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Zinc in PDB 5zon: Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis

Enzymatic activity of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis

All present enzymatic activity of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis:
3.1.3.15;

Protein crystallography data

The structure of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis, PDB code: 5zon was solved by B.Jha, D.Kumar, B.K.Biswal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.50 / 1.94
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.030, 71.062, 91.586, 92.16, 96.16, 101.94
R / Rfree (%) 21.2 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis (pdb code 5zon). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis, PDB code: 5zon:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5zon

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Zinc binding site 1 out of 8 in the Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:11.3
occ:1.00
OE1 A:GLU67 2.3 27.9 1.0
OE2 A:GLU68 2.4 31.2 1.0
O4 A:PO4303 2.5 42.4 1.0
OD1 A:ASP83 2.5 18.3 1.0
OD2 A:ASP44 2.5 27.2 1.0
O A:ILE85 2.7 20.0 1.0
O A:HOH441 2.7 27.5 1.0
O1 A:PO4303 2.9 38.5 1.0
OD1 A:ASP44 3.1 22.0 1.0
CG A:ASP44 3.1 27.1 1.0
P A:PO4303 3.3 34.4 1.0
CG A:ASP83 3.4 17.3 1.0
CD A:GLU67 3.5 29.7 1.0
CD A:GLU68 3.5 36.4 1.0
OD2 A:ASP83 3.6 16.1 1.0
C A:ILE85 3.7 20.0 1.0
O2 A:PO4303 4.0 32.1 0.9
OE1 A:GLU68 4.1 35.7 1.0
CG A:GLU67 4.2 25.7 1.0
N A:ILE85 4.2 19.6 1.0
CG2 A:THR88 4.2 24.3 1.0
ZN A:ZN302 4.2 10.9 1.0
OE2 A:GLU67 4.4 33.5 1.0
CA A:ILE85 4.4 17.6 1.0
O3 A:PO4303 4.5 31.4 1.0
CB A:GLU67 4.6 22.9 1.0
N A:ASP86 4.6 18.7 1.0
O A:HOH478 4.6 46.6 1.0
CB A:ASP44 4.6 24.1 1.0
CD A:PRO84 4.6 21.9 1.0
CG A:GLU68 4.7 31.5 1.0
O A:HOH435 4.7 41.6 1.0
CB A:ILE85 4.7 17.9 1.0
CB A:ASP83 4.8 17.8 1.0
CA A:ASP86 4.8 21.4 1.0
N A:PRO84 4.9 20.3 1.0

Zinc binding site 2 out of 8 in 5zon

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Zinc binding site 2 out of 8 in the Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:10.9
occ:1.00
O A:HOH435 2.0 41.6 1.0
O1 A:PO4303 2.1 38.5 1.0
OD2 A:ASP83 2.3 16.1 1.0
OD1 A:ASP213 2.4 26.3 1.0
OE2 A:GLU67 2.5 33.5 1.0
O A:HOH487 2.6 30.5 1.0
OD2 A:ASP213 2.6 34.7 1.0
OD1 A:ASP86 2.7 25.4 1.0
OE1 A:GLU67 2.8 27.9 1.0
CG A:ASP213 2.8 26.6 1.0
CD A:GLU67 3.0 29.7 1.0
CG A:ASP83 3.3 17.3 1.0
P A:PO4303 3.5 34.4 1.0
CG A:ASP86 3.8 26.2 1.0
OD1 A:ASP83 3.9 18.3 1.0
O A:HOH543 4.0 45.8 1.0
O2 A:PO4303 4.1 32.1 0.9
ZN A:ZN301 4.2 11.3 1.0
O3 A:PO4303 4.2 31.4 1.0
O A:HOH443 4.3 12.3 1.0
CA A:ASP86 4.3 21.4 1.0
CB A:ASP86 4.3 23.0 1.0
CB A:ASP83 4.3 17.8 1.0
CB A:ASP213 4.4 23.0 1.0
O4 A:PO4303 4.5 42.4 1.0
CG A:GLU67 4.5 25.7 1.0
O A:ILE85 4.7 20.0 1.0
OD2 A:ASP86 4.9 24.9 1.0
OG A:SER210 5.0 31.6 1.0

