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Mercury in PDB 1rhy: Crystal Structure of Imidazole Glycerol Phosphate Dehydratase

Enzymatic activity of Crystal Structure of Imidazole Glycerol Phosphate Dehydratase

All present enzymatic activity of Crystal Structure of Imidazole Glycerol Phosphate Dehydratase:
4.2.1.19;

Protein crystallography data

The structure of Crystal Structure of Imidazole Glycerol Phosphate Dehydratase, PDB code: 1rhy was solved by S.C.Sinha, B.N.Chaudhuri, J.W.Burgner, G.Yakovleva, V.J.Davisson, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.55 / 2.30
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 105.275, 105.275, 105.275, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.8

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Imidazole Glycerol Phosphate Dehydratase (pdb code 1rhy). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Crystal Structure of Imidazole Glycerol Phosphate Dehydratase, PDB code: 1rhy:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 1rhy

Go back to Mercury Binding Sites List in 1rhy
Mercury binding site 1 out of 6 in the Crystal Structure of Imidazole Glycerol Phosphate Dehydratase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Imidazole Glycerol Phosphate Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg5503

b:82.9
occ:1.00
 SG A:CYS62 2.4 69.2 1.0
O A:CYS62 2.9 53.5 1.0
O A:THR38 3.0 49.8 1.0
CB A:CYS62 3.2 57.2 1.0
C A:CYS62 3.3 59.1 1.0
O A:HOH5589 3.9 43.1 1.0
CA A:CYS62 3.9 60.0 1.0
C2 A:EMC5502 4.1 80.9 1.0
C A:THR38 4.1 52.2 1.0
N A:LYS63 4.1 65.3 1.0
C1 A:EMC5502 4.2 79.8 1.0
HG A:EMC5502 4.2 92.2 1.0
O A:LYS63 4.3 73.6 1.0
C A:LYS63 4.3 72.7 1.0
OG1 A:THR15 4.4 69.5 1.0
CA A:LYS63 4.4 71.1 1.0
CA A:THR38 4.9 50.5 1.0
N A:GLY64 4.9 78.0 1.0
N A:GLY39 4.9 51.5 1.0
O A:GLY64 4.9 91.0 1.0
CA A:GLY39 4.9 53.3 1.0
N A:CYS62 5.0 55.5 1.0

Mercury binding site 2 out of 6 in 1rhy

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Mercury binding site 2 out of 6 in the Crystal Structure of Imidazole Glycerol Phosphate Dehydratase


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 Imidazole Glycerol Phosphate Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg5501

b:72.9
occ:1.00
 HG A:EMC5501 0.0 72.9 1.0
C1 A:EMC5501 2.1 56.5 1.0
SG A:CYS124 2.4 50.6 1.0
C2 A:EMC5501 3.0 34.9 1.0
CB A:CYS124 3.1 28.8 1.0
N A:CYS124 3.2 32.1 1.0
CE2 A:PHE122 3.3 28.8 1.0
O B:HOH9614 3.4 85.7 1.0
CA A:CYS124 3.6 36.0 1.0
O A:HOH5509 3.6 33.5 1.0
O A:CYS124 3.7 41.4 1.0
CD2 A:PHE122 3.8 30.2 1.0
C A:CYS124 3.9 40.1 1.0
C A:MET123 4.0 35.3 1.0
CZ A:PHE122 4.2 29.6 1.0
O A:HOH5510 4.2 56.2 1.0
CA A:MET123 4.4 32.0 1.0
CB A:SER142 4.5 40.3 1.0
O A:MET123 4.8 35.8 1.0
O A:PHE122 4.9 30.5 1.0

Mercury binding site 3 out of 6 in 1rhy

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Mercury binding site 3 out of 6 in the Crystal Structure of Imidazole Glycerol Phosphate Dehydratase


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 Imidazole Glycerol Phosphate Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg5502

b:92.2
occ:1.00
 HG A:EMC5502 0.0 92.2 1.0
C1 A:EMC5502 2.1 79.8 1.0
SG A:CYS77 2.4 69.4 1.0
C2 A:EMC5502 3.1 80.9 1.0
CB A:CYS77 3.4 52.0 1.0
SG A:CYS62 3.5 69.2 1.0
O A:HOH5589 3.5 43.1 1.0
CB A:CYS62 3.7 57.2 1.0
O A:THR38 3.8 49.8 1.0
CA A:ALA74 3.9 61.6 1.0
CB A:THR38 4.1 42.5 1.0
HG A:HG5503 4.2 82.9 1.0
O A:ALA74 4.3 58.1 1.0
O A:THR73 4.3 80.7 1.0
N A:CYS77 4.4 41.1 1.0
CA A:CYS77 4.5 43.5 1.0
CA A:THR38 4.5 50.5 1.0
CB A:ALA74 4.5 59.1 1.0
C A:ALA74 4.6 60.1 1.0
C A:THR38 4.6 52.2 1.0
CG2 A:THR38 4.6 45.7 1.0
CD1 A:ILE17 4.7 51.3 1.0
N A:ALA74 4.9 73.8 1.0

