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Chlorine in PDB 5d8n: Tomato Leucine Aminopeptidase Mutant - K354E

Enzymatic activity of Tomato Leucine Aminopeptidase Mutant - K354E

All present enzymatic activity of Tomato Leucine Aminopeptidase Mutant - K354E:
3.4.11.1; 3.4.11.5;

Protein crystallography data

The structure of Tomato Leucine Aminopeptidase Mutant - K354E, PDB code: 5d8n was solved by K.T.Duprez, M.A.Scranton, L.L.Walling, L.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.15
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 127.112, 165.193, 168.275, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 17.9

Other elements in 5d8n:

The structure of Tomato Leucine Aminopeptidase Mutant - K354E also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Tomato Leucine Aminopeptidase Mutant - K354E (pdb code 5d8n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Tomato Leucine Aminopeptidase Mutant - K354E, PDB code: 5d8n:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5d8n

Go back to Chlorine Binding Sites List in 5d8n
Chlorine binding site 1 out of 8 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:31.4
occ:1.00
 OG1 A:THR454 2.8 31.6 1.0
N A:GLY370 3.1 18.7 1.0
N A:THR454 3.2 23.3 1.0
O A:HOH774 3.4 27.3 1.0
N A:GLY369 3.5 22.6 1.0
O A:LYS342 3.5 18.1 1.0
CB A:LYS342 3.5 21.9 1.0
CG2 A:THR454 3.6 25.0 1.0
CB A:THR454 3.7 25.2 1.0
N A:MET368 3.7 29.7 1.0
CE A:LYS342 3.7 28.6 1.0
CA A:GLY370 3.8 19.1 1.0
C A:MET368 3.8 26.6 1.0
CG A:LYS342 3.8 24.0 1.0
CA A:MET368 3.8 30.5 1.0
CD A:LYS342 3.9 28.2 1.0
CA A:ALA453 3.9 22.3 1.0
CA A:THR454 4.0 24.3 1.0
C A:ALA453 4.1 23.4 1.0
C A:GLY369 4.1 21.0 1.0
C A:LYS342 4.2 18.2 1.0
CA A:GLY369 4.2 23.1 1.0
CA A:LYS342 4.3 19.5 1.0
O A:ASN366 4.4 46.3 1.0
N A:ALA371 4.6 18.0 1.0
O A:MET368 4.6 26.6 1.0
N A:LYS342 4.7 20.4 1.0
O A:LEU452 4.7 18.0 1.0
C A:ASP367 4.7 41.5 1.0
C A:GLY370 4.8 19.0 1.0
CB A:ALA453 4.8 21.7 1.0
C A:THR454 4.9 24.6 1.0
O A:THR454 4.9 28.4 1.0
N A:ALA453 4.9 18.8 1.0
NZ A:LYS342 4.9 30.6 1.0

Chlorine binding site 2 out of 8 in 5d8n

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Chlorine binding site 2 out of 8 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:54.4
occ:0.96
 O A:HOH1033 3.2 47.7 1.0
NH1 A:ARG494 3.3 19.7 1.0
O A:HOH1024 3.3 40.8 1.0
CD A:ARG494 3.6 19.2 1.0
O A:HOH1094 3.8 32.0 1.0
CH2 C:TRP493 3.9 22.9 1.0
CZ A:ARG494 4.1 21.0 1.0
NE A:ARG494 4.2 20.0 1.0
CZ2 C:TRP493 4.4 21.3 1.0
O A:HOH1026 4.6 32.2 1.0
O A:HOH777 4.6 29.0 1.0
O A:HOH874 4.8 24.8 1.0
CG A:ARG494 4.8 19.1 1.0
CZ3 C:TRP493 4.8 21.0 1.0
CB A:ARG494 4.9 17.9 1.0

Chlorine binding site 3 out of 8 in 5d8n

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Chlorine binding site 3 out of 8 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:34.7
occ:1.00
 NE A:ARG431 3.2 23.5 1.0
N A:ARG431 3.2 20.5 1.0
O A:HOH764 3.4 34.0 1.0
C A:ALA428 3.5 25.6 1.0
CA A:ALA428 3.6 28.9 1.0
N A:GLY430 3.6 23.5 1.0
O A:ALA428 3.6 24.5 1.0
CG A:ARG431 3.8 19.7 1.0
CB A:ARG431 3.8 19.7 1.0
CD1 A:LEU455 3.8 23.9 1.0
NH2 A:ARG431 3.8 26.0 1.0
CB A:ALA428 3.8 30.2 1.0
O A:LEU455 3.8 29.0 1.0
CA A:GLY430 3.9 24.0 1.0
CZ A:ARG431 4.0 24.5 1.0
CG A:LEU455 4.0 23.6 1.0
C A:GLY430 4.0 24.2 1.0
N A:GLU429 4.1 26.9 1.0
CA A:ARG431 4.1 19.1 1.0
CD A:ARG431 4.1 20.2 1.0
C A:GLU429 4.4 25.6 1.0
C A:LEU455 4.7 26.4 1.0
CA A:LEU455 4.7 23.5 1.0
NZ A:LYS342 4.8 30.6 1.0
CA A:GLU429 4.8 27.4 1.0
O A:ASP427 4.9 37.2 1.0
N A:ALA428 4.9 29.1 1.0
CD2 A:LEU455 4.9 24.8 1.0

