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Zinc in PDB 3ea2: Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis

Enzymatic activity of Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis

All present enzymatic activity of Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis:
4.6.1.13;

Protein crystallography data

The structure of Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis, PDB code: 3ea2 was solved by X.Shi, C.Shao, X.Zhang, C.Zambonelli, A.G.Redfied, J.F.Head, B.A.Seaton, M.F.Roberts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.518, 97.226, 112.727, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis (pdb code 3ea2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis, PDB code: 3ea2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3ea2

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Zinc binding site 1 out of 6 in the Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:24.6
occ:1.00
 OD2 A:ASP224 1.9 20.9 1.0
ND1 A:HIS227 2.2 21.8 1.0
O A:HOH920 2.2 22.4 1.0
O A:HOH1045 2.3 26.1 1.0
O A:HOH1070 2.4 31.9 1.0
O A:HOH915 2.4 25.1 1.0
CG A:ASP224 2.9 20.7 1.0
CG A:HIS227 3.2 22.4 1.0
CE1 A:HIS227 3.2 22.9 1.0
OD1 A:ASP224 3.3 18.7 1.0
CB A:HIS227 3.4 22.5 1.0
ND2 A:ASN221 4.0 20.1 1.0
CB A:ASN193 4.1 23.0 1.0
CB A:ASP224 4.2 21.9 1.0
O A:HOH958 4.2 29.6 1.0
O A:HOH1106 4.2 33.6 1.0
OD1 A:ASN193 4.2 24.1 1.0
O A:HOH1082 4.3 43.5 1.0
CD2 A:HIS227 4.3 23.8 1.0
NE2 A:HIS227 4.3 22.9 1.0
CG A:ASN193 4.4 25.5 1.0
CA A:HIS227 4.4 20.9 1.0
ND2 A:ASN226 4.8 29.2 1.0
O A:HOH1145 4.9 35.0 1.0
N A:HIS227 4.9 22.3 1.0

Zinc binding site 2 out of 6 in 3ea2

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Zinc binding site 2 out of 6 in the Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:23.5
occ:1.00
 OE2 A:GLU278 1.6 27.4 1.0
CD A:GLU278 2.0 28.4 1.0
NE2 A:HIS61 2.1 16.0 1.0
OE1 A:GLU278 2.2 24.5 1.0
CE1 A:HIS61 3.0 17.6 1.0
CD2 A:HIS61 3.2 17.4 1.0
CG A:GLU278 3.3 24.3 1.0
O A:HOH906 3.4 4.8 1.0
OH A:TYR57 3.7 17.3 1.0
O A:HOH1154 3.8 23.9 1.0
CE2 A:TYR57 4.1 18.8 1.0
CZ A:TYR57 4.1 16.0 1.0
ND1 A:HIS61 4.1 16.0 1.0
CG A:HIS61 4.3 17.7 1.0
O A:HOH1221 4.4 35.3 1.0
O A:HOH1201 4.4 22.1 1.0
CB A:GLU278 4.4 22.7 1.0
O A:HOH1035 4.5 27.5 1.0
O A:HOH1150 4.6 42.6 1.0

Zinc binding site 3 out of 6 in 3ea2

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Zinc binding site 3 out of 6 in the Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:84.5
occ:1.00
 OE2 A:GLU93 2.4 18.7 1.0
O A:HOH1061 2.7 16.1 1.0
O A:HOH1083 2.7 26.9 1.0
CD A:GLU93 3.4 18.7 1.0
CG A:GLU93 3.7 18.0 1.0
CE A:LYS38 4.2 12.6 1.0
NZ A:LYS38 4.2 13.6 1.0
CZ A:PHE37 4.3 15.3 1.0
CE2 A:PHE37 4.3 14.0 1.0
O A:HOH1239 4.5 45.2 1.0
OE1 A:GLU93 4.5 20.2 1.0
CB A:ASP54 4.6 19.2 1.0
CG A:GLU97 4.7 19.6 1.0
CD2 A:PHE55 4.9 12.2 1.0
CD A:GLU97 5.0 24.0 1.0

