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Mercury in PDB 1n1b: Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage

Enzymatic activity of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage

All present enzymatic activity of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage:
5.5.1.8;

Protein crystallography data

The structure of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage, PDB code: 1n1b was solved by D.A.Whittington, M.L.Wise, M.Urbansky, R.M.Coates, R.B.Croteau, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.060, 116.770, 120.340, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 23.4

Other elements in 1n1b:

The structure of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage (pdb code 1n1b). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 11 binding sites of Mercury where determined in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage, PDB code: 1n1b:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 11 in 1n1b

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Mercury binding site 1 out of 11 in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage


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Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg903

b:33.6
occ:0.09
 SG A:CYS486 2.5 32.9 1.0
O A:TYR481 2.8 27.9 1.0
CB A:CYS486 3.3 28.1 1.0
OD2 A:ASP483 3.4 36.9 1.0
CA A:ASP483 3.9 27.1 1.0
N A:ASP483 4.0 26.3 1.0
O A:HIS482 4.0 25.0 1.0
C A:HIS482 4.0 26.3 1.0
C A:TYR481 4.0 33.0 1.0
CG A:ASP483 4.5 35.3 1.0
O A:HOH951 4.6 32.7 1.0
CA A:CYS486 4.7 24.7 1.0
NZ A:LYS449 4.7 36.6 1.0
CA A:HIS482 4.8 26.9 1.0
CB A:ASP483 4.8 30.8 1.0
N A:HIS482 4.8 28.7 1.0
CB A:TYR481 4.9 37.9 1.0
C A:ASP483 4.9 26.0 1.0
N A:CYS486 5.0 25.1 1.0

Mercury binding site 2 out of 11 in 1n1b

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Mercury binding site 2 out of 11 in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg904

b:23.4
occ:0.16
 SG A:CYS388 2.2 23.4 1.0
CE2 A:PHE306 2.7 34.7 1.0
CZ A:PHE306 3.2 34.3 1.0
CB A:CYS388 3.2 18.3 1.0
CA A:CYS388 3.4 18.2 1.0
CG1 A:VAL349 3.4 25.7 1.0
CD2 A:PHE306 3.5 34.3 1.0
O A:CYS388 3.8 18.9 1.0
C A:CYS388 4.0 18.8 1.0
CB A:VAL349 4.0 23.0 1.0
CG2 A:VAL392 4.2 19.1 1.0
CE1 A:PHE306 4.3 30.3 1.0
CD2 A:LEU346 4.4 20.2 1.0
CG1 A:ILE350 4.4 23.8 1.0
CG A:PHE306 4.6 33.2 1.0
N A:CYS388 4.7 20.0 1.0
O A:LEU346 4.7 20.6 1.0
CG2 A:VAL349 4.8 24.2 1.0
CD1 A:PHE306 4.9 33.0 1.0
N A:ILE350 4.9 23.1 1.0

Mercury binding site 3 out of 11 in 1n1b

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Mercury binding site 3 out of 11 in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg906

b:59.9
occ:0.25
 SG A:CYS221 2.5 58.5 1.0
O A:CYS221 3.3 56.6 1.0
CA A:CYS221 3.4 54.0 1.0
CB A:CYS221 3.4 54.1 1.0
C A:CYS221 3.6 55.4 1.0
HG A:HG907 3.7 57.3 0.1
O A:ALA188 3.8 62.7 1.0
CB A:ALA188 4.0 60.5 1.0
CB A:LYS225 4.3 65.9 1.0
C A:ALA188 4.5 61.7 1.0
N A:LYS225 4.6 65.1 1.0
CA A:ALA188 4.6 60.8 1.0
N A:LEU222 4.6 54.0 1.0
CB A:LYS224 4.8 64.3 1.0
N A:CYS221 4.8 50.8 1.0
CA A:LYS225 4.9 66.4 1.0

Mercury binding site 4 out of 11 in 1n1b

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Mercury binding site 4 out of 11 in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg907

b:57.3
occ:0.11
 SG A:CYS221 2.7 58.5 1.0
CD2 A:LEU222 3.2 49.8 1.0
N A:LEU222 3.2 54.0 1.0
CA A:LEU222 3.3 53.5 1.0
C A:CYS221 3.3 55.4 1.0
O A:CYS221 3.4 56.6 1.0
CB A:LYS225 3.5 65.9 1.0
HG A:HG906 3.7 59.9 0.2
CB A:CYS221 3.8 54.1 1.0
CG A:LEU222 3.9 51.7 1.0
CG A:LYS225 4.1 67.1 1.0
CG2 A:THR191 4.1 53.1 1.0
CB A:LEU222 4.1 53.4 1.0
CA A:CYS221 4.2 54.0 1.0
CB A:MET194 4.4 44.2 1.0
CA A:THR191 4.4 53.5 1.0
C A:LEU222 4.4 53.6 1.0
OG1 A:THR191 4.5 53.9 1.0
CB A:THR191 4.6 53.9 1.0
O A:LEU222 4.6 53.6 1.0
CG A:MET194 4.7 51.2 1.0
O A:ALA188 4.7 62.7 1.0
CA A:LYS225 4.8 66.4 1.0
O A:THR191 4.9 54.0 1.0
N A:LYS225 4.9 65.1 1.0

