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Mercury in PDB 1dkn: Crystal Structure of Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge

Enzymatic activity of Crystal Structure of Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge

All present enzymatic activity of Crystal Structure of Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge, PDB code: 1dkn 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 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.443, 74.701, 89.829, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 26.8

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge (pdb code 1dkn). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 5 binding sites of Mercury where determined in the Crystal Structure of Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge, PDB code: 1dkn:
Jump to Mercury binding site number: 1; 2; 3; 4; 5;

Mercury binding site 1 out of 5 in 1dkn

Go back to Mercury Binding Sites List in 1dkn
Mercury binding site 1 out of 5 in the Crystal Structure of Escherichia Coli Phytase at pH 5.0 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 Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg500

b:40.7
occ:1.00
ND1 A:HIS113 2.5 34.7 1.0
O A:HOH708 2.8 39.0 1.0
O A:TYR289 3.0 55.7 1.0
O A:HOH723 3.3 61.0 1.0
CE1 A:HIS113 3.4 33.1 1.0
CG A:HIS113 3.5 35.6 1.0
CB A:HIS113 3.7 31.0 1.0
C A:TYR289 4.1 53.3 1.0
O A:HOH630 4.1 56.5 1.0
CA A:HIS113 4.2 33.0 1.0
NE2 A:HIS113 4.6 38.2 1.0
CD2 A:HIS113 4.6 34.6 1.0
CA A:GLY290 4.8 54.7 1.0
N A:GLY290 5.0 53.8 1.0

Mercury binding site 2 out of 5 in 1dkn

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Mercury binding site 2 out of 5 in the Crystal Structure of Escherichia Coli Phytase at pH 5.0 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 Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg501

b:39.1
occ:1.00
NE2 A:HIS250 2.5 29.1 1.0
NH1 A:ARG16 2.5 30.7 1.0
OD2 A:ASP325 2.7 25.7 1.0
O A:HOH690 2.8 24.4 1.0
NH2 A:ARG16 2.8 26.5 1.0
OE1 A:GLU219 2.9 36.8 1.0
O A:HOH691 2.9 50.9 1.0
CZ A:ARG16 3.0 26.5 1.0
CD2 A:HIS250 3.2 31.5 1.0
OD1 A:ASP304 3.3 26.5 1.0
CG A:ASP325 3.6 27.7 1.0
CE1 A:HIS250 3.6 31.8 1.0
OD1 A:ASP325 3.7 23.0 1.0
CD A:GLU219 3.9 41.7 1.0
O A:THR327 3.9 31.6 1.0
CG A:GLU219 4.1 38.2 1.0
NE A:ARG16 4.2 25.8 1.0
O A:HOH627 4.2 22.9 1.0
CG A:ASP304 4.2 31.9 1.0
CB A:ASP304 4.3 27.4 1.0
CG A:HIS250 4.4 33.4 1.0
ND1 A:HIS250 4.6 34.4 1.0
OG1 A:THR327 4.7 33.3 1.0
C A:THR327 4.8 29.2 1.0
CB A:GLU219 4.9 38.6 1.0
O A:HOH656 4.9 27.6 1.0
CD A:ARG16 5.0 20.4 1.0
OE2 A:GLU219 5.0 43.5 1.0

Mercury binding site 3 out of 5 in 1dkn

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Mercury binding site 3 out of 5 in the Crystal Structure of Escherichia Coli Phytase at pH 5.0 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 Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg502

