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Nickel 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

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel 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 Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2c7v

Go back to Nickel Binding Sites List in 2c7v
Nickel binding site 1 out of 2 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 Nickel with other atoms in the Ni 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:Ni1273

b:49.3
occ:0.33
ND1 A:HIS179 2.1 19.8 1.0
ND1 C:HIS179 2.1 19.6 1.0
CE1 A:HIS179 2.9 19.9 1.0
CE1 C:HIS179 2.9 20.7 1.0
CG A:HIS179 3.3 18.1 1.0
CG C:HIS179 3.3 19.7 1.0
CB A:HIS179 3.8 16.5 1.0
CB C:HIS179 3.8 18.3 1.0
O A:HIS179 3.8 16.1 1.0
O C:HOH2120 3.9 36.9 1.0
O C:HIS179 3.9 17.8 1.0
CA A:HIS179 4.0 16.6 1.0
NE2 A:HIS179 4.1 19.9 1.0
NE2 C:HIS179 4.1 21.7 1.0
CA C:HIS179 4.1 17.8 1.0
O A:HOH2117 4.2 51.0 1.0
CD2 A:HIS179 4.3 20.1 1.0
C A:HIS179 4.3 16.5 1.0
CD2 C:HIS179 4.3 20.9 1.0
CB A:VAL182 4.4 16.8 1.0
C C:HIS179 4.4 17.7 1.0
CG1 A:VAL182 4.4 15.2 1.0
CG1 C:VAL182 4.6 16.5 1.0
CB C:VAL182 4.6 16.5 1.0
CG2 A:VAL182 4.8 15.6 1.0

Nickel binding site 2 out of 2 in 2c7v

Go back to Nickel Binding Sites List in 2c7v
Nickel binding site 2 out of 2 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 Nickel with other atoms in the Ni 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
B:Ni1273

b:43.1
occ:0.33
ND1 B:HIS179 1.8 18.6 1.0
ND1 D:HIS179 2.2 17.6 1.0
CE1 B:HIS179 2.6 19.8 1.0
CE1 D:HIS179 2.9 18.4 1.0
CG B:HIS179 3.0 17.2 1.0
CG D:HIS179 3.3 16.8 1.0
O D:HIS179 3.6 17.2 1.0
CB B:HIS179 3.6 16.2 1.0
CB D:HIS179 3.7 16.6 1.0
NE2 B:HIS179 3.8 19.9 1.0
O B:HIS179 3.9 16.0 1.0
CA D:HIS179 4.0 16.8 1.0
CD2 B:HIS179 4.0 19.2 1.0
O B:HOH2134 4.0 42.1 1.0
CA B:HIS179 4.0 16.0 1.0
NE2 D:HIS179 4.1 18.3 1.0
C D:HIS179 4.1 16.7 1.0
CB D:VAL182 4.3 15.0 1.0
CD2 D:HIS179 4.3 16.1 1.0
C B:HIS179 4.3 16.0 1.0
CG1 D:VAL182 4.4 13.6 1.0
CB B:VAL182 4.6 16.0 1.0
CG1 B:VAL182 4.7 15.2 1.0
CG2 D:VAL182 4.8 13.3 1.0
CG2 B:VAL182 5.0 13.5 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: Fri Sep 25 08:07:22 2020
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