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Magnesium 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:

Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 7 in 5d8n

Go back to Magnesium Binding Sites List in 5d8n
Magnesium binding site 1 out of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:47.6
occ:1.00
O A:HOH862 1.9 37.1 1.0
O A:HOH945 2.1 42.5 1.0
O A:HOH787 2.2 30.3 1.0
O A:HOH1085 2.3 44.1 1.0
O A:ILE74 2.4 34.3 1.0
O A:HOH705 2.5 40.7 1.0
C A:ILE74 3.5 30.4 1.0
N A:ILE74 3.6 28.6 1.0
O A:HOH733 3.8 29.9 1.0
CA A:ILE74 4.0 29.1 1.0
OE2 A:GLU249 4.1 33.0 1.0
OE1 A:GLU249 4.2 28.5 1.0
O A:HOH1013 4.3 45.2 1.0
CB A:ILE74 4.3 26.1 1.0
OE1 A:GLU242 4.5 41.9 1.0
CD A:GLU249 4.5 29.6 1.0
N A:GLY75 4.6 33.4 1.0
O A:HOH1007 4.7 46.8 1.0
C A:SER73 4.7 28.4 0.5
C A:SER73 4.7 28.7 0.5
CA A:GLY75 4.9 32.4 1.0

Magnesium binding site 2 out of 7 in 5d8n

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Magnesium binding site 2 out of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:50.3
occ:1.00
O A:ALA264 2.1 22.5 1.0
O A:HOH893 2.2 34.0 1.0
O A:HOH997 2.2 35.7 1.0
O A:HOH960 2.2 37.8 1.0
O A:VAL262 2.3 18.9 1.0
O A:HOH748 2.3 20.9 1.0
C A:ALA264 3.2 23.3 1.0
C A:VAL262 3.3 19.4 1.0
C A:ASN263 3.9 20.9 1.0
CA A:PRO265 3.9 21.4 1.0
N A:PRO265 4.0 22.2 1.0
N A:ALA264 4.0 20.3 1.0
CA A:VAL262 4.0 19.1 1.0
O A:HOH795 4.0 26.1 1.0
O A:LEU261 4.1 20.5 1.0
O A:ASN263 4.1 23.7 1.0
O A:HOH881 4.1 44.4 1.0
CA A:ALA264 4.2 20.6 1.0
O A:HOH754 4.3 40.4 1.0
N A:ASN263 4.3 20.2 1.0
C A:PRO265 4.4 20.4 1.0
O A:HOH952 4.5 40.4 1.0
CA A:ASN263 4.5 19.7 1.0
O A:HOH843 4.7 49.1 1.0
N A:ALA266 4.7 20.2 1.0
CG1 A:VAL262 4.8 19.3 1.0
O A:ASP367 4.8 36.8 1.0
C A:LEU261 4.9 20.4 1.0
N A:VAL262 4.9 20.1 1.0
O A:LYS365 5.0 51.3 1.0

Magnesium binding site 3 out of 7 in 5d8n

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Magnesium binding site 3 out of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:38.0
occ:1.00
O B:VAL262 2.1 18.1 1.0
O B:HOH762 2.1 38.2 1.0
O B:HOH980 2.2 38.7 1.0
O B:HOH1022 2.2 32.5 1.0
O B:ALA264 2.3 21.0 1.0
O B:HOH715 2.3 21.5 1.0
C B:VAL262 3.2 17.7 1.0
C B:ALA264 3.4 21.5 1.0
CA B:VAL262 3.8 18.5 1.0
C B:ASN263 4.0 18.1 1.0
O B:HOH943 4.0 18.6 1.0
O B:LEU261 4.1 16.0 1.0
N B:ALA264 4.1 18.3 1.0
CA B:PRO265 4.2 20.8 1.0
N B:PRO265 4.2 22.2 1.0
O B:ASN263 4.2 17.8 1.0
N B:ASN263 4.2 16.9 1.0
O B:HOH945 4.3 36.5 1.0
CA B:ALA264 4.4 19.9 1.0
O B:HOH720 4.4 30.4 1.0
O C:HOH1062 4.4 38.1 1.0
CG1 B:VAL262 4.5 19.0 1.0
CA B:ASN263 4.5 17.6 1.0
O B:ASP367 4.5 32.4 1.0
O B:HOH825 4.6 50.7 1.0
O B:LYS365 4.7 40.4 1.0
C B:PRO265 4.8 19.2 1.0
N B:VAL262 4.8 17.6 1.0
CB B:VAL262 4.8 18.8 1.0
C B:LEU261 4.8 16.6 1.0

