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Zinc in PDB 3h8f: High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida

Enzymatic activity of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida

All present enzymatic activity of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida:
3.4.11.1;

Protein crystallography data

The structure of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida, PDB code: 3h8f was solved by A.Kale, B.W.Dijkstra, T.Sonke, A.M.W.H.Thunnissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.45 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 95.786, 95.931, 96.308, 68.43, 76.31, 94.86
R / Rfree (%) 19.2 / 25.1

Other elements in 3h8f:

The structure of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida also contains other interesting chemical elements:

Potassium (K) 6 atoms
Manganese (Mn) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida (pdb code 3h8f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida, PDB code: 3h8f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3h8f

Go back to Zinc Binding Sites List in 3h8f
Zinc binding site 1 out of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:20.0
occ:1.00
 OD2 A:ASP290 2.0 10.8 1.0
OE1 A:GLU351 2.0 6.0 1.0
NZ A:LYS267 2.2 10.1 1.0
O A:HOH3681 2.3 14.2 1.0
OD2 A:ASP272 2.7 8.8 1.0
CG A:ASP290 2.9 7.9 1.0
CD A:GLU351 3.0 7.1 1.0
O A:HOH2219 3.1 26.4 1.0
CE A:LYS267 3.2 5.2 1.0
OD1 A:ASP290 3.2 11.8 1.0
MN A:MN502 3.3 38.0 1.0
OE2 A:GLU351 3.4 9.6 1.0
CG A:ASP272 3.5 6.0 1.0
O1 A:BCT504 3.7 10.1 1.0
CB A:ASP272 4.1 5.3 1.0
O A:THR376 4.3 11.3 1.0
CB A:ASP290 4.3 6.8 1.0
OD1 A:ASP272 4.4 5.4 1.0
CG A:GLU351 4.4 6.2 1.0
N A:GLY352 4.5 6.0 1.0
CD A:LYS267 4.5 4.7 1.0
CG1 A:ILE269 4.6 3.4 1.0
CB A:ILE269 4.6 3.2 1.0
CG2 A:ILE269 4.8 4.0 1.0
O A:ASP349 4.8 5.8 1.0
CA A:GLY352 4.9 5.2 1.0
C A:BCT504 4.9 12.0 1.0

Zinc binding site 2 out of 6 in 3h8f

Go back to Zinc Binding Sites List in 3h8f
Zinc binding site 2 out of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:21.2
occ:1.00
 O B:HOH3682 2.0 10.4 1.0
OE1 B:GLU351 2.0 3.4 1.0
OD2 B:ASP290 2.1 12.8 1.0
NZ B:LYS267 2.3 7.5 1.0
OD2 B:ASP272 2.8 7.1 1.0
CG B:ASP290 3.0 8.1 1.0
CD B:GLU351 3.0 5.1 1.0
CE B:LYS267 3.1 4.7 1.0
MN B:MN502 3.2 34.8 1.0
OD1 B:ASP290 3.3 7.7 1.0
OE2 B:GLU351 3.3 7.0 1.0
CG B:ASP272 3.6 5.7 1.0
O1 B:BCT504 3.7 12.7 1.0
CB B:ASP272 4.2 4.3 1.0
O B:THR376 4.3 13.5 1.0
CG B:GLU351 4.4 5.7 1.0
CB B:ASP290 4.4 7.3 1.0
OD1 B:ASP272 4.4 2.9 1.0
N B:GLY352 4.5 7.3 1.0
CD B:LYS267 4.6 6.3 1.0
CB B:ILE269 4.6 3.0 1.0
CG1 B:ILE269 4.6 2.7 1.0
CG2 B:ILE269 4.7 2.0 1.0
CA B:GLY352 4.8 7.9 1.0
C B:BCT504 4.9 13.0 1.0
O B:ASP349 4.9 5.8 1.0

Zinc binding site 3 out of 6 in 3h8f

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Zinc binding site 3 out of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:17.3
occ:1.00
 OD2 C:ASP290 2.0 8.4 1.0
OE1 C:GLU351 2.1 7.0 1.0
NZ C:LYS267 2.2 6.0 1.0
O C:HOH3683 2.5 14.6 1.0
CG C:ASP290 2.9 4.1 1.0
OD2 C:ASP272 2.9 3.4 1.0
OD1 C:ASP290 3.0 4.9 1.0
MN C:MN502 3.0 34.4 1.0
CD C:GLU351 3.1 6.6 1.0
CE C:LYS267 3.2 2.9 1.0
OE2 C:GLU351 3.4 7.1 1.0
CG C:ASP272 3.5 4.1 1.0
O3 C:BCT504 3.5 9.5 1.0
CB C:ASP272 4.0 2.0 1.0
CB C:ASP290 4.2 2.3 1.0
OD1 C:ASP272 4.3 5.5 1.0
O C:THR376 4.3 11.9 1.0
CG C:GLU351 4.4 4.5 1.0
CD C:LYS267 4.5 6.0 1.0
N C:GLY352 4.6 3.7 1.0
CG2 C:ILE269 4.6 2.0 1.0
CB C:ILE269 4.7 2.9 1.0
CG1 C:ILE269 4.7 2.0 1.0
O C:ASP349 4.8 2.8 1.0
C C:BCT504 4.8 9.1 1.0
CA C:GLY352 4.9 2.7 1.0

