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Mercury in PDB 3kbk: Epi-Isozizaene Synthase Complexed with Hg

Enzymatic activity of Epi-Isozizaene Synthase Complexed with Hg

All present enzymatic activity of Epi-Isozizaene Synthase Complexed with Hg:
4.2.3.37;

Protein crystallography data

The structure of Epi-Isozizaene Synthase Complexed with Hg, PDB code: 3kbk was solved by J.A.Aaron, X.Lin, D.E.Cane, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.74 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.693, 46.549, 75.551, 90.00, 92.34, 90.00
R / Rfree (%) 16.9 / 20.2

Other elements in 3kbk:

The structure of Epi-Isozizaene Synthase Complexed with Hg also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Epi-Isozizaene Synthase Complexed with Hg (pdb code 3kbk). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Epi-Isozizaene Synthase Complexed with Hg, PDB code: 3kbk:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 3kbk

Go back to Mercury Binding Sites List in 3kbk
Mercury binding site 1 out of 6 in the Epi-Isozizaene Synthase Complexed with Hg


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Epi-Isozizaene Synthase Complexed with Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg801

b:21.3
occ:0.77
 SG A:CYS68 2.4 15.3 1.0
CL A:CL701 2.6 31.6 0.6
CB A:CYS68 3.2 14.9 1.0
CE2 A:TYR63 3.6 12.1 1.0
O A:HOH376 3.6 13.8 1.0
O A:HOH467 3.7 21.3 1.0
CD2 A:TYR63 3.9 16.1 1.0
O A:TYR63 4.0 23.6 1.0
OG1 A:THR70 4.1 10.5 1.0
O A:HOH369 4.2 9.9 1.0
CA A:ALA64 4.2 25.2 1.0
CZ A:TYR63 4.3 14.2 1.0
CB A:THR70 4.5 11.8 1.0
C A:TYR63 4.6 23.8 1.0
OH A:TYR63 4.6 15.9 1.0
CA A:CYS68 4.7 13.8 1.0
CG2 A:THR45 4.7 16.1 1.0
N A:ALA64 4.8 24.6 1.0
CG A:TYR63 4.8 19.6 1.0
CB A:ALA64 4.9 31.8 1.0

Mercury binding site 2 out of 6 in 3kbk

Go back to Mercury Binding Sites List in 3kbk
Mercury binding site 2 out of 6 in the Epi-Isozizaene Synthase Complexed with Hg


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Epi-Isozizaene Synthase Complexed with Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg802

b:13.1
occ:0.59
 HG A:HG802 0.0 13.1 0.6
HG A:HG802 1.4 46.0 0.4
SG A:CYS283 2.4 17.0 1.0
CL A:CL703 2.5 37.4 0.6
O A:ARG279 3.0 12.8 1.0
OE1 A:GLU234 3.3 24.9 1.0
N A:CYS283 3.3 9.4 1.0
CB A:CYS283 3.4 10.8 1.0
CA A:CYS283 3.5 10.5 1.0
CD1 A:TRP238 3.7 17.9 1.0
NE1 A:TRP238 3.7 19.2 1.0
C A:ARG279 3.9 15.6 1.0
CD A:GLU234 3.9 27.7 1.0
C A:GLU282 4.2 10.4 1.0
CA A:ARG279 4.5 16.7 1.0
CB A:GLU282 4.5 14.1 1.0
CG A:GLU234 4.5 22.7 1.0
CB A:ARG279 4.6 20.6 1.0
OE2 A:GLU234 4.6 31.7 1.0
CG A:TRP238 4.6 18.1 1.0
CE2 A:TRP238 4.7 20.7 1.0
CG A:GLU282 4.7 20.7 1.0
O A:GLU282 4.8 11.2 1.0
CA A:GLU282 4.9 11.0 1.0
CD2 A:LEU231 4.9 12.2 1.0
N A:VAL280 4.9 14.8 1.0

Mercury binding site 3 out of 6 in 3kbk

Go back to Mercury Binding Sites List in 3kbk
Mercury binding site 3 out of 6 in the Epi-Isozizaene Synthase Complexed with Hg


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Epi-Isozizaene Synthase Complexed with Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg802

b:46.0
occ:0.41
 HG A:HG802 0.0 46.0 0.4
HG A:HG802 1.4 13.1 0.6
SG A:CYS283 2.3 17.0 1.0
OE1 A:GLU234 2.7 24.9 1.0
CD A:GLU234 3.0 27.7 1.0
CL A:CL703 3.1 37.4 0.6
OE2 A:GLU234 3.4 31.7 1.0
CB A:CYS283 3.5 10.8 1.0
CA A:CYS283 3.6 10.5 1.0
CD2 A:LEU231 3.7 12.2 1.0
CG A:GLU234 3.8 22.7 1.0
N A:CYS283 3.9 9.4 1.0
NE1 A:TRP238 4.1 19.2 1.0
CD1 A:TRP238 4.1 17.9 1.0
O A:ARG279 4.3 12.8 1.0
CB A:GLU234 4.4 13.5 1.0
C A:GLU282 4.7 10.4 1.0
OE1 A:GLU286 4.9 15.1 0.5
O A:HOH668 4.9 35.6 1.0