b:37.2
occ:0.50
O A:LEU293 2.6 48.8 1.0
NE2 A:HIS282 2.6 60.6 1.0
O A:HOH715 3.0 44.6 1.0
OE1 A:GLN287 3.1 68.7 1.0
OE1 A:GLN285 3.2 72.2 1.0
CD2 A:HIS282 3.3 58.2 1.0
CG A:GLN285 3.4 68.0 1.0
C A:LEU293 3.5 48.5 1.0
NE2 A:GLN287 3.5 62.1 1.0
CD A:GLN287 3.5 65.2 1.0
CD A:GLN285 3.6 71.0 1.0
CE1 A:HIS282 3.8 60.8 1.0
CB A:LEU293 4.0 49.8 1.0
CG2 A:THR277 4.1 45.5 1.0
N A:PRO294 4.2 48.8 1.0
CA A:LEU293 4.3 50.2 1.0
CD A:PRO294 4.3 45.3 1.0
O A:GLN285 4.5 61.8 1.0
O A:PRO283 4.5 59.0 1.0
CG A:HIS282 4.6 59.1 1.0
N A:LEU293 4.6 51.5 1.0
ND1 A:HIS282 4.7 61.8 1.0
CG A:GLN287 4.8 62.8 1.0
CB A:GLN287 4.8 57.9 1.0
N A:GLN285 4.8 60.2 1.0
CB A:GLN285 4.8 63.6 1.0
NE2 A:GLN285 4.8 71.8 1.0

Mercury binding site 4 out of 5 in 1dkn

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Mercury binding site 4 out of 5 in the Crystal Structure of Escherichia Coli Phytase at pH 5.0 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 Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg503

b:36.4
occ:0.30
O A:ALA278 2.7 36.5 1.0
N A:THR295 2.8 49.1 1.0
CA A:PRO294 2.9 49.2 1.0
CB A:PRO294 3.1 45.2 1.0
HG A:HG504 3.1 62.1 0.3
C A:PRO294 3.3 49.4 1.0
C A:ALA278 3.6 38.1 1.0
OG A:SER10 3.8 42.7 1.0
CA A:ALA278 3.8 36.5 1.0
CG2 A:THR295 3.9 53.0 1.0
CA A:THR295 3.9 48.8 1.0
C A:THR295 4.1 47.8 1.0
CG A:PRO294 4.1 43.6 1.0
N A:PRO294 4.2 48.8 1.0
CB A:ALA278 4.2 37.3 1.0
O A:THR295 4.3 49.6 1.0
CB A:THR295 4.5 50.9 1.0
O A:PRO294 4.5 51.0 1.0
CD2 A:LEU293 4.5 55.6 1.0
CA A:LEU293 4.6 50.2 1.0
CB A:LEU293 4.6 49.8 1.0
N A:SER296 4.6 44.0 1.0
N A:LEU279 4.8 38.5 1.0
C A:LEU293 4.9 48.5 1.0
CD A:PRO294 4.9 45.3 1.0

Mercury binding site 5 out of 5 in 1dkn

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Mercury binding site 5 out of 5 in the Crystal Structure of Escherichia Coli Phytase at pH 5.0 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 5 of Crystal Structure of Escherichia Coli Phytase at pH 5.0 with HG2+ Cation Acting As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg504

b:62.1
occ:0.30
O A:VAL11 3.1 36.2 1.0
HG A:HG503 3.1 36.4 0.3
OG A:SER10 3.2 42.7 1.0
O A:SER296 3.5 31.6 1.0
N A:LEU298 3.7 26.9 1.0
C A:SER296 3.7 35.9 1.0
CB A:LEU298 3.7 26.0 1.0
CG2 A:VAL12 3.8 28.6 1.0
CG2 A:THR295 3.9 53.0 1.0
C A:VAL297 3.9 30.1 1.0
N A:VAL297 3.9 34.2 1.0
C A:VAL11 3.9 35.8 1.0
N A:VAL11 4.0 36.5 1.0
CA A:VAL297 4.0 33.1 1.0
O A:ALA278 4.1 36.5 1.0
N A:SER296 4.2 44.0 1.0
CA A:LEU298 4.3 27.3 1.0
CA A:SER296 4.4 38.5 1.0
CB A:SER10 4.5 42.8 1.0
CB A:ALA278 4.5 37.3 1.0
O A:VAL297 4.5 29.3 1.0
C A:THR295 4.6 47.8 1.0
CA A:VAL11 4.6 36.2 1.0
CG A:LEU298 4.7 27.7 1.0
C A:ALA278 4.7 38.1 1.0
N A:THR295 4.7 49.1 1.0
N A:VAL12 4.8 32.3 1.0
C A:SER10 4.8 40.0 1.0
CA A:SER10 4.8 41.0 1.0
CA A:VAL12 4.9 30.5 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: Sun Dec 13 19:02:28 2020

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