Zinc binding site 4 out of 6 in 3ea2

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Zinc binding site 4 out of 6 in the Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn905

b:21.0
occ:1.00
 O A:HOH1011 2.1 18.9 1.0
OD2 A:ASP75 2.1 17.2 1.0
OD2 A:ASP74 2.1 20.0 1.0
O A:HOH1057 2.1 18.9 1.0
CG A:ASP75 2.9 17.9 1.0
CG A:ASP74 2.9 19.9 1.0
OD1 A:ASP74 3.1 19.6 1.0
OD1 A:ASP75 3.2 19.4 1.0
O A:HOH1064 3.7 23.8 1.0
O A:HOH909 4.1 14.8 1.0
CB A:ASP75 4.3 17.9 1.0
CB A:ASP74 4.3 17.7 1.0
N A:ASP75 4.4 17.5 1.0
O A:HOH1130 4.4 40.6 1.0
C A:ASP74 4.6 17.2 1.0
CA A:ASP75 4.6 16.7 1.0
O A:ASP74 5.0 16.4 1.0

Zinc binding site 5 out of 6 in 3ea2

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Zinc binding site 5 out of 6 in the Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn904

b:54.8
occ:1.00
 OE2 B:GLU278 1.8 18.4 1.0
NE2 B:HIS61 2.3 12.3 1.0
CE1 B:HIS61 2.8 13.4 1.0
CD B:GLU278 2.9 18.4 1.0
O B:HOH1066 3.3 37.1 1.0
OH B:TYR57 3.4 17.1 1.0
CG B:GLU278 3.4 17.6 1.0
CD2 B:HIS61 3.5 12.8 1.0
CE2 B:TYR57 3.7 14.3 1.0
CZ B:TYR57 3.8 15.7 1.0
OE1 B:GLU278 4.0 16.2 1.0
ND1 B:HIS61 4.1 12.6 1.0
CB B:GLU278 4.4 16.2 1.0
CG B:HIS61 4.4 14.3 1.0
CD2 B:TYR57 4.7 11.6 1.0
CE1 B:TYR57 5.0 13.1 1.0

Zinc binding site 6 out of 6 in 3ea2

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Zinc binding site 6 out of 6 in the Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Myo-Inositol Bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C From Bacillus Thuringiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn906

b:30.2
occ:1.00
 OD2 B:ASP224 1.9 29.1 1.0
O B:HOH952 2.2 28.7 1.0
ND1 B:HIS227 2.2 25.5 1.0
O B:HOH921 2.3 24.1 1.0
O B:HOH1067 2.4 33.7 1.0
O B:HOH1042 2.5 31.9 1.0
CG B:ASP224 3.0 28.3 1.0
CG B:HIS227 3.1 26.0 1.0
CE1 B:HIS227 3.3 25.5 1.0
CB B:HIS227 3.3 25.3 1.0
OD1 B:ASP224 3.4 28.0 1.0
ND2 B:ASN221 4.1 25.0 1.0
CB B:ASN193 4.1 29.9 1.0
CG B:ASN193 4.2 30.5 1.0
CB B:ASP224 4.2 28.5 1.0
CD2 B:HIS227 4.3 25.9 1.0
CA B:HIS227 4.3 24.0 1.0
NE2 B:HIS227 4.3 26.2 1.0
OD1 B:ASN193 4.4 29.9 1.0
O B:HOH1132 4.7 43.6 1.0
ND2 B:ASN193 4.7 28.6 1.0
N B:HIS227 4.8 25.0 1.0
OD1 B:ASN226 4.8 34.5 1.0

Reference:

X.Shi, C.Shao, X.Zhang, C.Zambonelli, A.G.Redfield, J.F.Head, B.A.Seaton, M.F.Roberts. Modulation of Bacillus Thuringiensis Phosphatidylinositol-Specific Phospholipase C Activity By Mutations in the Putative Dimerization Interface. J.Biol.Chem. V. 284 15607 2009.
ISSN: ISSN 0021-9258
PubMed: 19369255
DOI: 10.1074/JBC.M901601200
Page generated: Thu Oct 24 12:41:29 2024

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