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Zinc in PDB 4zi6: Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori

Enzymatic activity of Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori

All present enzymatic activity of Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori:
3.4.11.1; 3.4.11.10;

Protein crystallography data

The structure of Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori, PDB code: 4zi6 was solved by J.K.Modak, A.Roujeinikova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.40 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 96.310, 99.430, 99.680, 75.26, 61.08, 82.04
R / Rfree (%) 17.1 / 22.5

Other elements in 4zi6:

The structure of Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori (pdb code 4zi6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori, PDB code: 4zi6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 4zi6

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Zinc binding site 1 out of 12 in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori


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 Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:16.9
occ:0.60
 OE2 A:GLU342 2.1 13.1 1.0
OD2 A:ASP281 2.2 17.7 1.0
NZ A:LYS258 2.3 7.9 1.0
OD2 A:ASP263 2.4 15.8 1.0
O A:HOH635 2.5 14.8 1.0
O A:HOH812 2.5 26.4 1.0
CG A:ASP281 3.0 17.3 1.0
ZN A:ZN502 3.0 18.5 0.5
CD A:GLU342 3.0 16.1 1.0
OD1 A:ASP281 3.1 13.9 1.0
CE A:LYS258 3.2 11.9 1.0
OE1 A:GLU342 3.2 18.9 1.0
CG A:ASP263 3.3 15.7 1.0
O3 A:BCT503 3.7 12.1 1.0
CB A:ASP263 3.9 11.4 1.0
OD1 A:ASP263 4.3 14.3 1.0
O A:THR367 4.3 14.0 1.0
CB A:ASP281 4.4 12.5 1.0
CG A:GLU342 4.5 10.4 1.0
CG A:LEU260 4.5 14.9 1.0
CD A:LYS258 4.7 13.3 1.0
N A:GLY343 4.7 8.6 1.0
CB A:LEU260 4.7 14.7 1.0
O A:ASP340 4.9 15.0 1.0
CA A:GLY343 5.0 15.9 1.0

Zinc binding site 2 out of 12 in 4zi6

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Zinc binding site 2 out of 12 in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori


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 Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:18.5
occ:0.50
 OD2 A:ASP263 2.2 15.8 1.0
OD1 A:ASP340 2.2 18.6 1.0
OE1 A:GLU342 2.3 18.9 1.0
O A:HOH635 2.3 14.8 1.0
O A:ASP340 2.4 15.0 1.0
ZN A:ZN501 3.0 16.9 0.6
CG A:ASP340 3.1 19.4 1.0
CG A:ASP263 3.1 15.7 1.0
C A:ASP340 3.3 13.9 1.0
CD A:GLU342 3.3 16.1 1.0
OD1 A:ASP263 3.4 14.3 1.0
OE2 A:GLU342 3.5 13.1 1.0
O A:HOH812 3.6 26.4 1.0
CA A:ASP340 3.6 14.8 1.0
NZ A:LYS270 3.6 25.1 1.0
OD2 A:ASP340 3.9 23.7 1.0
CB A:ASP340 3.9 12.9 1.0
CE A:LYS270 4.0 22.3 1.0
O3 A:BCT503 4.1 12.1 1.0
N A:ALA341 4.4 14.1 1.0
N A:GLU342 4.5 12.3 1.0
CB A:ASP263 4.5 11.4 1.0
ND2 A:ASN313 4.6 8.6 1.0
CG A:GLU342 4.6 10.4 1.0
OD2 A:ASP281 4.8 17.7 1.0
CA A:ALA341 4.9 10.9 1.0
CA A:GLY265 4.9 13.6 1.0
NZ A:LYS258 4.9 7.9 1.0
C A:BCT503 5.0 19.3 1.0
O2 A:BCT503 5.0 27.0 0.7
N A:ASP340 5.0 13.0 1.0

Zinc binding site 3 out of 12 in 4zi6

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Zinc binding site 3 out of 12 in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori


