAF168 4.3 25.7 1.0
C12 A:MTX1272 4.3 25.0 1.0
O A:HOH2113 4.3 36.4 1.0
CH2 A:TRP221 4.5 24.5 1.0
CZ2 A:TRP221 4.9 24.7 1.0
C14 A:MTX1272 5.0 25.2 1.0

Arsenic binding site 3 out of 8 in 2c7v

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Arsenic binding site 3 out of 8 in the Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As59

b:38.0
occ:1.00
 AS B:CAF59 0.0 38.0 1.0
O1 B:CAF59 1.5 37.8 1.0
CE1 B:CAF59 1.7 38.4 1.0
CE2 B:CAF59 2.0 35.1 1.0
SG B:CAF59 2.2 28.5 1.0
CB B:CAF59 3.2 25.2 1.0
CA B:CAF59 3.6 24.2 1.0
O B:GLN60 4.0 22.0 1.0
N B:GLN60 4.0 23.2 1.0
C B:CAF59 4.0 23.7 1.0
O B:HOH2061 4.4 36.1 1.0
OG B:SER79 4.5 28.7 1.0
CB B:SER79 4.6 26.1 1.0
C B:GLN60 4.7 22.3 1.0
O B:HOH2064 4.8 22.9 1.0
O B:CAF59 4.8 23.3 1.0
O B:GLU75 4.9 24.9 1.0

Arsenic binding site 4 out of 8 in 2c7v

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Arsenic binding site 4 out of 8 in the Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As168

b:32.1
occ:0.50
 AS B:CAF168 0.0 32.1 0.5
O1 B:CAF168 1.5 32.6 0.5
CE1 B:CAF168 1.8 31.8 0.5
CE2 B:CAF168 1.8 32.5 0.5
SG B:CAF168 2.1 30.6 1.0
CB B:CAF168 3.1 24.6 1.0
O B:HOH2139 3.4 39.8 1.0
C15 B:MTX1272 3.8 22.9 1.0
C16 B:MTX1272 4.0 24.3 1.0
CA B:CAF168 4.4 24.7 1.0
CE2 B:PHE97 4.5 17.1 1.0
CZ B:PHE97 4.5 17.8 1.0
CH2 B:TRP221 4.5 25.5 1.0
O B:HOH2130 4.6 32.5 1.0
N B:CAF168 4.6 23.8 1.0
C14 B:MTX1272 4.7 23.4 1.0
O B:HOH2137 4.8 31.0 1.0
CZ2 B:TRP221 4.8 25.5 1.0
C11 B:MTX1272 4.9 24.5 1.0
CM B:MTX1272 5.0 21.0 1.0

Arsenic binding site 5 out of 8 in 2c7v

Go back to Arsenic Binding Sites List in 2c7v
Arsenic binding site 5 out of 8 in the Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As59

b:33.7
occ:1.00
 AS C:CAF59 0.0 33.7 1.0
O1 C:CAF59 1.7 33.6 1.0
CE1 C:CAF59 2.0 34.9 1.0
CE2 C:CAF59 2.0 34.1 1.0
SG C:CAF59 2.2 29.5 1.0
CB C:CAF59 3.2 26.0 1.0
CA C:CAF59 3.7 25.6 1.0
O C:GLN60 3.9 23.0 1.0
N C:GLN60 3.9 24.1 1.0
O C:HOH2049 4.0 46.1 1.0
C C:CAF59 4.0 25.0 1.0
C C:GLN60 4.6 22.9 1.0
CB C:SER79 4.7 23.4 1.0
O C:GLU75 4.8 22.8 1.0
CA C:GLN60 4.9 23.2 1.0
O C:CAF59 5.0 24.8 1.0
NH2 C:ARG82 5.0 37.1 1.0
OG C:SER79 5.0 24.3 1.0