Chlorine binding site 4 out of 8 in 5d8n

Go back to Chlorine Binding Sites List in 5d8n
Chlorine binding site 4 out of 8 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl605

b:32.9
occ:1.00
 OG1 B:THR454 2.9 29.2 1.0
N B:GLY370 3.1 15.2 1.0
N B:THR454 3.1 24.4 1.0
O B:HOH723 3.2 34.7 1.0
N B:GLY369 3.5 19.2 1.0
O B:LYS342 3.6 19.0 1.0
CB B:LYS342 3.6 20.0 1.0
CG2 B:THR454 3.6 24.5 1.0
CB B:THR454 3.7 25.2 1.0
CA B:GLY370 3.7 14.6 1.0
N B:MET368 3.7 28.5 1.0
CE B:LYS342 3.8 31.2 1.0
CG B:LYS342 3.9 24.0 1.0
C B:MET368 3.9 23.6 1.0
CA B:MET368 3.9 28.5 1.0
CA B:ALA453 3.9 20.8 1.0
CD B:LYS342 4.0 28.1 1.0
C B:ALA453 4.0 23.2 1.0
CA B:THR454 4.0 23.9 1.0
C B:GLY369 4.1 16.6 1.0
CA B:GLY369 4.1 17.9 1.0
C B:LYS342 4.2 19.2 1.0
CA B:LYS342 4.4 18.2 1.0
O B:ASN366 4.4 37.8 1.0
N B:ALA371 4.6 15.8 1.0
O B:MET368 4.6 23.4 1.0
N B:LYS342 4.7 15.8 1.0
O B:LEU452 4.7 16.9 1.0
C B:GLY370 4.7 16.1 1.0
C B:ASP367 4.7 40.1 1.0
CB B:ALA453 4.8 20.7 1.0
N B:ALA453 4.9 18.4 1.0
C B:THR454 4.9 22.5 1.0
NZ B:LYS342 5.0 39.9 1.0
O B:THR454 5.0 23.7 1.0

Chlorine binding site 5 out of 8 in 5d8n

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Chlorine binding site 5 out of 8 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl606

b:34.5
occ:1.00
 N B:ARG431 3.2 20.2 1.0
NE B:ARG431 3.3 19.9 1.0
N B:GLY430 3.5 24.9 1.0
CA B:ALA428 3.5 28.6 1.0
C B:ALA428 3.6 26.7 1.0
O B:ALA428 3.6 25.5 1.0
O B:HOH706 3.6 44.1 1.0
CD1 B:LEU455 3.8 21.2 1.0
O B:LEU455 3.8 30.4 1.0
CA B:GLY430 3.8 23.9 1.0
CB B:ARG431 3.8 16.6 1.0
CG B:ARG431 3.9 17.6 1.0
CB B:ALA428 3.9 31.5 1.0
NH2 B:ARG431 3.9 23.7 1.0
C B:GLY430 4.0 23.6 1.0
CG B:LEU455 4.0 22.0 1.0
CZ B:ARG431 4.1 21.5 1.0
N B:GLU429 4.1 26.3 1.0
CA B:ARG431 4.1 17.6 1.0
CD B:ARG431 4.2 19.3 1.0
C B:GLU429 4.4 25.5 1.0
C B:LEU455 4.7 28.0 1.0
CA B:LEU455 4.7 22.6 1.0
O B:ASP427 4.7 32.0 1.0
NZ B:LYS342 4.7 39.9 1.0
CA B:GLU429 4.8 26.6 1.0
N B:ALA428 4.9 30.0 1.0
CD2 B:LEU455 4.9 20.3 1.0