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 Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:23.2
occ:0.75
 OD2 B:ASP281 2.1 12.2 0.7
NZ B:LYS258 2.1 10.0 1.0
OE2 B:GLU342 2.2 19.4 1.0
O B:HOH813 2.5 16.4 1.0
OD2 B:ASP263 2.5 14.1 1.0
O B:HOH721 2.7 22.6 1.0
CG B:ASP281 2.9 16.0 1.0
CE B:LYS258 3.0 10.9 1.0
CD B:GLU342 3.1 15.2 1.0
OD1 B:ASP281 3.1 17.3 1.0
O B:HOH683 3.1 28.6 1.0
ZN B:ZN502 3.1 20.6 0.5
OE1 B:GLU342 3.3 10.5 1.0
CG B:ASP263 3.5 11.6 1.0
O1 B:BCT503 3.8 12.1 1.0
CB B:ASP263 3.9 12.7 1.0
O B:THR367 4.3 16.7 1.0
CB B:ASP281 4.3 14.0 1.0
OD1 B:ASP263 4.4 10.4 1.0
CD B:LYS258 4.5 14.2 1.0
CG B:GLU342 4.5 10.0 1.0
CG B:LEU260 4.6 12.0 1.0
N B:GLY343 4.6 11.5 1.0
CB B:LEU260 4.7 10.9 1.0
O B:ASP340 4.9 12.0 1.0
CA B:GLY343 4.9 11.7 1.0

Zinc binding site 4 out of 12 in 4zi6

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Zinc binding site 4 out of 12 in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori


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 Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:20.6
occ:0.50
 OD1 B:ASP340 2.2 14.4 1.0
OD2 B:ASP263 2.2 14.1 1.0
O B:HOH813 2.3 16.4 1.0
O B:ASP340 2.3 12.0 1.0
OE1 B:GLU342 2.3 10.5 1.0
ZN B:ZN501 3.1 23.2 0.8
CG B:ASP263 3.2 11.6 1.0
CG B:ASP340 3.2 18.6 1.0
C B:ASP340 3.2 14.7 1.0
O B:HOH721 3.2 22.6 1.0
CD B:GLU342 3.3 15.2 1.0
OD1 B:ASP263 3.4 10.4 1.0
CA B:ASP340 3.6 13.6 1.0
OE2 B:GLU342 3.6 19.4 1.0
NZ B:LYS270 3.9 23.6 1.0
CB B:ASP340 3.9 11.7 1.0
OD2 B:ASP340 4.0 20.5 1.0
CE B:LYS270 4.0 20.4 1.0
O1 B:BCT503 4.2 12.1 1.0
O B:HOH683 4.3 28.6 1.0
N B:ALA341 4.4 12.9 1.0
N B:GLU342 4.5 17.1 1.0
CB B:ASP263 4.5 12.7 1.0
ND2 B:ASN313 4.6 11.1 1.0
CG B:GLU342 4.6 10.0 1.0
OD2 B:ASP281 4.8 12.2 0.7
CA B:GLY265 4.8 12.0 1.0
CA B:ALA341 4.8 11.4 1.0
NZ B:LYS258 4.9 10.0 1.0
N B:ASP340 5.0 12.8 1.0
O B:HOH820 5.0 31.4 1.0

Zinc binding site 5 out of 12 in 4zi6

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Zinc binding site 5 out of 12 in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori


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 Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:27.7
occ:0.75
 OD2 C:ASP281 2.0 26.6 1.0
OE2 C:GLU342 2.1 19.4 1.0
NZ C:LYS258 2.4 8.4 1.0
O C:HOH648 2.5 19.3 1.0
OD2 C:ASP263 2.6 15.1 1.0
CG C:ASP281 2.9 19.4 1.0
O C:HOH848 3.0 28.0 1.0
CD C:GLU342 3.0 14.8 1.0
O C:HOH662 3.1 29.4 1.0
OD1 C:ASP281 3.1 19.6 1.0
CE C:LYS258 3.2 14.2 1.0
ZN C:ZN502 3.2 24.2 0.5
OE1 C:GLU342 3.3 17.4 1.0
CG C:ASP263 3.4 18.2 1.0
O1 C:BCT503 3.8 18.2 1.0
CB C:ASP263 3.9 16.9 1.0
CB C:ASP281 4.3 16.1 1.0
O C:THR367 4.4 23.4 1.0
CG C:GLU342 4.4 10.0 1.0
OD1 C:ASP263 4.4 16.9 1.0
CG C:LEU260 4.5 16.3 1.0
CD C:LYS258 4.6 15.6 1.0
CB C:LEU260 4.6 17.6 1.0
N C:GLY343 4.7 9.6 1.0
O C:HOH856 4.9 31.0 1.0
O C:ASP340 5.0 13.1 1.0
CA C:GLY343 5.0 12.6 1.0