Arsenic binding site 6 out of 8 in 2c7v

Go back to Arsenic Binding Sites List in 2c7v
Arsenic binding site 6 out of 8 in the Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As168

b:38.8
occ:0.50
 AS C:CAF168 0.0 38.8 0.5
O1 C:CAF168 1.7 36.6 0.5
CE1 C:CAF168 2.0 37.9 0.5
CE2 C:CAF168 2.0 37.4 0.5
SG C:CAF168 2.1 35.1 1.0
CB C:CAF168 3.1 27.9 1.0
O C:HOH2124 3.8 33.8 1.0
N C:CAF168 3.9 26.6 1.0
CA C:CAF168 4.0 27.5 1.0
O C:HOH2138 4.2 23.7 1.0
CH2 C:TRP221 4.3 25.8 1.0
C15 C:MTX1272 4.4 26.1 1.0
O C:HOH2122 4.5 34.5 1.0
C16 C:MTX1272 4.6 26.5 1.0
CB C:MET163 4.7 24.7 1.0
CZ3 C:TRP221 4.7 26.3 1.0
C C:PRO167 4.9 26.3 1.0
CG C:MET163 5.0 27.2 1.0
CZ2 C:TRP221 5.0 26.0 1.0

Arsenic binding site 7 out of 8 in 2c7v

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Arsenic binding site 7 out of 8 in the Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As59

b:35.4
occ:1.00
 AS D:CAF59 0.0 35.4 1.0
O1 D:CAF59 1.5 35.6 1.0
CE1 D:CAF59 1.8 37.4 1.0
CE2 D:CAF59 1.8 33.9 1.0
SG D:CAF59 2.2 30.7 1.0
CB D:CAF59 3.2 27.0 1.0
CA D:CAF59 3.6 26.5 1.0
O D:GLN60 3.7 25.3 1.0
N D:GLN60 3.8 25.7 1.0
C D:CAF59 3.9 26.0 1.0
O D:HOH2047 4.1 40.0 1.0
C D:GLN60 4.5 25.2 1.0
CA D:GLN60 4.8 25.8 1.0
O D:CAF59 4.8 25.0 1.0
CB D:SER79 4.9 24.8 1.0
N D:CAF59 5.0 26.5 1.0

Arsenic binding site 8 out of 8 in 2c7v

Go back to Arsenic Binding Sites List in 2c7v
Arsenic binding site 8 out of 8 in the Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of Structure of Trypanosoma Brucei Pteridine Reductase (PTR1) in Ternary Complex with Cofactor and the Antifolate Methotrexate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As168

b:39.4
occ:0.50
 AS D:CAF168 0.0 39.4 0.5
O1 D:CAF168 1.7 37.2 0.5
CE1 D:CAF168 2.0 38.3 0.5
CE2 D:CAF168 2.0 38.3 0.5
SG D:CAF168 2.1 34.9 1.0
CB D:CAF168 3.1 29.3 1.0
O D:HOH2109 3.6 40.9 1.0
N D:CAF168 4.0 27.9 1.0
CA D:CAF168 4.0 28.8 1.0
O D:HOH2110 4.1 36.4 1.0
O D:HOH2101 4.2 21.0 1.0
C15 D:MTX1272 4.4 27.3 1.0
CH2 D:TRP221 4.5 28.1 1.0
CB D:MET163 4.5 23.9 1.0
C16 D:MTX1272 4.6 28.4 1.0
CG D:MET163 4.8 27.7 1.0
CZ3 D:TRP221 4.8 28.3 1.0
C D:PRO167 5.0 27.4 1.0

Reference:

A.Dawson, F.Gibellini, N.Sienkiewicz, L.B.Tulloch, P.K.Fyfe, K.Mcluskey, A.H.Fairlamb, W.N.Hunter. Structure and Reactivity of Trypanosoma Brucei Pteridine Reductase: Inhibition By the Archetypal Antifolate Methotrexate Mol.Microbiol. V. 61 1457 2006.
ISSN: ISSN 0950-382X
PubMed: 16968221
DOI: 10.1111/J.1365-2958.2006.05332.X
Page generated: Wed Jul 10 11:20:07 2024

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