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Sodium in PDB 5yt7: Crystal Structure of Circularly Permutated Azurin 3

Protein crystallography data

The structure of Crystal Structure of Circularly Permutated Azurin 3, PDB code: 5yt7 was solved by H.H.Chen, H.P.Liu, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.02 / 1.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.888, 87.968, 66.096, 90.00, 110.22, 90.00
R / Rfree (%) 16.2 / 21.7

Other elements in 5yt7:

The structure of Crystal Structure of Circularly Permutated Azurin 3 also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
Chlorine (Cl) 2 atoms
Copper (Cu) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Circularly Permutated Azurin 3 (pdb code 5yt7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Circularly Permutated Azurin 3, PDB code: 5yt7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5yt7

Go back to Sodium Binding Sites List in 5yt7
Sodium binding site 1 out of 3 in the Crystal Structure of Circularly Permutated Azurin 3


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 Circularly Permutated Azurin 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:22.7
occ:1.00
O A:HOH390 2.3 31.8 1.0
O A:HOH382 2.3 35.0 1.0
O B:HOH424 2.3 37.7 1.0
O A:SER23 2.5 21.6 1.0
O B:HOH384 2.6 32.3 1.0
CG A:GLU21 3.3 42.4 1.0
C A:SER23 3.6 22.5 1.0
CD A:GLU21 4.1 45.3 1.0
O A:HOH393 4.2 29.6 1.0
OG A:SER23 4.2 28.2 1.0
N A:SER23 4.4 22.4 1.0
CA A:VAL24 4.4 22.1 1.0
N A:VAL24 4.4 21.2 1.0
CB A:GLU21 4.5 33.6 1.0
O A:GLU21 4.5 25.8 1.0
CA A:SER23 4.5 21.8 1.0
O B:ASN35 4.5 22.4 1.0
OE2 A:GLU21 4.6 34.2 1.0
OE1 A:GLU21 4.7 69.1 1.0
O B:HOH413 4.8 27.9 1.0
C A:GLU21 4.8 26.7 1.0
CB A:SER23 5.0 23.6 1.0

Sodium binding site 2 out of 3 in 5yt7

Go back to Sodium Binding Sites List in 5yt7
Sodium binding site 2 out of 3 in the Crystal Structure of Circularly Permutated Azurin 3


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 Circularly Permutated Azurin 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:37.2
occ:1.00
O A:HOH366 2.1 45.6 1.0
OD1 A:ASP42 2.3 28.1 1.0
O A:HOH391 2.3 45.7 1.0
O A:ILE16 2.4 23.3 1.0
CG A:ASP42 2.9 29.0 1.0
OD2 A:ASP42 2.9 34.3 1.0
N A:GLY19 2.9 27.8 1.0
CA A:GLY19 3.0 27.2 1.0
C A:ILE16 3.5 25.2 1.0
N A:ILE16 3.7 25.1 1.0
C A:GLY19 4.0 30.6 1.0
CA A:ILE16 4.1 22.2 1.0
OG A:SER44 4.1 44.2 1.0
C A:GLY18 4.1 28.5 1.0
C A:GLY15 4.3 27.1 1.0
CB A:ASP42 4.3 24.3 1.0
N A:GLY18 4.4 26.4 1.0
CB A:ILE16 4.4 24.2 1.0
CA A:GLY15 4.5 26.9 1.0
O A:GLY19 4.6 31.5 1.0
CB A:SER44 4.6 39.9 1.0
N A:ALA20 4.6 30.7 1.0
N A:PRO17 4.7 25.3 1.0
C A:PRO17 4.7 25.4 1.0
O A:HOH309 4.7 35.6 1.0
CA A:GLY18 4.8 28.0 1.0
CA A:PRO17 4.9 27.6 1.0
N A:SER44 4.9 31.7 1.0

Sodium binding site 3 out of 3 in 5yt7

Go back to Sodium Binding Sites List in 5yt7
Sodium binding site 3 out of 3 in the Crystal Structure of Circularly Permutated Azurin 3


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 Circularly Permutated Azurin 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na203

b:45.1
occ:1.00
OG C:SER44 2.4 40.5 1.0
OD2 C:ASP42 2.7 48.1 1.0
OD1 C:ASP42 3.0 44.6 1.0
C C:ILE16 3.1 58.5 1.0
CG C:ASP42 3.2 34.4 1.0
O C:ILE16 3.2 65.2 1.0
CB C:SER44 3.5 35.2 1.0
CA C:ILE16 4.4 57.3 1.0
N C:SER44 4.4 29.6 1.0
N C:ILE16 4.5 51.6 1.0
CA C:SER44 4.6 32.9 1.0
CB C:ASP42 4.7 30.8 1.0
N C:ALA20 4.9 40.5 1.0

Reference:

H.H.Chen, B.Su, T.T.Zhang, A.Huang, H.P.Liu, Y.Yu, J.Wang. Engineering the Metal-Binding Loop of A Blue Copper Protein By Circular Permutation Rsc Adv 56093 2017.
ISSN: ESSN 2046-2069
DOI: 10.1039/C7RA11512A
Page generated: Tue Dec 15 11:51:15 2020

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