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Sodium in PDB 2hb6: Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1)

Enzymatic activity of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1)

All present enzymatic activity of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1):
3.4.11.1;

Protein crystallography data

The structure of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1), PDB code: 2hb6 was solved by Y.Patskovsky, C.Zhan, B.C.Wengerter, U.Ramagopal, S.Milstein, M.Vidal, S.C.Almo, S.K.Burley, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 131.820, 131.820, 125.573, 90.00, 90.00, 120.00
R / Rfree (%) 14.7 / 18.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1) (pdb code 2hb6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1), PDB code: 2hb6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 2hb6

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Sodium binding site 1 out of 6 in the Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3001

b:28.1
occ:1.00
 OD2 A:ASP275 1.9 32.5 1.0
OE1 A:GLU336 2.3 23.4 0.5
NZ A:LYS252 2.3 18.1 1.0
NA A:NA3002 2.8 31.5 1.0
OD2 A:ASP257 2.8 40.1 1.0
CG A:ASP275 2.9 30.0 1.0
CE A:LYS252 3.1 16.3 1.0
O4 A:SO4492 3.3 23.6 1.0
OD1 A:ASP275 3.3 25.4 1.0
CD A:GLU336 3.4 42.4 0.5
CG A:ASP257 3.6 28.9 1.0
OE2 A:GLU336 3.7 34.5 0.5
CB A:ASP257 3.9 24.8 1.0
O1 A:SO4492 4.0 28.2 1.0
CB A:ASP275 4.2 18.5 1.0
S A:SO4492 4.3 26.8 1.0
CG1 A:VAL254 4.3 17.4 1.0
CG2 A:VAL254 4.4 14.9 1.0
CB A:VAL254 4.4 17.1 1.0
N A:GLY337 4.5 23.0 1.0
CD A:LYS252 4.5 17.9 1.0
OD1 A:ASP257 4.5 27.7 1.0
O A:THR362 4.5 22.9 1.0
CA A:GLY337 4.6 23.7 1.0
O A:HOH3379 4.6 50.0 1.0
CG A:GLU336 4.7 26.8 0.5

Sodium binding site 2 out of 6 in 2hb6

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Sodium binding site 2 out of 6 in the Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3002

b:31.5
occ:1.00
 OD2 A:ASP257 2.3 40.1 1.0
O A:ASP334 2.7 27.7 1.0
O4 A:SO4492 2.7 23.6 1.0
OE2 A:GLU336 2.7 34.5 0.5
NA A:NA3001 2.8 28.1 1.0
OD1 A:ASP334 2.9 39.3 1.0
O A:HOH3379 2.9 50.0 1.0
OE1 A:GLU336 3.3 23.4 0.5
CD A:GLU336 3.4 42.4 0.5
CG A:ASP257 3.5 28.9 1.0
C A:ASP334 3.5 27.6 1.0
CG A:ASP334 3.9 35.3 1.0
S A:SO4492 4.0 26.8 1.0
NZ A:LYS264 4.1 32.7 1.0
OD1 A:ASP257 4.1 27.7 1.0
CA A:ASP334 4.1 28.2 1.0
OD2 A:ASP275 4.2 32.5 1.0
O3 A:SO4492 4.2 24.7 1.0
NZ A:LYS252 4.4 18.1 1.0
N A:ALA335 4.4 20.9 1.0
N A:GLU336 4.5 25.9 1.0
CE A:LYS264 4.5 38.6 1.0
CB A:ASP257 4.5 24.8 1.0
CB A:ASP334 4.6 29.6 1.0
O1 A:SO4492 4.6 28.2 1.0
OD2 A:ASP334 4.6 41.4 1.0
CA A:ALA335 4.7 21.5 1.0
O A:LEU363 4.8 37.4 1.0
CG A:GLU336 4.9 26.8 0.5
N A:GLY337 5.0 23.0 1.0

Sodium binding site 3 out of 6 in 2hb6

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Sodium binding site 3 out of 6 in the Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3005

b:58.2
occ:1.00
 O3 A:SO4494 2.3 71.6 1.0
S A:SO4494 3.4 66.5 1.0
O4 A:SO4494 3.5 68.6 1.0
CA A:GLY140 3.9 33.2 1.0
N A:GLY140 3.9 35.6 1.0
O1 A:SO4494 3.9 73.1 1.0
NH2 A:ARG142 4.2 48.0 1.0
CB A:SER139 4.5 27.5 1.0
O2 A:SO4494 4.6 71.1 1.0
OG A:SER139 4.7 31.0 1.0
C A:SER139 4.7 34.9 1.0
O A:HOH3477 5.0 49.6 1.0

