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Zinc in PDB 1p6d: Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine

Enzymatic activity of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine

All present enzymatic activity of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine:
3.1.4.3;

Protein crystallography data

The structure of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine, PDB code: 1p6d 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 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.933, 89.933, 73.936, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.3

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 (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine (pdb code 1p6d). 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 (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine, PDB code: 1p6d:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1p6d

Go back to Zinc Binding Sites List in 1p6d
Zinc binding site 1 out of 3 in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine


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 (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn246

b:15.8
occ:1.00
 O3 A:3PC601 2.0 28.6 1.0
OD2 A:ASP122 2.1 10.2 1.0
ND1 A:HIS69 2.1 11.7 1.0
NE2 A:HIS118 2.1 8.3 1.0
OD1 A:ASN55 2.7 15.1 1.0
CE1 A:HIS69 3.0 11.2 1.0
CD2 A:HIS118 3.0 7.4 1.0
CG A:ASP122 3.0 11.4 1.0
P1 A:3PC601 3.0 32.6 1.0
CE1 A:HIS118 3.1 6.6 1.0
CG A:HIS69 3.2 11.1 1.0
C6 A:3PC601 3.3 36.5 1.0
OD1 A:ASP122 3.3 11.6 1.0
ZN A:ZN248 3.4 15.5 1.0
CB A:HIS69 3.6 9.3 1.0
CG A:ASN55 3.6 12.9 1.0
ND2 A:ASN55 3.9 11.1 1.0
O2 A:3PC601 4.0 30.6 1.0
NE2 A:HIS14 4.1 7.9 1.0
NE2 A:HIS69 4.1 10.4 1.0
O1 A:3PC601 4.2 33.2 1.0
CG A:HIS118 4.2 6.6 1.0
ND1 A:HIS118 4.2 5.9 1.0
CD2 A:HIS69 4.3 12.1 1.0
CB A:ASP122 4.4 9.2 1.0
CE1 A:HIS14 4.6 8.7 1.0
CE1 A:HIS128 4.6 8.3 1.0
C7 A:3PC601 4.8 42.7 1.0
CA A:HIS69 4.8 9.4 1.0
CD2 A:PHE66 4.9 18.3 1.0
CD2 A:HIS14 5.0 8.8 1.0

Zinc binding site 2 out of 3 in 1p6d

Go back to Zinc Binding Sites List in 1p6d
Zinc binding site 2 out of 3 in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine


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 (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn247

b:19.6
occ:1.00
 NE2 A:HIS128 2.0 12.1 1.0
NE2 A:HIS142 2.0 12.5 1.0
O2 A:3PC601 2.1 30.6 1.0
OE2 A:GLU146 2.2 13.8 1.0
OE1 A:GLU146 2.7 16.1 1.0
CD A:GLU146 2.7 12.3 1.0
CE1 A:HIS128 2.9 8.3 1.0
CE1 A:HIS142 3.0 11.2 1.0
CD2 A:HIS142 3.1 12.3 1.0
CD2 A:HIS128 3.1 11.3 1.0
P1 A:3PC601 3.3 32.6 1.0
C8 A:3PC601 3.8 46.4 1.0
C6 A:3PC601 3.9 36.5 1.0
N A:TRP1 3.9 11.1 1.0
C9 A:3PC601 4.0 49.8 1.0
ND1 A:HIS128 4.0 10.3 1.0
ND1 A:HIS142 4.1 10.8 1.0
CG A:GLU146 4.1 11.7 1.0
O1 A:3PC601 4.1 33.2 1.0
C7 A:3PC601 4.1 42.7 1.0
CG A:HIS128 4.2 9.9 1.0
CG A:HIS142 4.2 13.5 1.0
OE1 A:GLN125 4.3 13.6 1.0
C5 A:3PC601 4.3 37.3 1.0
O3 A:3PC601 4.5 28.6 1.0
ZN A:ZN248 4.5 15.5 1.0
OD1 A:ASP122 4.8 11.6 1.0
CA A:TRP1 4.8 11.3 1.0
O A:TRP1 4.9 11.6 1.0
CD A:GLN125 5.0 10.1 1.0
O5 A:3PC601 5.0 46.5 1.0

Zinc binding site 3 out of 3 in 1p6d

Go back to Zinc Binding Sites List in 1p6d
Zinc binding site 3 out of 3 in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus in Complex with (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine


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 (3S)-3,4,Di-N- Hexanoyloxybutyl-1-Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn248

b:15.5
occ:1.00
 NE2 A:HIS14 2.0 7.9 1.0
OD1 A:ASP122 2.1 11.6 1.0
O3 A:3PC601 2.1 28.6 1.0
O A:TRP1 2.3 11.6 1.0
N A:TRP1 2.3 11.1 1.0
O2 A:3PC601 2.8 30.6 1.0
CD2 A:HIS14 3.0 8.8 1.0
C A:TRP1 3.0 13.6 1.0
CE1 A:HIS14 3.0 8.7 1.0
P1 A:3PC601 3.0 32.6 1.0
CA A:TRP1 3.1 11.3 1.0
CG A:ASP122 3.2 11.4 1.0
ZN A:ZN246 3.4 15.8 1.0
OD2 A:ASP122 3.5 10.2 1.0
CB A:TRP1 3.7 10.6 1.0
NE2 A:HIS118 3.9 8.3 1.0
O1 A:3PC601 4.1 33.2 1.0
ND1 A:HIS14 4.1 8.9 1.0
CG A:HIS14 4.1 8.2 1.0
CE1 A:HIS118 4.2 6.6 1.0
N A:SER2 4.3 13.0 1.0
ND2 A:ASN55 4.3 11.1 1.0
CG A:TRP1 4.5 11.4 1.0
ZN A:ZN247 4.5 19.6 1.0
C5 A:3PC601 4.5 37.3 1.0
CB A:ASP122 4.5 9.2 1.0
OE2 A:GLU146 4.5 13.8 1.0
C6 A:3PC601 4.6 36.5 1.0
CD1 A:TRP1 4.6 10.8 1.0
NE2 A:HIS128 4.6 12.1 1.0
CE1 A:HIS128 4.6 8.3 1.0
CA A:ASP122 4.7 9.9 1.0
CD2 A:HIS118 4.8 7.4 1.0
OD1 A:ASN55 4.9 15.1 1.0
OE1 A:GLU146 5.0 16.1 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 Oct 16 17:44:04 2024

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