Mercury binding site 5 out of 11 in 1n1b

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Mercury binding site 5 out of 11 in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg908

b:52.9
occ:0.59
 SG A:CYS174 2.5 65.6 1.0
SG A:CYS139 2.5 64.5 1.0
O A:VAL171 3.2 48.3 1.0
O A:GLU144 3.3 74.3 1.0
CB A:CYS174 3.3 57.1 1.0
CB A:CYS139 3.6 60.7 1.0
C A:VAL171 4.1 48.1 1.0
CA A:CYS139 4.1 60.4 1.0
C A:GLU144 4.2 73.3 1.0
CG1 A:VAL171 4.3 55.6 1.0
O A:ASN143 4.3 70.9 1.0
O A:CYS139 4.4 60.5 1.0
CA A:VAL171 4.4 50.1 1.0
CA A:VAL145 4.5 72.1 1.0
CE1 A:PHE175 4.5 53.0 1.0
CA A:CYS174 4.6 56.6 1.0
C A:ASN143 4.6 70.7 1.0
C A:CYS139 4.7 59.8 1.0
N A:CYS174 4.7 55.5 1.0
N A:VAL145 4.8 73.3 1.0
CG2 A:THR153 4.8 38.8 1.0
OG1 A:THR153 4.9 37.8 1.0
N A:GLU146 5.0 71.9 1.0

Mercury binding site 6 out of 11 in 1n1b

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Mercury binding site 6 out of 11 in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg909

b:34.7
occ:0.09
 SG B:CYS486 2.4 28.0 1.0
O B:TYR481 2.9 25.0 1.0
CB B:CYS486 3.3 23.8 1.0
OD2 B:ASP483 3.6 37.5 1.0
C B:TYR481 4.1 30.9 1.0
O B:HIS482 4.1 17.7 1.0
CA B:ASP483 4.1 25.3 1.0
N B:ASP483 4.1 23.2 1.0
C B:HIS482 4.1 23.8 1.0
O B:HOH1081 4.2 41.7 1.0
O B:HOH955 4.5 27.4 1.0
NZ B:LYS449 4.6 33.0 1.0
CG B:ASP483 4.7 38.6 1.0
CA B:CYS486 4.7 19.9 1.0
CB B:TYR481 4.9 33.6 1.0
N B:HIS482 4.9 27.8 1.0
CA B:HIS482 4.9 24.3 1.0
O B:GLN480 4.9 42.2 1.0
N B:CYS486 5.0 20.9 1.0

Mercury binding site 7 out of 11 in 1n1b

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Mercury binding site 7 out of 11 in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg910

b:26.1
occ:0.57
 O B:TYR384 2.9 22.0 1.0
CB B:CYS388 3.2 28.4 0.5
CB B:CYS388 3.2 28.4 0.5
N B:CYS388 3.4 20.2 0.5
N B:CYS388 3.4 20.2 0.5
CA B:CYS388 3.5 22.3 0.5
CA B:CYS388 3.5 22.3 0.5
CD1 B:PHE306 3.8 32.9 1.0
CG B:PHE306 4.0 33.8 1.0
C B:TYR384 4.0 25.4 1.0
CE1 B:PHE306 4.1 33.1 1.0
HG B:HG911 4.1 24.8 0.3
CD1 B:LEU310 4.2 33.3 1.0
CB B:LEU387 4.2 23.9 1.0
C B:LEU387 4.2 21.8 1.0
CD2 B:PHE306 4.3 33.8 1.0
SG B:CYS388 4.4 39.0 0.5
SG B:CYS388 4.4 39.0 0.5
CZ B:PHE306 4.4 31.4 1.0
CE2 B:PHE306 4.5 29.4 1.0
CB B:PHE306 4.5 31.8 1.0
CA B:TYR384 4.5 22.8 1.0
CD1 B:ILE353 4.6 22.7 1.0
CB B:TYR384 4.6 25.9 1.0
CG1 B:VAL349 4.7 25.1 1.0
CA B:LEU387 4.8 22.2 1.0
O B:LEU387 4.9 19.7 1.0
CG B:LEU310 5.0 34.4 1.0
CD1 B:TYR384 5.0 26.3 1.0
CA B:PHE306 5.0 28.9 1.0

