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Mercury in PDB 2j0e: Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei

Enzymatic activity of Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei

All present enzymatic activity of Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei:
3.1.1.31;

Protein crystallography data

The structure of Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei, PDB code: 2j0e was solved by M.Delarue, N.Duclert-Savatier, E.Miclet, A.Haouz, D.Giganti, J.Ouazzani, P.Lopez, M.Nilges, V.Stoven, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 2.1
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.310, 80.850, 90.310, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.6

Other elements in 2j0e:

The structure of Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 2 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei (pdb code 2j0e). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei, PDB code: 2j0e:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 2j0e

Go back to Mercury Binding Sites List in 2j0e
Mercury binding site 1 out of 4 in the Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1267

b:50.7
occ:1.00
 SG A:CYS247 2.7 29.0 1.0
O A:LEU244 3.1 23.6 1.0
CD2 A:LEU244 3.2 22.1 1.0
CB A:CYS247 3.3 30.5 1.0
CB A:LEU244 3.3 22.2 1.0
CG2 A:VAL251 3.3 21.8 1.0
CG1 A:VAL214 3.5 16.9 1.0
CG1 A:VAL251 3.6 23.3 1.0
CA A:LEU244 3.7 24.1 1.0
CG A:LEU244 3.8 24.6 1.0
C A:LEU244 3.8 24.7 1.0
CB A:VAL214 3.8 17.6 1.0
CB A:VAL251 4.1 23.5 1.0
CG2 A:VAL214 4.3 11.8 1.0
CD1 A:LEU244 4.4 25.4 1.0
CA A:CYS247 4.7 28.7 1.0
N A:CYS247 4.9 29.8 1.0

Mercury binding site 2 out of 4 in 2j0e

Go back to Mercury Binding Sites List in 2j0e
Mercury binding site 2 out of 4 in the Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1268

b:50.5
occ:1.00
 SG A:CYS21 2.7 25.1 1.0
O A:HOH2057 2.7 29.2 1.0
NE2 A:HIS59 2.8 29.8 1.0
CB A:CYS21 3.2 21.1 1.0
N A:ARG22 3.3 23.5 1.0
C A:CYS21 3.3 22.0 1.0
O A:HOH2054 3.4 47.9 1.0
O A:CYS21 3.6 21.8 1.0
CE1 A:HIS59 3.6 29.0 1.0
CD2 A:HIS59 3.6 28.7 1.0
CA A:ARG22 3.6 25.1 1.0
O A:HOH2045 3.6 46.3 1.0
CA A:CYS21 3.9 22.4 1.0
CG2 A:VAL25 3.9 18.4 1.0
CB A:ARG22 4.3 30.6 1.0
CB A:VAL25 4.6 21.1 1.0
ND1 A:HIS59 4.6 29.7 1.0
CG A:HIS59 4.6 29.6 1.0
O A:ALA18 4.8 22.8 1.0
C A:ARG22 4.9 24.5 1.0

Mercury binding site 3 out of 4 in 2j0e

Go back to Mercury Binding Sites List in 2j0e
Mercury binding site 3 out of 4 in the Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1267

b:64.2
occ:1.00
 SG B:CYS247 2.7 29.8 1.0
CD2 B:LEU244 3.1 18.8 1.0
CG2 B:VAL251 3.2 19.8 1.0
CB B:LEU244 3.3 15.8 1.0
O B:LEU244 3.3 16.6 1.0
CB B:CYS247 3.4 28.9 1.0
CG1 B:VAL251 3.6 25.9 1.0
CG1 B:VAL214 3.7 12.8 1.0
CG B:LEU244 3.7 19.6 1.0
CA B:LEU244 3.7 16.8 1.0
CB B:VAL214 3.8 15.7 1.0
C B:LEU244 3.9 18.2 1.0
CB B:VAL251 4.0 23.4 1.0
CG2 B:VAL214 4.1 11.1 1.0
CD1 B:LEU244 4.3 22.1 1.0
CA B:CYS247 4.8 27.5 1.0
CA B:VAL251 4.9 21.7 1.0

Mercury binding site 4 out of 4 in 2j0e

Go back to Mercury Binding Sites List in 2j0e
Mercury binding site 4 out of 4 in the Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Three Dimensional Structure and Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1268

b:52.2
occ:1.00
 SG B:CYS21 2.6 27.0 1.0
NE2 B:HIS59 2.7 30.4 1.0
O B:HOH2022 2.9 31.8 1.0
O B:HOH2019 3.1 34.2 1.0
CB B:CYS21 3.2 22.2 1.0
O B:HOH2060 3.2 42.1 1.0
C B:CYS21 3.3 21.4 1.0
N B:ARG22 3.4 21.7 1.0
O B:CYS21 3.5 22.5 1.0
CD2 B:HIS59 3.5 28.9 1.0
CE1 B:HIS59 3.6 30.7 1.0
CA B:ARG22 3.7 23.6 1.0
CG2 B:VAL25 3.8 26.3 1.0
CA B:CYS21 3.9 23.6 1.0
CB B:ARG22 4.5 24.3 1.0
O B:ALA18 4.6 21.1 1.0
CG B:HIS59 4.6 31.4 1.0
ND1 B:HIS59 4.6 31.8 1.0
CB B:VAL25 4.7 25.8 1.0
C B:ARG22 5.0 23.6 1.0

Reference:

M.Delarue, N.Duclert-Savatier, E.Miclet, A.Haouz, D.Giganti, J.Ouazzani, P.Lopez, M.Nilges, V.Stoven. Three Dimensional Structure and Implications For the Catalytic Mechanism of 6- Phosphogluconolactonase From Trypanosoma Brucei. J.Mol.Biol. V. 366 868 2007.
ISSN: ISSN 0022-2836
PubMed: 17196981
DOI: 10.1016/J.JMB.2006.11.063
Page generated: Sun Dec 13 19:07:16 2020

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