Magnesium binding site 4 out of 7 in 5d8n

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Magnesium binding site 4 out of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg609

b:49.9
occ:1.00
O B:HOH830 2.0 36.2 1.0
O B:HOH989 2.3 41.0 1.0
O B:HOH1149 2.3 43.6 1.0
O B:ILE74 2.4 23.9 1.0
O B:HOH848 2.4 40.1 1.0
O B:HOH739 2.4 26.5 1.0
C B:ILE74 3.4 22.4 1.0
N B:ILE74 3.8 24.2 1.0
O B:HOH758 3.9 28.9 1.0
CA B:ILE74 4.1 23.1 1.0
O B:HOH1064 4.2 39.8 1.0
OE2 B:GLU249 4.3 23.2 1.0
OE1 B:GLU249 4.4 27.3 1.0
OE1 B:GLU242 4.4 33.9 1.0
CB B:ILE74 4.4 21.2 1.0
O B:HOH1144 4.5 42.6 1.0
N B:GLY75 4.5 23.0 1.0
CD B:GLU249 4.8 24.6 1.0
C B:SER73 4.8 24.6 0.5
C B:SER73 4.8 24.4 0.5
CA B:GLY75 4.8 23.6 1.0
O B:HOH1112 4.9 38.0 1.0
OG B:SER73 4.9 29.4 0.5

Magnesium binding site 5 out of 7 in 5d8n

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Magnesium binding site 5 out of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg610

b:47.1
occ:1.00
O B:HOH1156 2.0 53.3 1.0
O A:HOH973 2.1 41.9 1.0
O B:HOH1063 2.2 44.0 1.0
O B:HOH780 2.2 37.5 1.0
O A:HOH1001 2.5 52.1 1.0
O B:HOH778 2.7 41.2 1.0
O B:HOH1103 3.5 45.5 1.0
OE1 B:GLU129 4.1 37.2 1.0
O A:HOH1014 4.2 42.4 1.0
O B:SER138 4.3 30.5 1.0
O B:HOH951 4.3 28.0 1.0
CB B:GLU129 4.5 31.6 1.0
CB A:SER176 4.6 25.8 0.5
O A:SER176 4.7 29.3 0.5
O A:SER176 4.7 30.3 0.5
O B:HOH787 4.7 27.4 1.0
O B:HOH1123 4.8 48.0 1.0
CB A:SER176 4.8 29.5 0.5
CD B:GLU129 4.8 35.9 1.0
CG B:GLU129 4.8 34.7 1.0
O B:GLU129 4.9 27.3 1.0
OG A:SER176 5.0 30.1 0.5

Magnesium binding site 6 out of 7 in 5d8n

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Magnesium binding site 6 out of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg606

b:47.1
occ:1.00
O C:HOH952 2.1 37.5 1.0
O C:HOH955 2.2 43.1 1.0
O C:HOH748 2.2 28.1 1.0
O C:HOH1089 2.2 41.3 1.0
O C:ILE74 2.2 31.3 1.0
O C:HOH819 2.3 33.8 1.0
C C:ILE74 3.3 28.6 1.0
N C:ILE74 3.5 28.2 1.0
CA C:ILE74 3.9 27.6 1.0
OE2 C:GLU249 4.3 31.5 1.0
CB C:ILE74 4.4 29.2 1.0
N C:GLY75 4.4 28.5 1.0
O C:HOH711 4.4 27.7 1.0
OE1 C:GLU249 4.4 30.1 1.0
C C:SER73 4.5 28.3 0.5
C C:SER73 4.6 28.5 0.5
OE1 C:GLU242 4.6 35.6 1.0
OG C:SER73 4.8 29.3 0.5
CA C:GLY75 4.8 33.4 1.0
CD C:GLU249 4.8 30.3 1.0
CA C:SER73 4.8 29.2 0.5
CA C:SER73 4.9 29.4 0.5

Magnesium binding site 7 out of 7 in 5d8n

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg607

b:43.9
occ:1.00
O C:HOH857 2.0 39.3 1.0
O C:HOH731 2.0 22.0 1.0
O C:HOH1013 2.1 35.5 1.0
O C:VAL262 2.3 22.9 1.0
O C:HOH942 2.5 34.7 1.0
O C:ALA264 2.5 24.0 1.0
C C:VAL262 3.3 21.2 1.0
C C:ALA264 3.6 20.6 1.0
CA C:VAL262 3.7 20.5 1.0
O C:HOH880 3.8 48.0 1.0
O C:HOH804 3.9 46.4 1.0
O C:HOH893 3.9 29.8 1.0
O C:LEU261 4.0 22.6 1.0
O C:ASP367 4.2 32.1 1.0
C C:ASN263 4.3 20.5 1.0
N C:ALA264 4.3 19.7 1.0
CG1 C:VAL262 4.4 20.3 1.0
CA C:PRO265 4.4 21.6 1.0
N C:ASN263 4.4 19.4 1.0
N C:PRO265 4.4 22.0 1.0
O C:HOH990 4.6 38.3 1.0
CA C:ALA264 4.6 20.8 1.0
O C:ASN263 4.6 20.6 1.0
CG C:MET368 4.7 37.9 1.0
O C:LYS365 4.7 43.2 1.0
CB C:VAL262 4.7 21.6 1.0
N C:VAL262 4.7 20.7 1.0
C C:LEU261 4.8 20.9 1.0
CA C:ASN263 4.8 19.7 1.0
O C:HOH772 4.8 37.3 1.0
C C:PRO265 4.8 20.9 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: Mon Dec 14 20:10:32 2020

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