Zinc binding site 6 out of 12 in 4zi6

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Zinc binding site 6 out of 12 in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori


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 Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:24.2
occ:0.50
 OD1 C:ASP340 2.1 18.4 1.0
O C:HOH648 2.1 19.3 1.0
OE1 C:GLU342 2.3 17.4 1.0
O C:ASP340 2.3 13.1 1.0
OD2 C:ASP263 2.3 15.1 1.0
O C:HOH662 3.0 29.4 1.0
CG C:ASP340 3.0 22.4 1.0
C C:ASP340 3.2 13.5 1.0
ZN C:ZN501 3.2 27.7 0.8
CG C:ASP263 3.2 18.2 1.0
CD C:GLU342 3.3 14.8 1.0
OD1 C:ASP263 3.5 16.9 1.0
CA C:ASP340 3.5 14.9 1.0
OE2 C:GLU342 3.6 19.4 1.0
NZ C:LYS270 3.8 24.3 1.0
O C:HOH848 3.8 28.0 1.0
OD2 C:ASP340 3.8 21.3 1.0
CB C:ASP340 3.9 13.4 1.0
CE C:LYS270 3.9 23.0 1.0
O1 C:BCT503 4.3 18.2 1.0
N C:ALA341 4.4 13.0 1.0
N C:GLU342 4.5 11.8 1.0
O C:HOH856 4.6 31.0 1.0
ND2 C:ASN313 4.6 10.9 1.0
CB C:ASP263 4.6 16.9 1.0
CG C:GLU342 4.7 10.0 1.0
O3 C:BCT503 4.8 34.6 1.0
CA C:GLY265 4.8 12.4 1.0
CA C:ALA341 4.9 15.2 1.0
OD2 C:ASP281 4.9 26.6 1.0
N C:ASP340 4.9 9.8 1.0
C C:BCT503 5.0 19.8 1.0

Zinc binding site 7 out of 12 in 4zi6

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Zinc binding site 7 out of 12 in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:25.4
occ:0.75
 OD2 D:ASP281 2.1 12.9 0.7
OE2 D:GLU342 2.1 17.0 1.0
NZ D:LYS258 2.2 7.3 1.0
O D:HOH698 2.4 23.8 1.0
OD2 D:ASP263 2.6 13.2 0.8
O D:HOH852 2.8 28.2 1.0
CG D:ASP281 2.8 12.5 1.0
OD1 D:ASP281 3.0 15.5 1.0
CD D:GLU342 3.0 13.8 1.0
ZN D:ZN502 3.1 21.7 0.5
CE D:LYS258 3.1 11.1 1.0
OE1 D:GLU342 3.2 15.2 1.0
CG D:ASP263 3.5 16.1 1.0
O3 D:BCT503 3.7 17.0 1.0
CB D:ASP263 3.9 10.2 1.0
O D:THR367 4.2 18.4 1.0
CB D:ASP281 4.3 12.8 1.0
OD1 D:ASP263 4.4 11.1 1.0
CG D:GLU342 4.4 9.4 1.0
CD D:LYS258 4.5 12.8 1.0
CG D:LEU260 4.6 15.9 1.0
N D:GLY343 4.7 11.0 1.0
CB D:LEU260 4.8 11.6 1.0
O D:ASP340 4.9 14.3 1.0
CA D:GLY343 5.0 13.1 1.0

Zinc binding site 8 out of 12 in 4zi6

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Zinc binding site 8 out of 12 in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:21.7
occ:0.50
 O D:HOH698 2.2 23.8 1.0
OD2 D:ASP263 2.2 13.2 0.8
OD1 D:ASP340 2.3 14.1 1.0
O D:ASP340 2.4 14.3 1.0
OE1 D:GLU342 2.4 15.2 1.0
ZN D:ZN501 3.1 25.4 0.8
CG D:ASP263 3.2 16.1 1.0
CG D:ASP340 3.2 25.0 1.0
C D:ASP340 3.3 16.5 1.0
CD D:GLU342 3.3 13.8 1.0
OD1 D:ASP263 3.4 11.1 1.0
O D:HOH852 3.5 28.2 1.0
NZ D:LYS270 3.5 25.7 1.0
OE2 D:GLU342 3.6 17.0 1.0
CA D:ASP340 3.7 15.5 1.0
OD2 D:ASP340 3.9 25.4 1.0
CB D:ASP340 4.0 9.9 1.0
CE D:LYS270 4.2 25.1 1.0
O3 D:BCT503 4.2 17.0 1.0
N D:ALA341 4.5 13.9 1.0
CB D:ASP263 4.5 10.2 1.0
N D:GLU342 4.5 12.9 1.0
OD2 D:ASP281 4.7 12.9 0.7
CG D:GLU342 4.7 9.4 1.0
ND2 D:ASN313 4.8 10.5 1.0
CA D:ALA341 4.9 11.4 1.0
NZ D:LYS258 4.9 7.3 1.0
CA D:GLY265 5.0 11.6 1.0