Zinc binding site 3 out of 8 in 5zon

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Zinc binding site 3 out of 8 in the Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:42.3
occ:0.90
OD1 B:ASP86 2.5 36.5 1.0
O4 B:PO4304 2.8 62.5 0.5
O3 B:PO4304 2.9 50.8 1.0
OD2 B:ASP189 3.0 27.0 1.0
O B:HOH429 3.1 38.9 1.0
OD2 B:ASP213 3.3 46.5 1.0
O B:HOH586 3.3 23.4 1.0
CG B:ASP86 3.4 31.6 1.0
P B:PO4304 3.5 64.8 1.0
OD2 B:ASP86 3.5 31.6 1.0
CG B:ASP213 3.7 41.3 1.0
O B:HOH403 3.8 27.4 1.0
CG B:ASP189 4.0 25.5 1.0
OD1 B:ASP213 4.1 47.3 1.0
ZN B:ZN303 4.2 56.8 1.0
CB B:ASP189 4.2 21.9 1.0
O1 B:PO4304 4.3 45.6 1.0
O B:HOH447 4.4 28.0 1.0
CB B:ASP213 4.5 37.7 1.0
CA B:ASP189 4.5 22.0 1.0
N B:GLY87 4.6 20.7 1.0
O2 B:PO4304 4.7 54.5 1.0
CB B:ASP86 4.8 24.6 1.0
OE2 B:GLU206 4.8 39.1 1.0
O B:HOH508 4.9 34.5 1.0

Zinc binding site 4 out of 8 in 5zon

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Zinc binding site 4 out of 8 in the Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:56.8
occ:1.00
OD1 B:ASP213 2.1 47.3 1.0
OD2 B:ASP83 2.4 40.0 1.0
O3 B:PO4304 2.6 50.8 1.0
CG B:ASP213 2.8 41.3 1.0
OD2 B:ASP213 2.8 46.5 1.0
OD1 B:ASP86 3.0 36.5 1.0
O B:HOH403 3.3 27.4 1.0
CG B:ASP83 3.4 39.6 1.0
P B:PO4304 3.8 64.8 1.0
O1 B:PO4304 3.8 45.6 1.0
CG B:ASP86 4.0 31.6 1.0
OD1 B:ASP83 4.0 42.9 1.0
ZN B:ZN302 4.2 42.3 0.9
CB B:ASP213 4.2 37.7 1.0
CA B:ASP86 4.4 24.0 1.0
CB B:ASP86 4.4 24.6 1.0
CB B:ASP83 4.5 33.3 1.0
CA B:ASP213 4.8 29.8 1.0
O4 B:PO4304 4.8 62.5 0.5
O B:ILE85 4.8 27.3 1.0
O2 B:PO4304 4.8 54.5 1.0
OG B:SER210 4.9 30.5 1.0
O B:HOH414 4.9 42.2 1.0
N B:ASP213 5.0 27.8 1.0

Zinc binding site 5 out of 8 in 5zon

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Zinc binding site 5 out of 8 in the Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:10.4
occ:1.00
O4 C:PO4304 2.2 35.8 0.8
OD2 C:ASP83 2.3 14.4 1.0
OD1 C:ASP213 2.4 27.1 1.0
O C:HOH449 2.4 31.7 1.0
OE2 C:GLU67 2.5 31.6 1.0
O C:HOH508 2.5 45.6 1.0
OD2 C:ASP213 2.6 32.3 1.0
OD1 C:ASP86 2.8 23.7 1.0
OE1 C:GLU67 2.8 30.6 1.0
CG C:ASP213 2.9 25.5 1.0
CD C:GLU67 3.0 32.0 1.0
CG C:ASP83 3.3 15.8 1.0
P C:PO4304 3.6 34.0 1.0
CG C:ASP86 3.9 21.6 0.8
OD1 C:ASP83 4.0 16.8 1.0
O3 C:PO4304 4.1 32.7 1.0
ZN C:ZN302 4.2 11.7 1.0
O C:HOH466 4.2 10.7 1.0
O1 C:PO4304 4.3 29.3 1.0
CB C:ASP83 4.3 16.6 1.0
CA C:ASP86 4.4 17.6 1.0
CB C:ASP86 4.4 17.9 1.0
CB C:ASP213 4.4 23.4 1.0
CG C:GLU67 4.5 24.4 1.0
O C:HOH408 4.6 46.7 1.0
O C:HOH406 4.6 50.3 1.0
O2 C:PO4304 4.6 40.0 1.0
O C:HOH600 4.7 53.3 1.0
O C:ILE85 4.8 17.4 1.0
OD2 C:ASP86 4.9 21.0 1.0
OG C:SER210 4.9 33.2 0.9

