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Zinc in PDB 1p6e: Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine

Enzymatic activity of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine

All present enzymatic activity of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine:
3.1.4.3;

Protein crystallography data

The structure of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine, PDB code: 1p6e was solved by N.M.Antikainen, A.F.Monzingo, C.L.Franklin, J.D.Robertus, S.F.Martin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.795, 89.795, 74.206, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine (pdb code 1p6e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine, PDB code: 1p6e:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1p6e

Go back to Zinc Binding Sites List in 1p6e
Zinc binding site 1 out of 3 in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn246

b:24.3
occ:1.00
S3 A:PC5601 1.8 61.3 1.0
OD2 A:ASP122 2.1 12.3 1.0
ND1 A:HIS69 2.2 17.1 1.0
NE2 A:HIS118 2.2 10.6 1.0
OD1 A:ASN55 2.9 20.6 1.0
CE1 A:HIS69 3.0 18.4 1.0
CD2 A:HIS118 3.0 10.5 1.0
CG A:ASP122 3.1 13.6 1.0
CG A:HIS69 3.2 16.8 1.0
CE1 A:HIS118 3.3 7.0 1.0
P1 A:PC5601 3.3 23.4 1.0
OD1 A:ASP122 3.4 13.4 1.0
ZN A:ZN248 3.4 22.0 1.0
CB A:HIS69 3.6 13.8 1.0
O1 A:PC5601 3.7 69.9 1.0
CG A:ASN55 3.8 20.7 1.0
NE2 A:HIS14 4.0 15.9 1.0
ND2 A:ASN55 4.1 17.7 1.0
NE2 A:HIS69 4.1 19.8 1.0
CD2 A:HIS69 4.2 18.8 1.0
CG A:HIS118 4.2 8.5 1.0
ND1 A:HIS118 4.3 6.6 1.0
S2 A:PC5601 4.4 67.2 1.0
CB A:ASP122 4.4 12.9 1.0
O4 A:PC5601 4.5 64.6 1.0
CE1 A:HIS14 4.6 16.8 1.0
CE1 A:HIS128 4.7 12.8 1.0
CA A:HIS69 4.8 13.2 1.0
CD2 A:HIS14 4.9 15.7 1.0
CD2 A:PHE66 4.9 25.9 1.0
C7 A:PC5601 4.9 75.3 1.0
O A:HIS118 5.0 12.2 1.0

Zinc binding site 2 out of 3 in 1p6e

Go back to Zinc Binding Sites List in 1p6e
Zinc binding site 2 out of 3 in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn247

b:29.0
occ:1.00
S2 A:PC5601 2.0 67.2 1.0
NE2 A:HIS142 2.1 19.2 1.0
NE2 A:HIS128 2.1 12.1 1.0
OE2 A:GLU146 2.3 18.8 1.0
OE1 A:GLU146 2.7 22.4 1.0
CD A:GLU146 2.8 19.3 1.0
CE1 A:HIS128 3.0 12.8 1.0
CE1 A:HIS142 3.0 17.8 1.0
CD2 A:HIS142 3.1 18.1 1.0
CD2 A:HIS128 3.2 13.4 1.0
P1 A:PC5601 3.3 23.4 1.0
C7 A:PC5601 3.5 75.3 1.0
O1 A:PC5601 3.8 69.9 1.0
C8 A:PC5601 4.1 76.9 1.0
ND1 A:HIS142 4.1 19.7 1.0
O4 A:PC5601 4.1 64.6 1.0
ND1 A:HIS128 4.2 12.9 1.0
N A:TRP1 4.2 14.3 1.0
CG A:HIS142 4.2 19.0 1.0
CG A:GLU146 4.2 17.9 1.0
CG A:HIS128 4.3 13.4 1.0
C5 A:PC5601 4.3 63.9 1.0
OE1 A:GLN125 4.6 16.5 1.0
ZN A:ZN248 4.6 22.0 1.0
S3 A:PC5601 4.9 61.3 1.0

Zinc binding site 3 out of 3 in 1p6e

Go back to Zinc Binding Sites List in 1p6e
Zinc binding site 3 out of 3 in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with 1,2-Di-N-Pentanoyl-Sn- Glycero-3-Dithiophosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn248

b:22.0
occ:1.00
NE2 A:HIS14 2.1 15.9 1.0
OD1 A:ASP122 2.2 13.4 1.0
O A:TRP1 2.3 18.3 1.0
S3 A:PC5601 2.3 61.3 1.0
N A:TRP1 2.3 14.3 1.0
S2 A:PC5601 2.8 67.2 1.0
CD2 A:HIS14 3.0 15.7 1.0
C A:TRP1 3.1 16.7 1.0
P1 A:PC5601 3.1 23.4 1.0
CE1 A:HIS14 3.1 16.8 1.0
CA A:TRP1 3.2 15.3 1.0
CG A:ASP122 3.2 13.6 1.0
ZN A:ZN246 3.4 24.3 1.0
OD2 A:ASP122 3.5 12.3 1.0
CB A:TRP1 3.8 14.3 1.0
NE2 A:HIS118 4.0 10.6 1.0
CG A:HIS14 4.2 15.5 1.0
O4 A:PC5601 4.2 64.6 1.0
ND1 A:HIS14 4.2 14.5 1.0
N A:SER2 4.3 17.3 1.0
CE1 A:HIS118 4.4 7.0 1.0
CG A:TRP1 4.5 12.7 1.0
CB A:ASP122 4.5 12.9 1.0
CD1 A:TRP1 4.5 13.4 1.0
NE2 A:HIS128 4.5 12.1 1.0
OE2 A:GLU146 4.6 18.8 1.0
ND2 A:ASN55 4.6 17.7 1.0
O1 A:PC5601 4.6 69.9 1.0
ZN A:ZN247 4.6 29.0 1.0
CE1 A:HIS128 4.7 12.8 1.0
C5 A:PC5601 4.7 63.9 1.0
CA A:ASP122 4.8 12.3 1.0
CD2 A:HIS118 4.8 10.5 1.0
O A:SER2 4.9 18.1 1.0

Reference:

N.M.Antikainen, A.F.Monzingo, C.L.Franklin, J.D.Robertus, S.F.Martin. Using X-Ray Crystallography of the ASP55ASN Mutant of the Phosphatidylcholine-Preferring Phospholipase C From Bacillus Cereus to Support the Mechanistic Role of ASP55 As the General Base. Arch.Biochem.Biophys. V. 417 81 2003.
ISSN: ISSN 0003-9861
PubMed: 12921783
DOI: 10.1016/S0003-9861(03)00343-6
Page generated: Wed Dec 16 03:00:31 2020

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