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Zinc in PDB 4gyf: Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate

Enzymatic activity of Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate

All present enzymatic activity of Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate:
3.1.3.15;

Protein crystallography data

The structure of Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate, PDB code: 4gyf was solved by A.A.Fedorov, E.V.Fedorov, S.Ghodge, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.83 / 1.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.661, 86.679, 45.080, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.6

Other elements in 4gyf:

The structure of Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate (pdb code 4gyf). 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 Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate, PDB code: 4gyf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4gyf

Go back to Zinc Binding Sites List in 4gyf
Zinc binding site 1 out of 4 in the Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate


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 Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:7.7
occ:0.85
 OE2 A:GLU81 2.0 10.6 1.0
NE2 A:HIS109 2.1 8.1 1.0
NE2 A:HIS154 2.1 8.8 1.0
O A:HOH619 2.1 22.4 1.0
O3 A:PO4312 2.2 16.1 0.8
CE1 A:HIS109 2.9 10.8 1.0
CD A:GLU81 3.0 10.8 1.0
CD2 A:HIS154 3.0 9.1 1.0
CE1 A:HIS154 3.1 8.6 1.0
CD2 A:HIS109 3.2 8.8 1.0
OE1 A:GLU81 3.3 8.4 1.0
P A:PO4312 3.3 12.9 0.8
O1 A:PO4312 3.5 10.7 0.8
ZN A:ZN303 3.6 8.0 0.8
OG A:SER107 3.9 13.2 1.0
O2 A:PO4312 4.0 10.5 0.8
CE1 A:TYR157 4.1 11.6 1.0
ND1 A:HIS109 4.1 9.5 1.0
CB A:SER107 4.1 10.6 1.0
CE1 A:HIS42 4.2 10.0 1.0
ND1 A:HIS154 4.2 8.6 1.0
CG A:HIS154 4.2 7.9 1.0
CG A:HIS109 4.2 9.2 1.0
CG A:GLU81 4.3 10.8 1.0
N A:HSO313 4.3 13.3 0.8
CD1 A:TYR157 4.4 9.6 1.0
OD2 A:ASP228 4.4 11.7 1.0
O4 A:PO4312 4.5 11.9 0.8
CE1 A:HIS9 4.6 9.4 1.0
NE2 A:HIS9 4.7 7.2 1.0
ND1 A:HIS42 4.9 7.8 1.0
NH1 A:ARG160 5.0 13.8 1.0
CZ A:TYR157 5.0 13.4 1.0

Zinc binding site 2 out of 4 in 4gyf

Go back to Zinc Binding Sites List in 4gyf
Zinc binding site 2 out of 4 in the Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate


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 Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:7.7
occ:0.88
 O4 A:PO4312 2.0 11.9 0.8
OD2 A:ASP17 2.0 9.3 1.0
NE2 A:HIS42 2.0 7.7 1.0
NE2 A:HIS230 2.0 9.4 1.0
CG A:ASP17 2.8 8.2 1.0
OD1 A:ASP17 2.9 9.0 1.0
O1 A:PO4312 3.0 10.7 0.8
CD2 A:HIS42 3.0 6.9 1.0
CE1 A:HIS42 3.0 10.0 1.0
P A:PO4312 3.0 12.9 0.8
CE1 A:HIS230 3.0 10.2 1.0
CD2 A:HIS230 3.0 8.3 1.0
O3 A:PO4312 4.0 16.1 0.8
O2 A:PO4312 4.1 10.5 0.8
CA A:HSO313 4.1 19.3 0.8
O A:HSO313 4.1 27.8 0.8
ND1 A:HIS42 4.1 7.8 1.0
CG A:HIS42 4.1 8.3 1.0
ND1 A:HIS230 4.1 8.4 1.0
CG A:HIS230 4.2 7.5 1.0
CB A:ASP17 4.2 8.6 1.0
N A:HSO313 4.2 13.3 0.8
NE2 A:HIS11 4.3 7.6 1.0
CE1 A:HIS11 4.3 7.8 1.0
ND1 A:HIS11 4.4 8.5 1.0
CD2 A:HIS11 4.4 8.0 1.0
CG A:HIS11 4.5 5.8 1.0
ZN A:ZN303 4.5 8.0 0.8
C A:HSO313 4.6 23.4 0.8
CE1 A:PHE52 4.9 12.9 1.0