Zinc binding site 6 out of 8 in 5zon

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Zinc binding site 6 out of 8 in the Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:11.7
occ:1.00
OE1 C:GLU67 2.3 30.6 1.0
OE2 C:GLU68 2.4 32.5 1.0
OD1 C:ASP83 2.5 16.8 1.0
OD2 C:ASP44 2.5 24.9 1.0
O2 C:PO4304 2.6 40.0 1.0
O C:ILE85 2.7 17.4 1.0
O C:HOH422 2.7 28.9 1.0
O4 C:PO4304 2.8 35.8 0.8
OD1 C:ASP44 3.1 22.5 1.0
CG C:ASP44 3.2 24.4 1.0
P C:PO4304 3.3 34.0 1.0
CG C:ASP83 3.4 15.8 1.0
CD C:GLU67 3.4 32.0 1.0
CD C:GLU68 3.5 37.6 1.0
OD2 C:ASP83 3.5 14.4 1.0
C C:ILE85 3.7 16.4 0.7
OE1 C:GLU68 4.0 38.9 1.0
CG C:GLU67 4.1 24.4 1.0
ZN C:ZN301 4.2 10.4 1.0
O C:HOH555 4.2 58.5 1.0
O3 C:PO4304 4.2 32.7 1.0
N C:ILE85 4.2 19.0 1.0
OG1 C:THR88 4.3 27.9 1.0
OE2 C:GLU67 4.4 31.6 1.0
CA C:ILE85 4.5 17.0 1.0
O1 C:PO4304 4.5 29.3 1.0
CB C:GLU67 4.6 21.2 1.0
N C:ASP86 4.6 16.8 1.0
CB C:ASP44 4.7 21.3 1.0
O C:HOH552 4.7 39.2 1.0
CG C:GLU68 4.7 29.2 1.0
CD C:PRO84 4.7 17.7 1.0
CB C:ILE85 4.8 16.6 1.0
CB C:ASP83 4.8 16.6 1.0
CA C:ASP86 4.8 17.6 1.0
N C:PRO84 5.0 17.3 1.0

Zinc binding site 7 out of 8 in 5zon

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Zinc binding site 7 out of 8 in the Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:42.2
occ:0.80
O D:HOH411 2.4 31.4 1.0
OD1 D:ASP86 2.5 29.6 1.0
O1 D:PO4303 2.8 67.2 1.0
OD1 D:ASP189 2.9 27.3 1.0
O D:HOH413 3.1 31.1 1.0
CG D:ASP86 3.3 27.0 1.0
OD2 D:ASP86 3.4 24.0 1.0
OD2 D:ASP213 3.4 38.5 0.8
O D:HOH540 3.6 29.5 1.0
CG D:ASP213 3.8 33.4 0.4
CG D:ASP189 3.9 24.9 1.0
O D:HOH402 3.9 32.8 1.0
CB D:ASP189 4.1 23.0 1.0
P D:PO4303 4.1 68.5 1.0
ZN D:ZN302 4.2 63.5 1.0
O2 D:PO4303 4.2 46.0 1.0
OD1 D:ASP213 4.2 43.2 1.0
O D:HOH481 4.3 27.1 1.0
CA D:ASP189 4.4 20.1 1.0
N D:GLY87 4.5 22.6 1.0
CB D:ASP213 4.6 32.0 1.0
CB D:ASP86 4.7 22.2 1.0
OE2 D:GLU206 4.8 32.5 1.0
O D:HOH431 4.9 28.1 1.0
O4 D:PO4303 5.0 48.2 1.0

Zinc binding site 8 out of 8 in 5zon

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Zinc binding site 8 out of 8 in the Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:63.5
occ:1.00
OD1 D:ASP213 2.0 43.2 1.0
O D:HOH411 2.3 31.4 1.0
OD2 D:ASP83 2.3 37.6 1.0
CG D:ASP213 2.8 33.4 0.4
OD1 D:ASP86 2.8 29.6 1.0
OD2 D:ASP213 2.9 38.5 0.8
O D:HOH454 2.9 44.6 1.0
CG D:ASP83 3.4 33.7 1.0
O D:HOH402 3.6 32.8 1.0
CG D:ASP86 3.7 27.0 1.0
O2 D:PO4303 3.9 46.0 1.0
OD1 D:ASP83 4.0 39.7 1.0
CB D:ASP86 4.1 22.2 1.0
CA D:ASP86 4.1 22.1 1.0
ZN D:ZN301 4.2 42.2 0.8
CB D:ASP213 4.2 32.0 1.0
O1 D:PO4303 4.5 67.2 1.0
CB D:ASP83 4.5 28.6 1.0
O D:ILE85 4.7 24.3 1.0
CA D:ASP213 4.7 26.0 1.0
OD2 D:ASP86 4.8 24.0 1.0
P D:PO4303 4.8 68.5 1.0
N D:ASP86 5.0 22.1 1.0
N D:ASP213 5.0 23.2 1.0

Reference:

B.Jha, D.Kumar, A.Sharma, A.Dwivedy, R.Singh, B.K.Biswal. Identification and Structural Characterization of A Histidinol Phosphate Phosphatase From Mycobacterium Tuberculosis J. Biol. Chem. V. 293 10102 2018.
ISSN: ESSN 1083-351X
PubMed: 29752410
DOI: 10.1074/JBC.RA118.002299
Page generated: Wed Dec 16 11:27:36 2020

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