Mercury in PDB 1k1e: Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)

The structure of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679), PDB code: 1k1e was solved by K.Lim, O.Herzberg, Structure 2 Function Project (S2F), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.67
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.300, 109.100, 179.100, 90.00, 107.60, 90.00
R / Rfree (%)	17.8 / 22.5

The structure of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) also contains other interesting chemical elements:

Cobalt

(Co)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Mercury atom in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) (pdb code 1k1e). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 12 binding sites of Mercury where determined in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679), PDB code: 1k1e:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 12 in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg301 b:19.3 occ:1.00 SG A:CYS118 2.3 19.3 1.0 SG A:CYS88 2.4 21.8 1.0 O A:ALA114 2.9 23.1 1.0 CB A:CYS88 3.1 10.3 1.0 CB A:CYS118 3.3 15.3 1.0 N A:CYS118 3.6 16.2 1.0 CD1 A:TYR104 3.7 13.6 1.0 CA A:CYS118 3.8 15.2 1.0 C A:ALA114 3.8 20.9 1.0 CD1 A:ILE12 3.9 13.8 1.0 CE A:MET92 4.1 13.3 1.0 CB A:TYR104 4.1 10.8 1.0 CA A:ALA114 4.1 10.6 1.0 CG A:TYR104 4.1 10.3 1.0 C A:ALA117 4.2 19.8 1.0 CB A:ALA117 4.2 14.8 1.0 CA A:CYS88 4.3 11.0 1.0 CB A:ALA114 4.3 15.5 1.0 CE1 A:TYR104 4.5 13.8 1.0 CA A:ALA117 4.7 13.7 1.0 O A:ALA117 4.9 19.2 1.0 CG2 A:THR102 4.9 12.1 1.0

Mercury binding site 2 out of 12 in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg302 b:18.0 occ:1.00 SG B:CYS118 2.3 20.8 1.0 SG B:CYS88 2.5 21.1 1.0 O B:ALA114 2.9 17.0 1.0 CB B:CYS88 3.2 14.5 1.0 CB B:CYS118 3.3 10.7 1.0 N B:CYS118 3.7 16.6 1.0 CD1 B:TYR104 3.7 11.0 1.0 C B:ALA114 3.8 18.4 1.0 CA B:CYS118 3.8 17.9 1.0 CE B:MET92 4.0 18.0 1.0 CD1 B:ILE12 4.0 11.9 1.0 CA B:ALA114 4.1 16.5 1.0 CB B:ALA117 4.1 19.7 1.0 CB B:TYR104 4.2 16.3 1.0 C B:ALA117 4.2 20.9 1.0 CG B:TYR104 4.2 14.6 1.0 CB B:ALA114 4.3 15.2 1.0 CA B:CYS88 4.3 13.1 1.0 CE1 B:TYR104 4.6 15.6 1.0 CA B:ALA117 4.7 17.4 1.0 O B:ALA117 4.7 27.8 1.0 CB B:ILE12 5.0 13.1 1.0

Mercury binding site 3 out of 12 in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) within 5.0Å range: probe atom residue distance (Å) B Occ C:Hg303 b:18.0 occ:1.00 SG C:CYS118 2.3 19.3 1.0 SG C:CYS88 2.4 19.1 1.0 O C:ALA114 3.0 13.9 1.0 CB C:CYS88 3.0 15.8 1.0 CB C:CYS118 3.2 14.6 1.0 N C:CYS118 3.7 20.2 1.0 CD1 C:TYR104 3.8 10.7 1.0 CA C:CYS118 3.8 12.9 1.0 C C:ALA114 3.8 15.8 1.0 CE C:MET92 4.0 20.2 1.0 CD1 C:ILE12 4.0 21.8 1.0 CB C:TYR104 4.0 15.3 1.0 CA C:ALA114 4.0 13.7 1.0 CB C:ALA117 4.1 19.8 1.0 CB C:ALA114 4.1 23.0 1.0 CG C:TYR104 4.2 10.1 1.0 C C:ALA117 4.2 18.7 1.0 CA C:CYS88 4.3 11.4 1.0 CE1 C:TYR104 4.6 16.1 1.0 CA C:ALA117 4.7 10.5 1.0 O C:ALA117 4.9 24.2 1.0

