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Nickel in PDB 3tq0: Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex with Fumarate

Enzymatic activity of Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex with Fumarate

All present enzymatic activity of Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex with Fumarate:
1.3.3.1;

Protein crystallography data

The structure of Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex with Fumarate, PDB code: 3tq0 was solved by A.T.Cordeiro, P.R.Feliciano, M.C.Nonato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.81 / 1.90
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 140.833, 140.833, 68.348, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 18.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex with Fumarate (pdb code 3tq0). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex with Fumarate, PDB code: 3tq0:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3tq0

Go back to Nickel Binding Sites List in 3tq0
Nickel binding site 1 out of 2 in the Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex with Fumarate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex with Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni316

b:63.4
occ:0.50
NI A:NI316 0.0 63.4 0.5
NI A:NI316 1.5 52.0 0.5
O B:HOH390 2.5 17.5 1.0
O A:HOH389 3.7 19.6 1.0
ND1 B:HIS174 3.9 19.4 1.0
CE2 B:TYR142 3.9 15.3 1.0
CD1 B:PHE170 4.0 10.9 1.0
CZ B:TYR142 4.1 15.5 1.0
CE1 B:HIS174 4.2 19.9 1.0
CD2 B:TYR142 4.3 14.3 1.0
OH B:TYR142 4.4 13.2 1.0
CD1 A:PHE170 4.6 9.3 1.0
CE1 B:TYR142 4.6 15.6 1.0
CZ A:TYR142 4.7 12.2 1.0
O B:HOH421 4.7 36.3 1.0
CE1 A:HIS174 4.7 19.4 1.0
CE1 B:PHE170 4.7 7.9 1.0
O B:PRO168 4.8 8.7 1.0
CD2 B:TYR169 4.8 11.5 1.0
CE1 A:TYR142 4.8 12.3 1.0
CG B:TYR142 4.8 15.3 1.0
N B:PHE170 4.8 10.2 1.0
ND1 A:HIS174 4.9 18.6 1.0
CE2 A:TYR142 4.9 12.4 1.0
CA B:TYR169 4.9 9.8 1.0
CD1 B:TYR142 5.0 14.9 1.0

Nickel binding site 2 out of 2 in 3tq0

Go back to Nickel Binding Sites List in 3tq0
Nickel binding site 2 out of 2 in the Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex with Fumarate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex with Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni316

b:52.0
occ:0.50
NI A:NI316 0.0 52.0 0.5
NI A:NI316 1.5 63.4 0.5
O A:HOH389 2.5 19.6 1.0
O B:HOH390 3.7 17.5 1.0
CD1 A:PHE170 3.9 9.3 1.0
CE2 A:TYR142 4.0 12.4 1.0
ND1 A:HIS174 4.0 18.6 1.0
CZ A:TYR142 4.1 12.2 1.0
CE1 A:HIS174 4.2 19.4 1.0
OH A:TYR142 4.3 12.0 1.0
CD2 A:TYR142 4.4 12.5 1.0
CD1 B:PHE170 4.5 10.9 1.0
CE1 A:PHE170 4.6 8.1 1.0
CE1 A:TYR142 4.6 12.3 1.0
CZ B:TYR142 4.7 15.5 1.0
O A:PRO168 4.7 9.8 1.0
CD2 A:TYR169 4.7 11.5 1.0
N A:PHE170 4.7 10.8 1.0
CA A:TYR169 4.8 10.4 1.0
CE1 B:TYR142 4.8 15.6 1.0
CE2 B:TYR142 4.8 15.3 1.0
CE1 B:HIS174 4.9 19.9 1.0
CG A:TYR142 4.9 12.0 1.0
CG A:PHE170 4.9 11.1 1.0
OH B:TYR142 4.9 13.2 1.0
ND1 B:HIS174 4.9 19.4 1.0
CD1 A:TYR142 4.9 12.3 1.0
CB A:PHE170 5.0 10.6 1.0

Reference:

A.T.Cordeiro, P.R.Feliciano, M.P.Pinheiro, M.C.Nonato. Crystal Structure of Dihydroorotate Dehydrogenase From Leishmania Major. Biochimie V. 94 1739 2012.
ISSN: ISSN 0300-9084
PubMed: 22542640
DOI: 10.1016/J.BIOCHI.2012.04.003
Page generated: Fri Sep 25 08:35:18 2020
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