Mercury binding site 4 out of 6 in 3kbk

Go back to Mercury Binding Sites List in 3kbk
Mercury binding site 4 out of 6 in the Epi-Isozizaene Synthase Complexed with Hg


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Epi-Isozizaene Synthase Complexed with Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg803

b:20.8
occ:0.78
 CL A:CL704 2.5 23.3 0.6
SG A:CYS243 2.5 22.7 1.0
CB A:CYS243 3.1 23.6 1.0
O A:HOH692 3.2 29.9 1.0
CD2 A:TYR239 3.2 12.2 1.0
ND1 A:HIS333 3.3 24.4 1.0
CE2 A:TYR239 3.3 17.7 1.0
O A:TYR239 3.3 12.6 1.0
CG A:HIS333 3.4 18.9 1.0
CE1 A:HIS333 3.6 21.1 1.0
CD2 A:HIS333 3.7 22.0 1.0
C A:TYR239 3.8 13.5 1.0
NE2 A:HIS333 3.8 23.9 1.0
CG A:TYR239 3.8 12.0 1.0
CB A:HIS333 3.9 18.3 1.0
CA A:ASN240 3.9 16.5 1.0
N A:ASN240 4.0 11.3 1.0
CZ A:TYR239 4.1 16.2 1.0
CB A:TYR239 4.5 10.1 1.0
CA A:CYS243 4.5 24.7 1.0
CD1 A:TYR239 4.5 15.4 1.0
CE1 A:TYR239 4.6 17.6 1.0
N A:CYS243 4.6 18.3 1.0
CA A:TYR239 4.8 12.3 1.0
OD1 A:ASN240 4.8 22.4 1.0
C A:ASN240 4.8 19.5 1.0
CB A:ASN240 4.9 15.4 1.0
OH A:TYR239 4.9 15.2 1.0
O A:ASN240 4.9 20.8 1.0

Mercury binding site 5 out of 6 in 3kbk

Go back to Mercury Binding Sites List in 3kbk
Mercury binding site 5 out of 6 in the Epi-Isozizaene Synthase Complexed with Hg


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Epi-Isozizaene Synthase Complexed with Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg804

b:52.4
occ:0.48
 HG A:HG804 0.0 52.4 0.5
HG A:HG804 2.1 43.5 0.5
SG A:CYS213 2.9 20.9 0.4
CB A:CYS213 3.0 15.3 0.6
CB A:CYS213 3.2 15.5 0.4
O A:HOH424 3.2 19.0 1.0
CA A:CYS213 3.5 16.5 0.6
CA A:CYS213 3.5 16.5 0.4
SG A:CYS213 3.7 18.5 0.6
OE1 A:GLU310 3.7 38.6 1.0
NH1 A:ARG307 3.7 27.3 1.0
O A:GLY212 3.7 16.8 1.0
C A:CYS213 4.4 14.7 1.0
N A:CYS213 4.5 14.2 1.0
N A:GLU214 4.5 13.0 1.0
C A:GLY212 4.5 16.3 1.0
O A:HOH656 4.8 29.6 1.0
O A:HOH419 4.9 26.4 1.0
O A:HOH529 4.9 28.7 1.0
CZ A:ARG307 4.9 36.1 1.0
CD A:GLU310 4.9 44.7 1.0

Mercury binding site 6 out of 6 in 3kbk

Go back to Mercury Binding Sites List in 3kbk
Mercury binding site 6 out of 6 in the Epi-Isozizaene Synthase Complexed with Hg


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Epi-Isozizaene Synthase Complexed with Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg804

b:43.5
occ:0.52
 HG A:HG804 0.0 43.5 0.5
HG A:HG804 2.1 52.4 0.5
SG A:CYS213 2.4 18.5 0.6
NH1 A:ARG307 2.7 27.3 1.0
CB A:CYS213 2.9 15.3 0.6
CB A:CYS213 3.0 15.5 0.4
SG A:CYS213 3.2 20.9 0.4
CZ A:ARG307 3.6 36.1 1.0
NH2 A:ARG307 3.7 33.4 1.0
CD2 A:LEU311 3.8 20.2 1.0
CA A:CYS213 3.8 16.5 0.4
CA A:CYS213 3.8 16.5 0.6
O A:GLU214 3.9 12.4 1.0
O A:HOH424 4.1 19.0 1.0
C A:CYS213 4.3 14.7 1.0
N A:GLU214 4.4 13.0 1.0
OE1 A:GLU310 4.4 38.6 1.0
C A:GLU214 4.7 13.3 1.0
NE A:ARG307 4.7 38.7 1.0
CG A:LEU311 4.8 22.1 1.0
CB A:GLU310 5.0 23.8 1.0
O A:HOH656 5.0 29.6 1.0

Reference:

J.A.Aaron, X.Lin, D.E.Cane, D.W.Christianson. Structure of Epi-Isozizaene Synthase From Streptomyces Coelicolor A3(2), A Platform For New Terpenoid Cyclization Templates Biochemistry V. 49 1787 2010.
ISSN: ISSN 0006-2960
PubMed: 20131801
DOI: 10.1021/BI902088Z
Page generated: Sun Aug 11 04:00:31 2024

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