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Zinc in PDB 5hif: Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph.

Enzymatic activity of Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph.

All present enzymatic activity of Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph.:
3.1.1.35;

Protein crystallography data

The structure of Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph., PDB code: 5hif was solved by F.Baier, P.D.Carr, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.60 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.600, 88.150, 119.800, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.6

Other elements in 5hif:

The structure of Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph. (pdb code 5hif). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph., PDB code: 5hif:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5hif

Go back to Zinc Binding Sites List in 5hif
Zinc binding site 1 out of 4 in the Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph.


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 A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:11.0
occ:1.00
 O A:HOH507 2.0 10.4 1.0
NE2 A:HIS268 2.1 8.6 1.0
NE2 A:HIS119 2.1 7.9 1.0
OD2 A:ASP118 2.1 9.1 1.0
OD2 A:ASP221 2.2 11.1 1.0
CE1 A:HIS268 2.9 10.7 1.0
CG A:ASP221 3.0 9.5 1.0
CD2 A:HIS119 3.0 7.7 1.0
CG A:ASP118 3.0 9.3 1.0
OD1 A:ASP221 3.1 8.7 1.0
CE1 A:HIS119 3.1 8.8 1.0
CD2 A:HIS268 3.1 8.9 1.0
ZN A:ZN402 3.2 13.1 1.0
OD1 A:ASP118 3.3 10.7 1.0
O A:HOH646 3.9 14.9 1.0
NE2 A:HIS114 4.0 9.8 1.0
CE1 A:HIS114 4.0 10.5 1.0
ND1 A:HIS268 4.1 9.4 1.0
C4 A:PEG403 4.2 48.7 1.0
ND1 A:HIS119 4.2 9.0 1.0
CG A:HIS119 4.2 8.1 1.0
CG A:HIS268 4.2 8.9 1.0
O2 A:PEG403 4.4 52.0 1.0
CB A:ASP221 4.4 9.8 1.0
CB A:ASP118 4.4 9.7 1.0
NE2 A:HIS224 4.8 12.1 1.0
C3 A:PEG403 4.9 54.3 1.0
CB A:HIS116 4.9 10.8 1.0
CB A:ALA267 4.9 8.9 1.0
ND1 A:HIS116 5.0 11.0 1.0

Zinc binding site 2 out of 4 in 5hif

Go back to Zinc Binding Sites List in 5hif
Zinc binding site 2 out of 4 in the Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph.


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 A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:13.1
occ:1.00
 O A:HOH507 1.9 10.4 1.0
OD2 A:ASP221 2.2 11.1 1.0
ND1 A:HIS116 2.2 11.0 1.0
NE2 A:HIS114 2.2 9.8 1.0
NE2 A:HIS200 2.2 10.6 1.0
O A:HOH646 2.3 14.9 1.0
CE1 A:HIS116 3.1 12.8 1.0
CD2 A:HIS114 3.1 8.9 1.0
CE1 A:HIS200 3.2 10.2 1.0
CG A:HIS116 3.2 10.3 1.0
CD2 A:HIS200 3.2 9.3 1.0
CE1 A:HIS114 3.2 10.5 1.0
ZN A:ZN401 3.2 11.0 1.0
CG A:ASP221 3.2 9.5 1.0
CB A:HIS116 3.6 10.8 1.0
CB A:ASP221 3.8 9.8 1.0
NE2 A:HIS119 4.1 7.9 1.0
NE2 A:HIS116 4.2 11.1 1.0
NE2 A:HIS224 4.2 12.1 1.0
CG A:HIS114 4.3 9.4 1.0
OD1 A:ASP221 4.3 8.7 1.0
ND1 A:HIS114 4.3 9.6 1.0
ND1 A:HIS200 4.3 9.3 1.0
CD2 A:HIS116 4.3 11.8 1.0
CD2 A:HIS119 4.3 7.7 1.0
CG A:HIS200 4.4 9.4 1.0
OD1 A:ASP118 4.5 10.7 1.0
C1 A:PEG403 4.7 50.6 1.0
OD2 A:ASP118 4.8 9.1 1.0
CE1 A:HIS224 4.8 13.0 1.0
NE2 A:HIS268 4.9 8.6 1.0
O2 A:PEG403 4.9 52.0 1.0

Zinc binding site 3 out of 4 in 5hif

Go back to Zinc Binding Sites List in 5hif
Zinc binding site 3 out of 4 in the Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph.


