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Sodium in PDB 3fz3: Crystal Structure of Almond PRU1 Protein

Protein crystallography data

The structure of Crystal Structure of Almond PRU1 Protein, PDB code: 3fz3 was solved by T.C.Jin, Y.Z.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.08 / 2.40
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 151.021, 151.021, 165.367, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.9

Other elements in 3fz3:

The structure of Crystal Structure of Almond PRU1 Protein also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Almond PRU1 Protein (pdb code 3fz3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of Almond PRU1 Protein, PDB code: 3fz3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 3fz3

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Sodium binding site 1 out of 9 in the Crystal Structure of Almond PRU1 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na552

b:53.0
occ:1.00
 OD1 A:ASN296 3.8 47.0 1.0
NE2 B:GLN449 4.1 49.5 1.0
O A:HOH565 4.2 48.9 1.0
OD2 B:ASP460 4.5 50.1 1.0
CA A:ASN296 4.5 49.1 1.0
CB A:ASN296 4.6 49.0 1.0
CG A:ASN296 4.6 47.6 1.0
O B:HOH708 4.7 45.6 1.0

Sodium binding site 2 out of 9 in 3fz3

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Sodium binding site 2 out of 9 in the Crystal Structure of Almond PRU1 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9

b:50.2
occ:1.00
 O D:HOH1025 2.1 43.9 1.0
O A:HOH604 3.2 51.0 1.0
NH1 A:ARG505 3.4 51.6 1.0
NH1 A:ARG510 3.7 35.0 1.0
NH2 A:ARG510 3.8 39.3 1.0
CZ A:ARG510 4.2 37.1 1.0
CG A:ARG505 4.3 42.9 1.0
NH2 D:ARG510 4.4 36.1 1.0
CD A:ARG505 4.4 46.8 1.0
CZ A:ARG505 4.5 45.9 1.0
NE A:ARG505 4.9 47.8 1.0

Sodium binding site 3 out of 9 in 3fz3

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Sodium binding site 3 out of 9 in the Crystal Structure of Almond PRU1 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na552

b:40.7
occ:1.00
 ND2 B:ASN296 3.4 30.4 1.0
NE2 C:GLN449 3.8 41.6 1.0
CA B:ASN296 4.0 34.3 1.0
O B:HOH728 4.1 45.2 1.0
CB B:ASN296 4.2 34.9 1.0
CG B:ASN296 4.3 35.2 1.0
OD2 C:ASP460 4.3 52.5 1.0
N B:ASN296 4.4 34.0 1.0
O C:HOH828 4.5 43.2 1.0

Sodium binding site 4 out of 9 in 3fz3

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Sodium binding site 4 out of 9 in the Crystal Structure of Almond PRU1 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na552

b:51.1
occ:1.00
 O C:HOH641 3.2 39.2 1.0
ND2 C:ASN296 3.7 47.8 1.0
CA C:ASN296 3.9 47.5 1.0
CB C:ASN296 4.0 48.2 1.0
NE2 A:GLN449 4.2 48.9 1.0
CG C:ASN296 4.3 49.2 1.0
N C:ASN296 4.4 46.5 1.0
OD2 A:ASP460 4.7 62.5 1.0

Sodium binding site 5 out of 9 in 3fz3

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Sodium binding site 5 out of 9 in the Crystal Structure of Almond PRU1 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na552

b:58.3
occ:1.00
 NE2 E:GLN449 4.0 48.6 1.0
ND2 D:ASN296 4.0 51.5 1.0
CA D:ASN296 4.1 48.6 1.0
OD2 E:ASP460 4.2 62.6 1.0
CB D:ASN296 4.3 49.3 1.0
N D:ASN296 4.4 47.0 1.0
CG D:ASN296 4.5 51.1 1.0