Mercury binding site 4 out of 6 in 1rhy

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Mercury binding site 4 out of 6 in the Crystal Structure of Imidazole Glycerol Phosphate Dehydratase


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 Imidazole Glycerol Phosphate Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg9503

b:77.7
occ:1.00
 SG B:CYS62 2.4 51.0 1.0
O B:THR38 3.1 43.2 1.0
O B:CYS62 3.1 54.2 1.0
CB B:CYS62 3.3 45.8 1.0
C B:CYS62 3.4 53.8 1.0
C1 B:EMC9502 3.8 63.1 1.0
C B:LYS63 3.9 69.9 1.0
N B:LYS63 3.9 58.5 1.0
N B:GLY64 4.0 77.1 1.0
CA B:CYS62 4.0 51.9 1.0
C B:THR38 4.1 50.8 1.0
C2 B:EMC9502 4.1 55.5 1.0
HG B:EMC9502 4.1 79.5 1.0
O B:LYS63 4.2 68.3 1.0
CA B:LYS63 4.2 67.8 1.0
CA B:GLY64 4.4 83.7 1.0
CA B:GLY39 4.7 50.6 1.0
N B:GLY39 4.8 50.1 1.0
CA B:THR38 5.0 49.8 1.0

Mercury binding site 5 out of 6 in 1rhy

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Mercury binding site 5 out of 6 in the Crystal Structure of Imidazole Glycerol Phosphate Dehydratase


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 Imidazole Glycerol Phosphate Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg9501

b:70.7
occ:1.00
 HG B:EMC9501 0.0 70.7 1.0
C1 B:EMC9501 2.1 60.6 1.0
SG B:CYS124 2.4 50.3 1.0
C2 B:EMC9501 3.0 62.8 1.0
CB B:CYS124 3.1 27.3 1.0
N B:CYS124 3.3 22.8 1.0
CE2 B:PHE122 3.4 20.4 1.0
O B:HOH9509 3.4 38.5 1.0
OG B:SER142 3.4 50.8 1.0
CA B:CYS124 3.6 24.4 1.0
O B:CYS124 3.7 29.8 1.0
O B:HOH9506 3.8 42.2 1.0
CD2 B:PHE122 3.9 18.2 1.0
C B:CYS124 3.9 30.1 1.0
C B:MET123 4.0 27.4 1.0
CZ B:PHE122 4.2 26.9 1.0
CA B:MET123 4.5 25.2 1.0
CB B:SER142 4.7 34.8 1.0
O B:MET123 4.8 29.4 1.0
O B:HOH9561 4.8 71.6 1.0

Mercury binding site 6 out of 6 in 1rhy

Go back to Mercury Binding Sites List in 1rhy
Mercury binding site 6 out of 6 in the Crystal Structure of Imidazole Glycerol Phosphate Dehydratase


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 Imidazole Glycerol Phosphate Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg9502

b:79.5
occ:1.00
 HG B:EMC9502 0.0 79.5 1.0
C1 B:EMC9502 2.1 63.1 1.0
SG B:CYS77 2.4 54.6 1.0
C2 B:EMC9502 2.9 55.5 1.0
CB B:CYS77 3.3 39.4 1.0
SG B:CYS62 3.4 51.0 1.0
O B:THR38 3.6 43.2 1.0
CB B:CYS62 3.8 45.8 1.0
N B:CYS77 3.9 30.4 1.0
CA B:ALA74 4.0 58.0 1.0
CA B:CYS77 4.1 34.2 1.0
HG B:HG9503 4.1 77.7 1.0
CD1 B:ILE17 4.2 39.2 1.0
O B:THR73 4.2 65.3 1.0
O B:ALA74 4.3 59.6 1.0
CB B:THR38 4.3 41.9 1.0
C B:THR38 4.4 50.8 1.0
CA B:THR38 4.4 49.8 1.0
C B:ALA74 4.6 57.4 1.0
N B:ALA74 4.7 65.2 1.0
C B:THR73 4.8 68.4 1.0
CB B:ALA74 4.9 56.6 1.0
C B:ASP76 4.9 35.4 1.0
CG1 B:ILE17 5.0 43.1 1.0

Reference:

S.C.Sinha, B.N.Chaudhuri, J.W.Burgner, G.Yakovleva, V.J.Davisson, J.L.Smith. Crystal Structure of Imidazole Glycerol-Phosphate Dehydratase: Duplication of An Unusual Fold J.Biol.Chem. V. 279 15491 2004.
ISSN: ISSN 0021-9258
PubMed: 14724278
DOI: 10.1074/JBC.M312733200
Page generated: Sun Aug 11 01:27:00 2024

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