Chlorine binding site 6 out of 8 in 5d8n

Go back to Chlorine Binding Sites List in 5d8n
Chlorine binding site 6 out of 8 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl607

b:59.0
occ:1.00
 N B:ASP475 3.1 24.1 1.0
O B:PRO473 3.5 25.9 1.0
CA B:ASN474 3.8 23.4 1.0
CB B:ASP475 3.9 25.0 1.0
C B:ASN474 3.9 24.3 1.0
CG B:ASP475 4.0 29.7 1.0
CA B:ASP475 4.1 24.3 1.0
OD2 B:ASP475 4.1 33.4 1.0
C B:PRO473 4.4 24.2 1.0
OD1 B:ASP475 4.5 28.2 1.0
N B:ASN474 4.6 26.1 1.0
CB B:ASN474 4.9 25.8 1.0
N B:ASP476 4.9 23.5 0.5
N B:ASP476 4.9 24.4 0.5
OD1 B:ASP476 4.9 27.1 0.5

Chlorine binding site 7 out of 8 in 5d8n

Go back to Chlorine Binding Sites List in 5d8n
Chlorine binding site 7 out of 8 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl604

b:32.5
occ:1.00
 OG1 C:THR454 2.8 32.2 1.0
N C:GLY370 3.1 18.2 1.0
O C:HOH801 3.2 33.6 1.0
N C:THR454 3.2 24.8 1.0
N C:GLY369 3.5 20.5 1.0
O C:LYS342 3.5 19.8 1.0
CB C:LYS342 3.6 21.9 1.0
CG2 C:THR454 3.6 26.5 1.0
CB C:THR454 3.6 26.4 1.0
CD C:LYS342 3.7 24.8 1.0
N C:MET368 3.7 26.1 1.0
CA C:MET368 3.8 28.5 1.0
CA C:GLY370 3.8 20.4 1.0
C C:MET368 3.8 24.0 1.0
CG C:LYS342 3.8 22.4 1.0
CA C:ALA453 4.0 22.6 1.0
CA C:THR454 4.0 25.7 1.0
C C:ALA453 4.0 23.2 1.0
CE C:LYS342 4.1 30.6 1.0
C C:GLY369 4.1 18.8 1.0
CA C:GLY369 4.1 19.9 1.0
C C:LYS342 4.2 20.2 1.0
CA C:LYS342 4.4 19.8 1.0
O C:ASN366 4.4 37.1 1.0
O C:MET368 4.6 22.5 1.0
N C:ALA371 4.6 19.9 1.0
C C:ASP367 4.7 34.7 1.0
N C:LYS342 4.7 17.2 1.0
O C:LEU452 4.8 18.3 1.0
C C:GLY370 4.8 21.6 1.0
CB C:ALA453 4.8 23.7 1.0
C C:THR454 4.9 26.3 1.0
N C:ALA453 4.9 20.7 1.0
O C:THR454 4.9 27.0 1.0

Chlorine binding site 8 out of 8 in 5d8n

Go back to Chlorine Binding Sites List in 5d8n
Chlorine binding site 8 out of 8 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl605

b:38.8
occ:1.00
 NE C:ARG431 3.1 19.9 1.0
N C:ARG431 3.2 20.2 1.0
O C:HOH733 3.5 43.5 1.0
C C:ALA428 3.6 25.6 1.0
CA C:ALA428 3.6 27.3 1.0
N C:GLY430 3.6 24.1 1.0
O C:ALA428 3.6 25.0 1.0
CB C:ARG431 3.7 18.1 1.0
CG C:ARG431 3.7 18.6 1.0
NH2 C:ARG431 3.8 25.7 1.0
O C:LEU455 3.8 31.6 1.0
CD1 C:LEU455 3.8 22.8 1.0
CB C:ALA428 3.8 28.4 1.0
CA C:GLY430 3.9 23.9 1.0
CZ C:ARG431 3.9 23.1 1.0
CG C:LEU455 3.9 22.6 1.0
CD C:ARG431 4.0 18.9 1.0
C C:GLY430 4.0 24.1 1.0
CA C:ARG431 4.0 19.4 1.0
N C:GLU429 4.1 28.4 1.0
C C:GLU429 4.5 27.8 1.0
NZ C:LYS342 4.7 45.0 1.0
C C:LEU455 4.7 27.6 1.0
CA C:LEU455 4.7 24.3 1.0
CD2 C:LEU455 4.9 22.6 1.0
CA C:GLU429 4.9 29.5 1.0
O C:ASP427 4.9 32.9 1.0
N C:ALA428 4.9 27.8 1.0
CB C:LEU455 5.0 23.4 1.0

Reference:

K.T.Duprez, M.A.Scranton, L.L.Walling, L.Fan. Structural Insights Into Chaperone-Activity Enhancement By A K354E Mutation in Tomato Acidic Leucine Aminopeptidase. Acta Crystallogr D Struct V. 72 694 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27139632
DOI: 10.1107/S205979831600509X
Page generated: Fri Jul 26 06:35:06 2024

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