Zinc binding site 4 out of 6 in 3h8f

Go back to Zinc Binding Sites List in 3h8f
Zinc binding site 4 out of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:21.2
occ:1.00
 OD2 D:ASP290 2.0 11.8 1.0
NZ D:LYS267 2.1 4.5 1.0
O D:HOH3684 2.1 2.0 1.0
OE1 D:GLU351 2.2 9.3 1.0
OD2 D:ASP272 2.8 7.2 1.0
CG D:ASP290 2.9 9.4 1.0
CE D:LYS267 3.1 3.3 1.0
MN D:MN502 3.1 35.4 1.0
OD1 D:ASP290 3.2 9.8 1.0
CD D:GLU351 3.2 8.4 1.0
OE2 D:GLU351 3.5 8.1 1.0
O2 D:BCT504 3.5 13.0 1.0
CG D:ASP272 3.6 9.2 1.0
CB D:ASP272 4.1 6.7 1.0
CB D:ASP290 4.3 9.2 1.0
O D:THR376 4.3 14.9 1.0
CG2 D:ILE269 4.4 6.6 1.0
CD D:LYS267 4.4 2.0 1.0
CG1 D:ILE269 4.5 7.4 1.0
CB D:ILE269 4.5 9.0 1.0
N D:GLY352 4.5 5.8 1.0
CG D:GLU351 4.5 6.2 1.0
OD1 D:ASP272 4.6 11.4 1.0
CA D:GLY352 4.7 5.6 1.0
C D:BCT504 4.8 12.9 1.0
O D:ASP349 4.9 6.0 1.0

Zinc binding site 5 out of 6 in 3h8f

Go back to Zinc Binding Sites List in 3h8f
Zinc binding site 5 out of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:18.3
occ:1.00
 OD2 E:ASP290 2.0 5.1 1.0
O E:HOH3685 2.1 2.7 1.0
NZ E:LYS267 2.2 2.0 1.0
OE1 E:GLU351 2.2 8.5 1.0
OD2 E:ASP272 2.6 4.5 1.0
CG E:ASP290 2.9 6.3 1.0
CE E:LYS267 3.0 2.0 1.0
OD1 E:ASP290 3.0 6.6 1.0
CD E:GLU351 3.1 8.1 1.0
MN E:MN502 3.2 33.9 1.0
OE2 E:GLU351 3.4 8.1 1.0
CG E:ASP272 3.5 3.8 1.0
O3 E:BCT504 3.7 7.9 1.0
CB E:ASP272 4.1 3.4 1.0
CB E:ASP290 4.3 6.9 1.0
OD1 E:ASP272 4.3 3.7 1.0
O E:THR376 4.3 12.2 1.0
CD E:LYS267 4.5 2.0 1.0
CG E:GLU351 4.5 4.8 1.0
N E:GLY352 4.6 3.1 1.0
CG2 E:ILE269 4.7 2.0 1.0
CB E:ILE269 4.7 3.0 1.0
CG1 E:ILE269 4.8 2.0 1.0
C E:BCT504 4.9 7.7 1.0
CA E:GLY352 4.9 3.2 1.0
O E:ASP349 4.9 4.9 1.0

Zinc binding site 6 out of 6 in 3h8f

Go back to Zinc Binding Sites List in 3h8f
Zinc binding site 6 out of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:20.6
occ:1.00
 OD2 F:ASP290 2.0 7.1 1.0
OE1 F:GLU351 2.1 5.1 1.0
O F:HOH3686 2.2 13.8 1.0
NZ F:LYS267 2.3 16.1 1.0
OD2 F:ASP272 2.5 12.3 1.0
CG F:ASP290 3.0 7.4 1.0
CE F:LYS267 3.0 14.3 1.0
CD F:GLU351 3.1 8.1 1.0
OD1 F:ASP290 3.2 6.4 1.0
MN F:MN502 3.3 37.8 1.0
OE2 F:GLU351 3.3 8.0 1.0
CG F:ASP272 3.4 5.4 1.0
O3 F:BCT504 3.7 12.8 1.0
CB F:ASP272 4.0 3.2 1.0
OD1 F:ASP272 4.3 5.1 1.0
CB F:ASP290 4.3 7.4 1.0
O F:THR376 4.4 13.0 1.0
CG F:GLU351 4.5 6.4 1.0
CD F:LYS267 4.5 13.2 1.0
N F:GLY352 4.5 7.9 1.0
CG1 F:ILE269 4.7 7.1 1.0
CB F:ILE269 4.7 8.0 1.0
CG2 F:ILE269 4.8 7.0 1.0
CA F:GLY352 4.8 8.7 1.0
O F:ASP349 4.9 3.9 1.0
C F:BCT504 4.9 11.8 1.0

Reference:

A.Kale, T.Pijning, T.Sonke, B.W.Dijkstra, A.M.Thunnissen. Crystal Structure of the Leucine Aminopeptidase From Pseudomonas Putida Reveals the Molecular Basis For Its Enantioselectivity and Broad Substrate Specificity. J.Mol.Biol. V. 398 703 2010.
ISSN: ISSN 0022-2836
PubMed: 20359484
DOI: 10.1016/J.JMB.2010.03.042
Page generated: Thu Oct 24 14:17:58 2024

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