Sodium binding site 4 out of 6 in 2hb6

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Sodium binding site 4 out of 6 in the Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3003

b:28.8
occ:1.00
 OD2 B:ASP275 1.9 32.6 1.0
OE1 B:GLU336 2.3 23.4 0.5
NZ B:LYS252 2.3 18.1 1.0
OD2 B:ASP257 2.7 40.2 1.0
NA B:NA3004 2.7 31.6 1.0
CG B:ASP275 2.9 30.1 1.0
CE B:LYS252 3.1 16.5 1.0
O4 B:SO4492 3.3 25.0 1.0
OD1 B:ASP275 3.3 25.3 1.0
CD B:GLU336 3.3 42.3 0.5
CG B:ASP257 3.6 29.0 1.0
OE2 B:GLU336 3.7 34.5 0.5
CB B:ASP257 3.9 24.7 1.0
O3 B:SO4492 4.0 28.9 1.0
CB B:ASP275 4.2 18.6 1.0
S B:SO4492 4.3 27.0 1.0
CG1 B:VAL254 4.4 17.1 1.0
CG2 B:VAL254 4.4 14.8 1.0
CB B:VAL254 4.5 17.1 1.0
N B:GLY337 4.5 23.2 1.0
O B:HOH3300 4.5 48.4 1.0
OD1 B:ASP257 4.5 27.6 1.0
O B:THR362 4.5 22.4 1.0
CD B:LYS252 4.6 17.9 1.0
CA B:GLY337 4.6 23.6 1.0
CG B:GLU336 4.7 26.8 0.5

Sodium binding site 5 out of 6 in 2hb6

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Sodium binding site 5 out of 6 in the Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3004

b:31.6
occ:1.00
 OD2 B:ASP257 2.3 40.2 1.0
O B:ASP334 2.7 27.7 1.0
O4 B:SO4492 2.7 25.0 1.0
NA B:NA3003 2.7 28.8 1.0
OE2 B:GLU336 2.8 34.5 0.5
O B:HOH3300 2.8 48.4 1.0
OD1 B:ASP334 2.9 39.3 1.0
OE1 B:GLU336 3.3 23.4 0.5
CD B:GLU336 3.4 42.3 0.5
CG B:ASP257 3.5 29.0 1.0
C B:ASP334 3.5 27.4 1.0
CG B:ASP334 3.8 35.4 1.0
S B:SO4492 4.0 27.0 1.0
NZ B:LYS264 4.1 32.7 1.0
CA B:ASP334 4.1 28.2 1.0
OD1 B:ASP257 4.1 27.6 1.0
OD2 B:ASP275 4.2 32.6 1.0
O2 B:SO4492 4.2 22.4 1.0
NZ B:LYS252 4.4 18.1 1.0
N B:ALA335 4.4 21.0 1.0
N B:GLU336 4.5 25.8 1.0
CE B:LYS264 4.5 38.5 1.0
CB B:ASP334 4.6 29.7 1.0
CB B:ASP257 4.6 24.7 1.0
OD2 B:ASP334 4.6 41.3 1.0
O3 B:SO4492 4.6 28.9 1.0
CA B:ALA335 4.7 21.6 1.0
O B:LEU363 4.8 35.3 1.0
CG B:GLU336 4.9 26.8 0.5
N B:GLY337 5.0 23.2 1.0

Sodium binding site 6 out of 6 in 2hb6

Go back to Sodium Binding Sites List in 2hb6
Sodium binding site 6 out of 6 in the Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3006

b:67.4
occ:1.00
 O1 B:SO4493 2.3 73.8 1.0
S B:SO4493 3.2 67.5 1.0
O4 B:SO4493 3.3 64.5 1.0
O2 B:SO4493 3.7 71.5 1.0
N B:GLY140 3.9 35.7 1.0
CA B:GLY140 3.9 33.2 1.0
NH2 B:ARG142 4.0 48.0 1.0
O3 B:SO4493 4.5 62.8 1.0
CB B:SER139 4.6 27.6 1.0
C B:SER139 4.8 35.0 1.0
OG B:SER139 4.8 30.9 1.0
CZ B:ARG142 4.9 46.9 1.0

Reference:

C.Zhan, Y.Patskovsky, B.C.Wengerter, U.Ramagopal, S.Milstein, M.Vidal, S.C.Almo. Crystal Structure of Caenorhabditis Elegans Leucine Aminopeptidase To Be Published.
Page generated: Mon Oct 7 02:45:19 2024

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