Zinc binding site 9 out of 12 in 4zi6

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Zinc binding site 9 out of 12 in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:23.4
occ:0.70
 OD2 E:ASP281 2.0 19.5 1.0
OE2 E:GLU342 2.2 15.4 1.0
NZ E:LYS258 2.2 11.4 1.0
O E:HOH688 2.4 14.1 1.0
OD2 E:ASP263 2.6 12.8 1.0
O E:HOH853 2.8 28.8 1.0
CG E:ASP281 2.9 16.3 1.0
ZN E:ZN502 3.1 17.9 0.5
OD1 E:ASP281 3.1 16.4 1.0
CE E:LYS258 3.1 17.4 1.0
CD E:GLU342 3.2 17.7 1.0
CG E:ASP263 3.4 15.6 1.0
OE1 E:GLU342 3.4 15.9 1.0
CB E:ASP263 3.7 11.4 1.0
O3 E:BCT503 3.8 13.1 1.0
O E:HOH870 4.2 27.7 1.0
O E:THR367 4.3 12.1 1.0
CB E:ASP281 4.3 13.6 1.0
OD1 E:ASP263 4.3 13.1 1.0
CG E:LEU260 4.5 15.3 1.0
CD E:LYS258 4.5 9.4 1.0
CG E:GLU342 4.6 16.5 1.0
CB E:LEU260 4.7 15.0 1.0
N E:GLY343 4.7 12.9 1.0
CA E:GLY343 4.9 13.2 1.0
O E:ASP340 5.0 14.1 1.0

Zinc binding site 10 out of 12 in 4zi6

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Zinc binding site 10 out of 12 in the Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:17.9
occ:0.50
 OD2 E:ASP263 2.2 12.8 1.0
OD1 E:ASP340 2.3 14.1 1.0
O E:HOH688 2.3 14.1 1.0
OE1 E:GLU342 2.4 15.9 1.0
O E:ASP340 2.4 14.1 1.0
O E:HOH870 2.5 27.7 1.0
CG E:ASP263 3.1 15.6 1.0
ZN E:ZN501 3.1 23.4 0.7
CG E:ASP340 3.1 18.7 1.0
C E:ASP340 3.2 17.0 1.0
CD E:GLU342 3.3 17.7 1.0
OD1 E:ASP263 3.3 13.1 1.0
OE2 E:GLU342 3.5 15.4 1.0
CA E:ASP340 3.6 11.9 1.0
OD2 E:ASP340 3.9 24.1 1.0
O E:HOH853 3.9 28.8 1.0
CB E:ASP340 4.0 16.8 1.0
CE E:LYS270 4.0 19.5 1.0
NZ E:LYS270 4.1 31.3 1.0
O3 E:BCT503 4.1 13.1 1.0
N E:ALA341 4.4 13.9 1.0
CB E:ASP263 4.4 11.4 1.0
N E:GLU342 4.5 12.5 1.0
ND2 E:ASN313 4.6 10.1 1.0
CG E:GLU342 4.7 16.5 1.0
OD2 E:ASP281 4.7 19.5 1.0
O E:HOH753 4.8 31.7 1.0
CA E:ALA341 4.8 15.8 1.0
CA E:GLY265 4.9 12.3 1.0
NZ E:LYS258 4.9 11.4 1.0

Reference:

J.K.Modak, W.Rut, L.C.Wijeyewickrema, R.N.Pike, M.Drag, A.Roujeinikova. Structural Basis For Substrate Specificity of Helicobacter Pylori M17 Aminopeptidase. Biochimie V. 121 60 2016.
ISSN: ISSN 0300-9084
PubMed: 26616008
DOI: 10.1016/J.BIOCHI.2015.11.021
Page generated: Sun Oct 27 11:47:54 2024

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