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Mercury in PDB 1dko: Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge

Enzymatic activity of Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge

All present enzymatic activity of Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge, PDB code: 1dko was solved by D.Lim, S.Golovan, C.W.Forsberg, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.642, 74.952, 89.653, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.2

Other elements in 1dko:

The structure of Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge also contains other interesting chemical elements:

Tungsten (W) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge (pdb code 1dko). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge, PDB code: 1dko:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 1dko

Go back to Mercury Binding Sites List in 1dko
Mercury binding site 1 out of 4 in the Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge


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 Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg500

b:24.9
occ:1.00
 ND1 A:HIS113 2.5 24.7 1.0
O A:HOH612 2.9 22.4 1.0
O A:TYR289 3.0 53.6 1.0
CG A:HIS113 3.3 23.9 1.0
CB A:HIS113 3.4 20.9 1.0
CE1 A:HIS113 3.5 26.1 1.0
CA A:HIS113 4.1 21.2 1.0
C A:TYR289 4.2 52.9 1.0
CD2 A:HIS113 4.5 24.8 1.0
NE2 A:HIS113 4.6 28.5 1.0
CG2 A:THR111 4.8 29.2 1.0
CA A:GLY290 4.9 54.7 1.0
O A:GLY290 4.9 55.8 1.0

Mercury binding site 2 out of 4 in 1dko

Go back to Mercury Binding Sites List in 1dko
Mercury binding site 2 out of 4 in the Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge


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 Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg501

b:34.9
occ:0.27
 NE2 A:HIS250 2.7 17.5 1.0
OD2 A:ASP325 2.7 19.9 1.0
NH1 A:ARG16 2.9 18.4 1.0
OD1 A:ASP304 2.9 12.3 1.0
OE2 A:GLU219 3.1 25.6 1.0
OE1 A:GLU219 3.2 26.0 1.0
CD A:GLU219 3.2 25.1 1.0
CZ A:ARG16 3.2 16.7 1.0
NH2 A:ARG16 3.3 16.5 1.0
O A:THR327 3.4 17.7 1.0
CE1 A:HIS250 3.4 17.8 1.0
CG A:ASP325 3.5 18.4 1.0
OD1 A:ASP325 3.6 19.6 1.0
CD2 A:HIS250 3.7 18.1 1.0
CG A:ASP304 3.8 16.0 1.0
OG1 A:THR327 3.9 18.5 1.0
CB A:ASP304 3.9 14.9 1.0
O A:HOH631 4.0 29.5 1.0
NE A:ARG16 4.2 16.2 1.0
CG A:GLU219 4.3 20.6 1.0
C A:THR327 4.4 17.3 1.0
ND1 A:HIS250 4.5 20.4 1.0
CZ A:PHE254 4.6 17.1 1.0
CG A:HIS250 4.7 20.4 1.0
CD A:ARG16 4.9 15.9 1.0
CB A:THR327 4.9 18.3 1.0
CE1 A:PHE254 5.0 17.1 1.0
OD2 A:ASP304 5.0 15.4 1.0
CB A:ASP325 5.0 19.4 1.0

Mercury binding site 3 out of 4 in 1dko

Go back to Mercury Binding Sites List in 1dko
Mercury binding site 3 out of 4 in the Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge


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 Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg502

b:40.4
occ:0.27
 O A:LEU293 2.7 47.7 1.0
CB A:GLN285 3.1 64.4 1.0
O A:LYS286 3.2 58.8 1.0
NE2 A:GLN285 3.5 71.2 1.0
C A:GLN285 3.6 61.3 1.0
C A:LEU293 3.6 47.0 1.0
N A:LYS286 3.7 60.1 1.0
CA A:GLN285 3.7 62.0 1.0
N A:GLN285 4.0 60.6 1.0
O A:GLN285 4.0 61.5 1.0
C A:LYS286 4.0 58.7 1.0
CG A:GLN285 4.1 68.3 1.0
CD A:GLN285 4.2 70.5 1.0
CB A:LEU293 4.2 47.2 1.0
CA A:LYS286 4.3 59.5 1.0
CD A:PRO294 4.3 43.6 1.0
OG1 A:THR277 4.4 33.2 1.0
N A:PRO294 4.4 45.8 1.0
ND1 A:HIS282 4.4 59.4 1.0
CA A:LEU293 4.4 48.5 1.0
O A:PRO283 4.5 53.5 1.0
N A:LEU293 4.7 50.4 1.0

Mercury binding site 4 out of 4 in 1dko

Go back to Mercury Binding Sites List in 1dko
Mercury binding site 4 out of 4 in the Crystal Structure of Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge


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 Tungstate Complex of Escherichia Coli Phytase at pH 6.6 with Tungstate Bound at the Active Site and with HG2+ Cation Acting As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg503

b:43.9
occ:0.30
 O A:ALA278 2.6 20.5 1.0
N A:THR295 2.7 41.1 1.0
O A:HOH843 3.0 38.4 1.0
CA A:PRO294 3.0 44.7 1.0
C A:PRO294 3.3 43.3 1.0
CB A:PRO294 3.4 44.1 1.0
C A:ALA278 3.4 23.8 1.0
CA A:ALA278 3.6 23.5 1.0
CB A:ALA278 3.8 21.5 1.0
CA A:THR295 3.8 39.3 1.0
O A:HOH630 3.9 29.0 1.0
OG A:SER10 4.0 31.6 1.0
CD2 A:LEU293 4.0 47.7 1.0
C A:THR295 4.1 37.7 1.0
OG1 A:THR295 4.1 44.8 1.0
CB A:THR295 4.2 41.0 1.0
O A:THR295 4.3 38.5 1.0
N A:PRO294 4.3 45.8 1.0
CG A:PRO294 4.5 43.3 1.0
CB A:LEU293 4.5 47.2 1.0
O A:PRO294 4.5 43.5 1.0
CA A:LEU293 4.6 48.5 1.0
N A:LEU279 4.7 24.7 1.0
N A:SER296 4.7 32.7 1.0
CG A:LEU293 4.8 47.7 1.0
C A:LEU293 5.0 47.0 1.0

Reference:

D.Lim, S.Golovan, C.W.Forsberg, Z.Jia. Crystal Structures of Escherichia Coli Phytase and Its Complex with Phytate. Nat.Struct.Biol. V. 7 108 2000.
ISSN: ISSN 1072-8368
PubMed: 10655611
DOI: 10.1038/72371
Page generated: Sat Aug 10 23:34:28 2024

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