Mercury binding site 4 out of 12 in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) within 5.0Å range: probe atom residue distance (Å) B Occ D:Hg304 b:19.8 occ:1.00 SG D:CYS118 2.3 20.0 1.0 SG D:CYS88 2.4 21.3 1.0 O D:ALA114 2.9 14.2 1.0 CB D:CYS88 3.1 16.5 1.0 CB D:CYS118 3.3 17.9 1.0 CD1 D:TYR104 3.6 12.3 1.0 N D:CYS118 3.6 19.1 1.0 C D:ALA114 3.8 17.8 1.0 CA D:CYS118 3.9 23.8 1.0 CE D:MET92 4.0 21.2 1.0 CB D:TYR104 4.0 12.7 1.0 CA D:ALA114 4.1 19.7 1.0 CD1 D:ILE12 4.1 20.4 1.0 CG D:TYR104 4.1 15.2 1.0 CB D:ALA117 4.2 18.8 1.0 CB D:ALA114 4.2 15.0 1.0 C D:ALA117 4.2 22.9 1.0 CA D:CYS88 4.2 18.9 1.0 CE1 D:TYR104 4.5 11.7 1.0 CA D:ALA117 4.7 20.6 1.0 O D:ALA117 4.9 17.9 1.0 CG2 D:THR102 4.9 18.6 1.0 N D:PHE115 5.0 14.4 1.0

Mercury binding site 5 out of 12 in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) within 5.0Å range: probe atom residue distance (Å) B Occ E:Hg305 b:18.2 occ:1.00 SG E:CYS88 2.3 18.3 1.0 SG E:CYS118 2.4 19.1 1.0 CB E:CYS88 3.1 24.1 1.0 O E:ALA114 3.1 14.4 1.0 CB E:CYS118 3.4 14.2 1.0 CD1 E:TYR104 3.7 15.2 1.0 N E:CYS118 3.8 14.8 1.0 C E:ALA114 3.9 19.1 1.0 CA E:CYS118 3.9 16.0 1.0 CB E:TYR104 4.0 11.8 1.0 CA E:ALA114 4.0 13.4 1.0 CD1 E:ILE12 4.0 14.8 1.0 CB E:ALA117 4.1 16.8 1.0 CB E:ALA114 4.1 14.4 1.0 CG E:TYR104 4.1 10.3 1.0 CE E:MET92 4.1 21.9 1.0 C E:ALA117 4.2 19.9 1.0 CA E:CYS88 4.2 17.6 1.0 CE1 E:TYR104 4.6 18.5 1.0 CA E:ALA117 4.7 17.6 1.0 O E:ALA117 4.7 26.5 1.0 OG1 E:THR102 4.9 38.6 1.0 CB E:ILE12 5.0 11.1 1.0

Mercury binding site 6 out of 12 in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) within 5.0Å range: probe atom residue distance (Å) B Occ F:Hg306 b:22.0 occ:1.00 SG F:CYS118 2.3 23.3 1.0 SG F:CYS88 2.5 23.4 1.0 O F:ALA114 3.0 19.1 1.0 CB F:CYS88 3.1 17.8 1.0 CB F:CYS118 3.3 13.5 1.0 CD1 F:TYR104 3.7 13.7 1.0 N F:CYS118 3.7 23.1 1.0 C F:ALA114 3.8 18.2 1.0 CA F:CYS118 3.9 16.8 1.0 CE F:MET92 3.9 18.2 1.0 CB F:TYR104 4.0 18.2 1.0 CA F:ALA114 4.0 23.0 1.0 CB F:ALA114 4.1 16.8 1.0 CD1 F:ILE12 4.1 14.5 1.0 CG F:TYR104 4.2 8.7 1.0 C F:ALA117 4.3 28.9 1.0 CA F:CYS88 4.3 17.5 1.0 CB F:ALA117 4.4 26.7 1.0 CE1 F:TYR104 4.5 19.1 1.0 O F:ALA117 4.8 21.8 1.0 CA F:ALA117 4.8 19.7 1.0

Mercury binding site 7 out of 12 in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) within 5.0Å range: probe atom residue distance (Å) B Occ G:Hg307 b:19.8 occ:1.00 SG G:CYS118 2.4 22.4 1.0 SG G:CYS88 2.4 22.0 1.0 O G:ALA114 3.0 19.9 1.0 CB G:CYS88 3.2 22.4 1.0 CB G:CYS118 3.3 22.5 1.0 N G:CYS118 3.7 24.0 1.0 C G:ALA114 3.8 13.1 1.0 CE G:MET92 3.8 25.0 1.0 CD1 G:TYR104 3.9 13.8 1.0 CA G:ALA114 3.9 16.4 1.0 CA G:CYS118 3.9 22.9 1.0 CB G:ALA114 4.0 13.3 1.0 CD1 G:ILE12 4.1 19.5 1.0 CB G:ALA117 4.2 22.2 1.0 CB G:TYR104 4.2 12.8 1.0 CA G:CYS88 4.3 14.8 1.0 CG G:TYR104 4.3 15.4 1.0 C G:ALA117 4.3 26.9 1.0 CE1 G:TYR104 4.7 22.3 1.0 CA G:ALA117 4.8 21.9 1.0 OG1 G:THR102 4.9 34.4 1.0 N G:PHE115 5.0 14.9 1.0 O G:ALA117 5.0 23.8 1.0 CB G:ILE12 5.0 15.0 1.0

