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Zinc in PDB 5yht: Crystal Structure of A Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate

Enzymatic activity of Crystal Structure of A Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate

All present enzymatic activity of Crystal Structure of A Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate:
3.1.3.15;

Protein crystallography data

The structure of Crystal Structure of A Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate, PDB code: 5yht was solved by B.K.Biswal, B.Jha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.80 / 2.87
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.664, 142.446, 48.723, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate (pdb code 5yht). 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 Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate, PDB code: 5yht:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5yht

Go back to Zinc Binding Sites List in 5yht
Zinc binding site 1 out of 4 in the Crystal Structure of A Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate


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 Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:43.4
occ:1.00
 OD2 A:ASP83 2.0 61.5 1.0
OP3 A:HSA303 2.1 70.8 1.0
OD1 A:ASP213 2.3 64.0 1.0
OE1 A:GLU67 2.3 80.7 1.0
O A:HOH402 2.6 33.0 1.0
OD2 A:ASP213 2.9 80.0 1.0
CG A:ASP213 3.0 71.8 1.0
CG A:ASP83 3.1 53.6 1.0
CD A:GLU67 3.3 82.9 1.0
P A:HSA303 3.5 88.0 1.0
OE2 A:GLU67 3.5 74.1 1.0
CD2 A:HSA303 3.6 70.5 1.0
OD1 A:ASP83 3.8 57.0 1.0
OD1 A:ASP86 3.8 67.7 1.0
ZN A:ZN302 3.9 43.6 1.0
OP2 A:HSA303 3.9 0.6 1.0
CG A:ASP86 4.2 66.0 1.0
CB A:ASP83 4.2 47.3 1.0
CA A:ASP86 4.3 54.2 1.0
OP1 A:HSA303 4.4 78.0 1.0
CB A:ASP86 4.4 58.7 1.0
CB A:ASP213 4.5 69.1 1.0
OP4 A:HSA303 4.5 93.5 1.0
CG A:HSA303 4.6 78.9 1.0
NE2 A:HSA303 4.6 68.9 1.0
O A:ILE85 4.6 59.5 1.0
CB A:HSA303 4.6 78.8 1.0
CG A:GLU67 4.7 87.2 1.0
C A:HSA303 4.7 85.5 1.0
CA A:HSA303 4.7 81.4 1.0
OD2 A:ASP86 5.0 74.1 1.0
N A:ASP86 5.0 53.3 1.0

Zinc binding site 2 out of 4 in 5yht

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Zinc binding site 2 out of 4 in the Crystal Structure of A Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate


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 Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:43.6
occ:1.00
 OD1 A:ASP83 2.3 57.0 1.0
OD2 A:ASP44 2.4 83.3 1.0
OP1 A:HSA303 2.4 78.0 1.0
OE2 A:GLU67 2.6 74.1 1.0
O A:ILE85 2.8 59.5 1.0
OP3 A:HSA303 3.1 70.8 1.0
P A:HSA303 3.2 88.0 1.0
CG A:ASP83 3.2 53.6 1.0
CG A:ASP44 3.3 80.0 1.0
OD1 A:ASP44 3.4 88.4 1.0
OD2 A:ASP83 3.5 61.5 1.0
CD A:GLU68 3.6 67.1 1.0
CD A:GLU67 3.6 82.9 1.0
C A:ILE85 3.7 48.5 1.0
ZN A:ZN301 3.9 43.4 1.0
OE1 A:GLU67 4.0 80.7 1.0
N A:ILE85 4.1 45.4 1.0
OP2 A:HSA303 4.2 0.6 1.0
CA A:ILE85 4.4 44.6 1.0
OP4 A:HSA303 4.6 93.5 1.0
N A:ASP86 4.6 53.3 1.0
CB A:ASP83 4.6 47.3 1.0
CD A:PRO84 4.7 46.9 1.0
CB A:ASP44 4.7 74.3 1.0
CG2 A:THR88 4.7 57.0 1.0
CB A:ILE85 4.7 44.2 1.0
CG A:GLU67 4.8 87.2 1.0
N A:PRO84 4.8 48.8 1.0
CG A:GLU68 4.8 68.0 1.0
CB A:GLU67 4.9 84.0 1.0
CA A:ASP86 5.0 54.2 1.0
CA A:ASP83 5.0 47.9 1.0
C A:ASP83 5.0 47.5 1.0

Zinc binding site 3 out of 4 in 5yht

Go back to Zinc Binding Sites List in 5yht
Zinc binding site 3 out of 4 in the Crystal Structure of A Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate


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 Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:70.0
occ:1.00
 OD1 B:ASP213 2.5 73.9 1.0
OD2 B:ASP83 2.6 62.5 1.0
OD2 B:ASP213 2.6 85.4 1.0
OE1 B:GLU67 2.6 98.2 1.0
CG B:ASP213 2.9 79.3 1.0
O1 B:PO4304 3.2 0.9 1.0
O4 B:PO4304 3.2 99.2 1.0
CD B:GLU67 3.6 98.8 1.0
CG B:ASP83 3.7 71.4 1.0
P B:PO4304 3.8 0.6 1.0
OE2 B:GLU67 3.8 0.7 1.0
O B:HOH405 3.8 29.9 1.0
OD1 B:ASP86 3.9 62.8 1.0
ZN B:ZN303 4.1 75.2 1.0
OD1 B:ASP83 4.2 79.1 1.0
CG B:ASP86 4.4 70.9 1.0
CB B:ASP213 4.4 73.3 1.0
O2 B:PO4304 4.4 0.2 1.0
CA B:ASP86 4.5 63.5 1.0
CB B:ASP86 4.7 68.4 1.0
CB B:ASP83 4.8 70.4 1.0
O B:ILE85 4.9 59.7 1.0
CG B:GLU67 5.0 92.7 1.0

Zinc binding site 4 out of 4 in 5yht

Go back to Zinc Binding Sites List in 5yht
Zinc binding site 4 out of 4 in the Crystal Structure of A Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate


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 Phosphatase From Mycobacterium Tuberculosis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:75.2
occ:1.00
 OD1 B:ASP86 2.3 62.8 1.0
O B:HOH412 2.4 53.5 1.0
O4 B:PO4304 2.6 99.2 1.0
CG B:ASP86 3.3 70.9 1.0
OD2 B:ASP213 3.4 85.4 1.0
OD2 B:ASP189 3.5 76.5 1.0
OD2 B:ASP86 3.5 80.5 1.0
CG B:ASP213 3.8 79.3 1.0
P B:PO4304 3.8 0.6 1.0
O3 B:PO4304 4.1 0.4 1.0
OD1 B:ASP213 4.1 73.9 1.0
ZN B:ZN302 4.1 70.0 1.0
CB B:ASP189 4.1 61.7 1.0
CG B:ASP189 4.2 72.0 1.0
O1 B:PO4304 4.3 0.9 1.0
CA B:ASP189 4.5 57.6 1.0
CB B:ASP213 4.5 73.3 1.0
O B:HOH403 4.6 45.6 1.0
N B:GLY87 4.6 54.7 1.0
CB B:ASP86 4.7 68.4 1.0
OE2 B:GLU206 4.8 64.7 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 Frommycobacterium Tuberculosis J. Biol. Chem. V. 293 10102 2018.
ISSN: ESSN 1083-351X
PubMed: 29752410
DOI: 10.1074/JBC.RA118.002299
Page generated: Mon Oct 28 15:44:30 2024

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