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Mercury in PDB 1dkq: Crystal Structure of Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge

Enzymatic activity of Crystal Structure of Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge

All present enzymatic activity of Crystal Structure of Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge, PDB code: 1dkq 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 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.445, 75.141, 89.957, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.7

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge (pdb code 1dkq). 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 Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge, PDB code: 1dkq:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 1dkq

Go back to Mercury Binding Sites List in 1dkq
Mercury binding site 1 out of 4 in the Crystal Structure of Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts 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 Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg500

b:32.3
occ:1.00
 ND1 A:HIS113 2.5 30.3 1.0
O A:TYR289 2.8 30.9 1.0
O A:HOH674 2.9 26.4 1.0
CG A:HIS113 3.4 30.9 1.0
CE1 A:HIS113 3.4 34.1 1.0
CB A:HIS113 3.5 24.8 1.0
O A:HOH800 3.8 41.5 1.0
C A:TYR289 3.9 28.4 1.0
CA A:HIS113 4.1 26.0 1.0
CA A:GLY290 4.5 31.4 1.0
CD2 A:HIS113 4.5 31.1 1.0
NE2 A:HIS113 4.5 33.2 1.0
CG2 A:THR111 4.6 30.3 1.0
N A:GLY290 4.6 28.2 1.0
CA A:TYR289 4.9 28.4 1.0
C A:GLY290 4.9 35.8 1.0

Mercury binding site 2 out of 4 in 1dkq

Go back to Mercury Binding Sites List in 1dkq
Mercury binding site 2 out of 4 in the Crystal Structure of Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts 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 Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg501

b:32.2
occ:0.75
 NE2 A:HIS282 2.5 45.0 1.0
OE1 A:GLN287 2.6 46.4 1.0
O A:HOH769 2.8 35.6 1.0
O A:LEU293 2.9 35.9 1.0
NE2 A:GLN287 3.1 38.9 1.0
CD A:GLN287 3.2 45.5 1.0
CD2 A:HIS282 3.4 44.2 1.0
CE1 A:HIS282 3.5 46.0 1.0
CG A:GLN285 3.5 57.8 1.0
OE1 A:GLN285 3.5 63.2 1.0
C A:LEU293 3.6 34.1 1.0
CD A:GLN285 4.0 61.7 1.0
CB A:LEU293 4.1 31.9 1.0
OG1 A:THR277 4.1 40.0 1.0
N A:PRO294 4.2 33.6 1.0
CA A:LEU293 4.3 34.6 1.0
CD A:PRO294 4.4 27.7 1.0
O A:GLN285 4.4 44.4 1.0
ND1 A:HIS282 4.5 47.1 1.0
CG A:HIS282 4.5 44.2 1.0
O A:PRO283 4.7 46.0 1.0
N A:LEU293 4.7 36.3 1.0
N A:GLN285 4.7 46.1 1.0
CG A:GLN287 4.7 41.6 1.0
CB A:GLN285 4.9 52.0 1.0

Mercury binding site 3 out of 4 in 1dkq

Go back to Mercury Binding Sites List in 1dkq
Mercury binding site 3 out of 4 in the Crystal Structure of Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts 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 Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg502

b:35.5
occ:0.23
 HG A:HG503 1.8 10.9 0.2
NE2 A:HIS250 2.6 26.7 1.0
OD2 A:ASP325 2.7 25.1 1.0
NH1 A:ARG16 2.8 19.9 1.0
OD1 A:ASP304 3.0 32.6 1.0
OE2 A:GLU219 3.2 28.4 1.0
O24 A:IHP550 3.2 33.8 0.8
CZ A:ARG16 3.3 20.5 1.0
CD A:GLU219 3.3 27.3 1.0
OE1 A:GLU219 3.4 24.3 1.0
OD1 A:ASP325 3.4 20.3 1.0
CE1 A:HIS250 3.4 24.5 1.0
CG A:ASP325 3.5 27.8 1.0
CD2 A:HIS250 3.5 23.7 1.0
NH2 A:ARG16 3.5 18.0 1.0
O A:THR327 3.5 26.2 1.0
CG A:ASP304 3.9 30.4 1.0
CB A:ASP304 3.9 26.4 1.0
OG1 A:THR327 4.0 29.8 1.0
CG A:GLU219 4.2 22.1 1.0
NE A:ARG16 4.2 19.3 1.0
C A:THR327 4.4 23.4 1.0
ND1 A:HIS250 4.5 28.4 1.0
CG A:HIS250 4.6 26.5 1.0
P4 A:IHP550 4.6 34.6 0.8
CZ A:PHE254 4.8 25.3 1.0
CD A:ARG16 4.8 20.0 1.0
CB A:GLU219 4.9 22.9 1.0
CB A:ASP325 4.9 24.5 1.0

Mercury binding site 4 out of 4 in 1dkq

Go back to Mercury Binding Sites List in 1dkq
Mercury binding site 4 out of 4 in the Crystal Structure of Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts 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 Phytate Complex Escherichia Coli Phytase at pH 5.0. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg503

b:10.9
occ:0.18
 HG A:HG502 1.8 35.5 0.2
OG1 A:THR327 2.4 29.8 1.0
OD1 A:ASP325 2.6 20.3 1.0
NE2 A:HIS250 2.7 26.7 1.0
O A:THR327 3.0 26.2 1.0
OD2 A:ASP325 3.2 25.1 1.0
CG A:ASP325 3.2 27.8 1.0
CD2 A:HIS250 3.3 23.7 1.0
O A:HOH600 3.5 18.3 1.0
OD1 A:ASP304 3.6 32.6 1.0
C A:THR327 3.6 23.4 1.0
CB A:THR327 3.7 26.8 1.0
CB A:ASP304 3.7 26.4 1.0
CE1 A:HIS250 3.9 24.5 1.0
NH1 A:ARG16 3.9 19.9 1.0
CA A:THR327 4.0 22.9 1.0
N A:THR327 4.0 20.9 1.0
CG A:ASP304 4.1 30.4 1.0
CE2 A:PHE254 4.4 25.6 1.0
CZ A:PHE254 4.4 25.3 1.0
OE2 A:GLU219 4.4 28.4 1.0
CZ A:ARG16 4.5 20.5 1.0
CG A:HIS250 4.6 26.5 1.0
O24 A:IHP550 4.6 33.8 0.8
N A:PRO328 4.6 23.4 1.0
CD2 A:PHE254 4.7 24.9 1.0
CE1 A:PHE254 4.7 25.3 1.0
CB A:ASP325 4.7 24.5 1.0
CG2 A:THR327 4.8 19.7 1.0
ND1 A:HIS250 4.8 28.4 1.0
CD A:GLU219 4.9 27.3 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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