Sodium binding site 6 out of 9 in 3fz3

Go back to Sodium Binding Sites List in 3fz3
Sodium binding site 6 out of 9 in the Crystal Structure of Almond PRU1 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na552

b:67.8
occ:1.00
 ND2 E:ASN296 2.9 45.1 1.0
NH2 F:ARG447 3.9 54.9 1.0
CG E:ASN296 3.9 47.5 1.0
CB E:ASN296 4.0 48.2 1.0
NE2 F:GLN449 4.1 46.9 1.0
CA E:ASN296 4.1 47.8 1.0
OD2 F:ASP460 4.6 51.9 1.0
O E:HOH578 4.8 41.2 1.0
CZ F:ARG447 4.9 52.3 1.0
N E:ASN296 4.9 48.9 1.0
O E:PHE295 5.0 50.7 1.0

Sodium binding site 7 out of 9 in 3fz3

Go back to Sodium Binding Sites List in 3fz3
Sodium binding site 7 out of 9 in the Crystal Structure of Almond PRU1 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na8

b:44.8
occ:1.00
 O C:HOH1018 2.2 48.8 1.0
NH2 E:ARG510 3.4 43.5 1.0
NH1 E:ARG505 3.7 55.3 1.0
OE1 E:GLN536 4.0 61.5 1.0
NH1 E:ARG510 4.3 39.4 1.0
CZ E:ARG510 4.3 42.2 1.0
NH2 B:ARG189 4.4 63.5 1.0
NH2 C:ARG510 4.5 34.3 1.0
CD E:ARG505 4.7 48.8 1.0
O E:HOH565 4.8 44.9 1.0
CZ E:ARG505 4.8 47.8 1.0
CD E:GLN536 5.0 58.5 1.0

Sodium binding site 8 out of 9 in 3fz3

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Sodium binding site 8 out of 9 in the Crystal Structure of Almond PRU1 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na552

b:44.0
occ:1.00
 O F:HOH626 3.2 49.6 1.0
O F:HOH1011 3.2 39.5 1.0
O F:HOH992 3.8 39.0 1.0
ND2 F:ASN296 3.8 35.0 1.0
CA F:ASN296 4.0 34.0 1.0
NE2 D:GLN449 4.3 35.4 1.0
CB F:ASN296 4.3 34.0 1.0
N F:ASN296 4.4 34.8 1.0
CG F:ASN296 4.5 34.6 1.0
OD2 D:ASP460 4.7 52.4 1.0

Sodium binding site 9 out of 9 in 3fz3

Go back to Sodium Binding Sites List in 3fz3
Sodium binding site 9 out of 9 in the Crystal Structure of Almond PRU1 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na7

b:53.6
occ:1.00
 O B:HOH1019 2.2 55.9 1.0
NH2 F:ARG510 2.8 42.9 1.0
NH1 F:ARG505 3.7 66.3 1.0
NH2 B:ARG510 4.0 46.2 1.0
CZ F:ARG510 4.1 44.2 1.0
NH2 E:ARG185 4.2 77.3 1.0
CD F:ARG505 4.4 50.8 1.0
NH1 B:ARG505 4.6 61.7 1.0
NH1 E:ARG185 4.7 77.3 1.0
CZ E:ARG185 4.7 93.4 1.0
NE2 F:GLN536 4.7 56.1 1.0
CZ F:ARG505 4.8 50.7 1.0
NH2 A:ARG189 4.8 58.3 1.0
NH1 F:ARG510 4.8 45.7 1.0
CZ B:ARG510 5.0 44.2 1.0
NH1 B:ARG510 5.0 46.7 1.0
NE F:ARG510 5.0 39.0 1.0

Reference:

T.Jin, S.M.Albillos, F.Guo, A.Howard, T.J.Fu, M.H.Kothary, Y.Z.Zhang. Crystal Structure of Prunin-1, A Major Component of the Almond (Prunus Dulcis) Allergen Amandin. J.Agric.Food Chem. V. 57 8643 2009.
ISSN: ISSN 0021-8561
PubMed: 19694440
DOI: 10.1021/JF9017355
Page generated: Mon Oct 7 09:51:57 2024

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