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 A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:11.7
occ:1.00
 O B:HOH508 2.0 10.7 1.0
NE2 B:HIS268 2.0 10.2 1.0
NE2 B:HIS119 2.1 9.9 1.0
OD2 B:ASP118 2.1 12.7 1.0
OD2 B:ASP221 2.2 10.7 1.0
CG B:ASP221 2.9 10.1 1.0
CE1 B:HIS268 2.9 11.1 1.0
CD2 B:HIS119 3.0 9.6 1.0
CG B:ASP118 3.1 12.3 1.0
OD1 B:ASP221 3.1 9.7 1.0
CE1 B:HIS119 3.1 9.0 1.0
CD2 B:HIS268 3.1 11.2 1.0
ZN B:ZN402 3.2 14.1 1.0
OD1 B:ASP118 3.4 12.1 1.0
O B:HOH585 3.8 17.5 1.0
NE2 B:HIS114 4.0 11.3 1.0
CE1 B:HIS114 4.1 9.8 1.0
ND1 B:HIS268 4.1 9.9 1.0
C1 B:PEG403 4.1 38.1 1.0
CG B:HIS119 4.2 10.4 1.0
CG B:HIS268 4.2 10.1 1.0
ND1 B:HIS119 4.2 9.3 1.0
O2 B:PEG403 4.3 42.8 1.0
CB B:ASP221 4.4 10.1 1.0
CB B:ASP118 4.4 12.2 1.0
NE2 B:HIS224 4.7 13.3 1.0
C2 B:PEG403 4.7 37.6 1.0
CB B:ALA267 5.0 9.4 1.0
CB B:HIS116 5.0 12.0 1.0
O1 B:PEG403 5.0 39.4 1.0

Zinc binding site 4 out of 4 in 5hif

Go back to Zinc Binding Sites List in 5hif
Zinc binding site 4 out of 4 in the Crystal Structure of A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph.


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 A Reconstructed Lactonase Ancestor, ANC1-Mph, of the Bacterial Methyl Parathion Hydrolase, Mph. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:14.1
occ:1.00
 O B:HOH508 2.0 10.7 1.0
OD2 B:ASP221 2.1 10.7 1.0
NE2 B:HIS200 2.2 9.8 1.0
NE2 B:HIS114 2.2 11.3 1.0
ND1 B:HIS116 2.2 11.0 1.0
O B:HOH585 2.3 17.5 1.0
CE1 B:HIS116 3.1 12.6 1.0
CE1 B:HIS200 3.1 9.8 1.0
CD2 B:HIS114 3.1 10.6 1.0
CD2 B:HIS200 3.2 9.1 1.0
CE1 B:HIS114 3.2 9.8 1.0
CG B:HIS116 3.2 12.2 1.0
ZN B:ZN401 3.2 11.7 1.0
CG B:ASP221 3.3 10.1 1.0
CB B:HIS116 3.6 12.0 1.0
CB B:ASP221 3.7 10.1 1.0
NE2 B:HIS119 4.1 9.9 1.0
NE2 B:HIS224 4.2 13.3 1.0
NE2 B:HIS116 4.3 13.1 1.0
ND1 B:HIS200 4.3 8.7 1.0
CG B:HIS114 4.3 11.0 1.0
ND1 B:HIS114 4.3 10.8 1.0
OD1 B:ASP221 4.3 9.7 1.0
CG B:HIS200 4.3 9.9 1.0
CD2 B:HIS116 4.3 13.5 1.0
CD2 B:HIS119 4.4 9.6 1.0
OD1 B:ASP118 4.5 12.1 1.0
OD2 B:ASP118 4.8 12.7 1.0
CE1 B:HIS224 4.8 12.2 1.0
NE2 B:HIS268 4.9 10.2 1.0
C4 B:PEG403 4.9 50.4 1.0
O4 B:PEG403 4.9 57.0 1.0
O2 B:PEG403 5.0 42.8 1.0

Reference:

F.Baier, P.D.Carr, C.J.Jackson. To Be Published To Be Published.
Page generated: Sun Oct 27 17:29:01 2024

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