Zinc binding site 3 out of 4 in 4gyf

Go back to Zinc Binding Sites List in 4gyf
Zinc binding site 3 out of 4 in the Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate


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 Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:8.0
occ:0.84
 O1 A:PO4312 1.9 10.7 0.8
O A:HOH619 2.1 22.4 1.0
NE2 A:HIS9 2.1 7.2 1.0
NE2 A:HIS11 2.2 7.6 1.0
OE1 A:GLU81 2.2 8.4 1.0
OD1 A:ASP228 2.2 11.6 1.0
CE1 A:HIS11 3.0 7.8 1.0
CE1 A:HIS9 3.1 9.4 1.0
CG A:ASP228 3.1 11.2 1.0
CD A:GLU81 3.1 10.8 1.0
CD2 A:HIS9 3.1 6.7 1.0
CD2 A:HIS11 3.2 8.0 1.0
P A:PO4312 3.2 12.9 0.8
OD2 A:ASP228 3.3 11.7 1.0
OE2 A:GLU81 3.5 10.6 1.0
ZN A:ZN301 3.6 7.7 0.8
O3 A:PO4312 3.7 16.1 0.8
CE1 A:HIS42 3.8 10.0 1.0
O2 A:PO4312 3.9 10.5 0.8
CE1 A:HIS230 4.2 10.2 1.0
ND1 A:HIS11 4.2 8.5 1.0
ND1 A:HIS9 4.2 8.2 1.0
NE2 A:HIS42 4.2 7.7 1.0
CG A:HIS9 4.3 7.2 1.0
CG A:HIS11 4.3 5.8 1.0
O4 A:PO4312 4.3 11.9 0.8
CG A:GLU81 4.4 10.8 1.0
CB A:ASP228 4.5 10.2 1.0
ZN A:ZN302 4.5 7.7 0.9
ND1 A:HIS42 4.6 7.8 1.0
NE2 A:HIS230 4.6 9.4 1.0
CB A:GLU81 4.7 10.5 1.0
CA A:ASP228 4.8 8.3 1.0
NE2 A:HIS154 5.0 8.8 1.0

Zinc binding site 4 out of 4 in 4gyf

Go back to Zinc Binding Sites List in 4gyf
Zinc binding site 4 out of 4 in the Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate


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 Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L- Histidinol and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:8.9
occ:0.87
 NE2 A:HSO314 2.0 11.4 1.0
NE2 A:HIS32 2.0 12.9 1.0
NE2 A:HIS240 2.0 10.8 1.0
CL A:CL306 2.2 14.1 1.0
CE1 A:HSO314 2.9 10.6 1.0
CD2 A:HIS240 3.0 9.6 1.0
CD2 A:HIS32 3.0 10.5 1.0
CE1 A:HIS32 3.0 9.1 1.0
CE1 A:HIS240 3.1 10.9 1.0
CD2 A:HSO314 3.1 13.9 1.0
ND1 A:HSO314 4.1 16.9 1.0
ND1 A:HIS32 4.1 11.3 1.0
CG A:HIS32 4.1 10.0 1.0
CG A:HIS240 4.1 10.3 1.0
ND1 A:HIS240 4.2 11.5 1.0
CG A:HSO314 4.2 16.1 1.0
CE3 A:TRP236 4.4 12.1 1.0
CZ3 A:TRP236 5.0 14.3 1.0
CD2 A:TRP236 5.0 11.5 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, S.Ghodge, F.M.Raushel, S.C.Almo. Crystal Structure of Histidinol Phosphate Phosphatase (Hisk) From Lactococcus Lactis Subsp. Lactis IL1403 Complexed with Zn, L-Histidinol and Phosphate To Be Published.
Page generated: Wed Dec 16 05:21:16 2020

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