Mercury binding site 8 out of 11 in 1n1b

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Mercury binding site 8 out of 11 in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg911

b:24.8
occ:0.29
 CE2 B:PHE306 2.4 29.4 1.0
SG B:CYS388 2.4 39.0 0.5
SG B:CYS388 2.4 39.0 0.5
CZ B:PHE306 3.0 31.4 1.0
CD2 B:PHE306 3.1 33.8 1.0
CB B:CYS388 3.2 28.4 0.5
CB B:CYS388 3.2 28.4 0.5
CG1 B:VAL349 3.4 25.1 1.0
CA B:CYS388 3.4 22.3 0.5
CA B:CYS388 3.4 22.3 0.5
CB B:VAL349 3.9 21.9 1.0
O B:CYS388 4.0 18.5 0.5
O B:CYS388 4.0 18.5 0.5
CE1 B:PHE306 4.1 33.1 1.0
C B:CYS388 4.1 20.3 0.5
C B:CYS388 4.1 20.3 0.5
HG B:HG910 4.1 26.1 0.6
CG B:PHE306 4.2 33.8 1.0
CD2 B:LEU346 4.4 19.5 1.0
CG2 B:VAL392 4.5 16.2 1.0
CD1 B:PHE306 4.5 32.9 1.0
CG1 B:ILE350 4.6 24.6 1.0
N B:CYS388 4.7 20.2 0.5
N B:CYS388 4.7 20.2 0.5
CG2 B:VAL349 4.7 20.3 1.0
O B:LEU346 4.8 20.5 1.0

Mercury binding site 9 out of 11 in 1n1b

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Mercury binding site 9 out of 11 in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg913

b:53.2
occ:0.23
 SG B:CYS221 2.5 62.2 1.0
O B:CYS221 3.2 55.5 1.0
CA B:CYS221 3.4 54.3 1.0
CB B:CYS221 3.4 56.5 1.0
O B:ALA188 3.5 53.4 1.0
C B:CYS221 3.6 55.5 1.0
HG B:HG914 3.6 58.7 0.1
CB B:ALA188 3.8 51.0 1.0
C B:ALA188 4.2 52.4 1.0
CA B:ALA188 4.2 51.6 1.0
CB B:LYS225 4.4 68.1 1.0
N B:LYS225 4.7 65.9 1.0
N B:LEU222 4.7 54.6 1.0
CB B:LYS224 4.7 64.9 1.0
N B:CYS221 4.8 52.5 1.0

Mercury binding site 10 out of 11 in 1n1b

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Mercury binding site 10 out of 11 in the Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Crystal Structure of (+)-Bornyl Diphosphate Synthase From Sage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg914

b:58.7
occ:0.12
 SG B:CYS221 2.5 62.2 1.0
C B:CYS221 3.1 55.5 1.0
N B:LEU222 3.2 54.6 1.0
O B:CYS221 3.2 55.5 1.0
CD1 B:LEU222 3.2 56.6 1.0
CA B:LEU222 3.4 55.1 1.0
CB B:CYS221 3.5 56.5 1.0
HG B:HG913 3.6 53.2 0.2
CB B:LYS225 3.8 68.1 1.0
CA B:CYS221 3.9 54.3 1.0
CB B:MET194 3.9 43.9 1.0
CG B:LEU222 4.0 55.5 1.0
CG B:MET194 4.1 50.1 1.0
CB B:LEU222 4.2 55.5 1.0
O B:ALA188 4.2 53.4 1.0
OG1 B:THR191 4.3 55.9 1.0
CA B:THR191 4.3 52.9 1.0
CG B:LYS225 4.4 70.2 1.0
CG2 B:THR191 4.4 54.5 1.0
C B:LEU222 4.5 55.7 1.0
CB B:THR191 4.6 53.2 1.0
O B:LEU222 4.9 55.2 1.0

Reference:

D.A.Whittington, M.L.Wise, M.Urbansky, R.M.Coates, R.B.Croteau, D.W.Christianson. Bornyl Diphosphate Synthase: Structure and Strategy For Carbocation Manipulation By A Terpenoid Cyclase Proc.Natl.Acad.Sci.Usa V. 99 15375 2002.
ISSN: ISSN 0027-8424
PubMed: 12432096
DOI: 10.1073/PNAS.232591099
Page generated: Sun Aug 11 00:38:50 2024

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