Mercury binding site 8 out of 12 in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) within 5.0Å range: probe atom residue distance (Å) B Occ H:Hg308 b:25.3 occ:1.00 SG H:CYS118 2.2 22.8 1.0 SG H:CYS88 2.5 26.4 1.0 O H:ALA114 3.0 21.0 1.0 CB H:CYS88 3.2 20.4 1.0 CB H:CYS118 3.4 23.1 1.0 CD1 H:TYR104 3.7 14.7 1.0 N H:CYS118 3.7 22.9 1.0 CE H:MET92 3.8 26.5 1.0 C H:ALA114 3.9 22.9 1.0 CA H:CYS118 4.0 21.9 1.0 CB H:TYR104 4.0 14.4 1.0 CD1 H:ILE12 4.1 18.1 1.0 CA H:ALA114 4.1 19.4 1.0 CG H:TYR104 4.2 22.0 1.0 CB H:ALA114 4.2 16.9 1.0 CA H:CYS88 4.3 17.6 1.0 CB H:ALA117 4.3 23.4 1.0 C H:ALA117 4.3 26.5 1.0 CE1 H:TYR104 4.5 17.9 1.0 CA H:ALA117 4.8 22.2 1.0 OG1 H:THR102 4.8 32.6 1.0 CB H:ILE12 5.0 13.8 1.0

Mercury binding site 9 out of 12 in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) within 5.0Å range: probe atom residue distance (Å) B Occ I:Hg309 b:19.6 occ:1.00 SG I:CYS118 2.3 21.2 1.0 SG I:CYS88 2.4 20.5 1.0 O I:ALA114 3.0 18.2 1.0 CB I:CYS88 3.1 21.7 1.0 CB I:CYS118 3.3 11.8 1.0 N I:CYS118 3.6 16.9 1.0 CD1 I:TYR104 3.7 14.9 1.0 CA I:CYS118 3.9 11.8 1.0 C I:ALA114 3.9 20.8 1.0 CB I:TYR104 4.0 18.8 1.0 CA I:ALA114 4.1 20.2 1.0 CD1 I:ILE12 4.1 14.2 1.0 CE I:MET92 4.1 12.7 1.0 CG I:TYR104 4.1 14.5 1.0 CB I:ALA114 4.2 18.6 1.0 CA I:CYS88 4.3 18.4 1.0 C I:ALA117 4.3 19.4 1.0 CB I:ALA117 4.3 14.0 1.0 CE1 I:TYR104 4.5 11.2 1.0 CA I:ALA117 4.8 20.2 1.0 O I:ALA117 4.9 25.9 1.0 CB I:ILE12 5.0 12.9 1.0

Mercury binding site 10 out of 12 in the Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Structure of the Cobalt-Bound Form of the Deoxy-D-Mannose-Octulosonate 8-Phosphate Phosphatase (Yrbi) From Haemophilus Influenzae (HI1679) within 5.0Å range: probe atom residue distance (Å) B Occ J:Hg310 b:24.9 occ:1.00 SG J:CYS118 2.4 24.4 1.0 SG J:CYS88 2.5 29.8 1.0 O J:ALA114 3.0 20.9 1.0 CB J:CYS88 3.2 27.9 1.0 CB J:CYS118 3.4 16.1 1.0 CE J:MET92 3.6 26.1 1.0 N J:CYS118 3.8 20.7 1.0 CD1 J:TYR104 3.8 13.8 1.0 C J:ALA114 3.9 19.9 1.0 CA J:CYS118 4.0 20.4 1.0 CB J:ALA117 4.0 27.2 1.0 CB J:TYR104 4.1 13.4 1.0 CA J:ALA114 4.2 19.6 1.0 C J:ALA117 4.2 27.2 1.0 CD1 J:ILE12 4.2 20.1 1.0 CG J:TYR104 4.2 17.3 1.0 CB J:ALA114 4.3 23.6 1.0 CA J:CYS88 4.3 19.3 1.0 CA J:ALA117 4.6 20.0 1.0 CE1 J:TYR104 4.7 19.0 1.0 O J:ALA117 4.8 25.6 1.0

J.F.Parsons, K.Lim, A.Tempczyk, W.Krajewski, E.Eisenstein, O.Herzberg. From Structure to Function: Yrbi From Haemophilus Influenzae (HI1679) Is A Phosphatase. Proteins V. 46 393 2002.
ISSN: ISSN 0887-3585
PubMed: 11835514
DOI: 10.1002/PROT.10057