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Sodium in PDB 7chl: Crystal Structure of Hybrid Arabinose Isomerase Ai-10

Enzymatic activity of Crystal Structure of Hybrid Arabinose Isomerase Ai-10

All present enzymatic activity of Crystal Structure of Hybrid Arabinose Isomerase Ai-10:
5.3.1.4;

Protein crystallography data

The structure of Crystal Structure of Hybrid Arabinose Isomerase Ai-10, PDB code: 7chl was solved by T.P.Cao, I.Dhanasingh, J.Y.Sung, S.M.Shin, D.W.Lee, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.54 / 3.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 152.086, 164.297, 151.973, 90, 119.92, 90
R / Rfree (%) 20.8 / 26.4

Other elements in 7chl:

The structure of Crystal Structure of Hybrid Arabinose Isomerase Ai-10 also contains other interesting chemical elements:

Manganese (Mn) 12 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10 (pdb code 7chl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10, PDB code: 7chl:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 7chl

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Sodium binding site 1 out of 12 in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10


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 Hybrid Arabinose Isomerase Ai-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:35.9
occ:1.00
 O A:ASP268 2.9 56.0 1.0
CE1 A:PHE265 3.9 55.4 1.0
C A:ASP268 3.9 55.5 1.0
OH A:TYR208 4.0 40.3 1.0
CE2 A:TYR208 4.0 42.0 1.0
CZ A:PHE265 4.3 55.4 1.0
CD1 A:PHE265 4.3 54.5 1.0
CZ A:TYR208 4.3 41.0 1.0
CE1 A:PHE271 4.4 38.1 1.0
CB A:ASP268 4.4 57.9 1.0
O A:PHE265 4.5 48.0 1.0
CA A:GLY269 4.6 56.1 1.0
N A:GLY269 4.6 58.5 1.0
OH A:TYR216 4.7 50.7 1.0
CA A:ASP268 4.8 56.2 1.0
CZ A:PHE271 4.9 37.7 1.0
CD2 A:TYR208 5.0 41.9 1.0

Sodium binding site 2 out of 12 in 7chl

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Sodium binding site 2 out of 12 in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10


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 Hybrid Arabinose Isomerase Ai-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:28.6
occ:1.00
 OD2 B:ASP268 3.3 75.9 1.0
CE2 B:TYR208 3.8 35.9 1.0
CA B:GLY269 3.9 58.7 1.0
OH B:TYR208 4.0 35.0 1.0
CE1 B:PHE265 4.2 48.7 1.0
CZ B:PHE265 4.2 48.1 1.0
N B:GLY269 4.2 64.9 1.0
CZ B:TYR208 4.2 35.1 1.0
CE2 B:PHE271 4.4 48.3 1.0
CG B:ASP268 4.5 74.0 1.0
C B:ASP268 4.7 62.1 1.0
CD2 B:TYR208 4.8 37.7 1.0
CD1 B:PHE265 4.8 50.1 1.0
O B:PHE265 4.9 56.6 1.0
CZ B:PHE271 4.9 48.4 1.0
CE2 B:PHE265 4.9 48.4 1.0
OH B:TYR216 4.9 57.9 1.0
O B:ASP268 4.9 61.2 1.0

Sodium binding site 3 out of 12 in 7chl

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Sodium binding site 3 out of 12 in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10


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 Hybrid Arabinose Isomerase Ai-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:25.7
occ:1.00
 CE2 C:TYR208 4.0 43.4 1.0
OH C:TYR208 4.1 43.0 1.0
CA C:GLY269 4.1 50.9 1.0
N C:GLY269 4.2 53.0 1.0
CZ C:PHE265 4.3 48.9 1.0
CE2 C:PHE265 4.3 49.5 1.0
CE2 C:PHE271 4.3 45.4 1.0
CZ C:TYR208 4.4 42.8 1.0
OH C:TYR216 4.5 60.0 1.0
CB C:ASP268 4.5 57.5 1.0
O C:PHE265 4.6 49.4 1.0
C C:ASP268 4.6 52.1 1.0
CZ C:PHE271 4.7 45.7 1.0
CE1 C:PHE265 4.8 48.5 1.0
CD2 C:PHE265 4.8 49.7 1.0
O C:ASP268 4.9 51.1 1.0
OD2 C:ASP268 4.9 61.9 1.0
CD2 C:TYR208 4.9 43.1 1.0

Sodium binding site 4 out of 12 in 7chl

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Sodium binding site 4 out of 12 in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10


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 Hybrid Arabinose Isomerase Ai-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:39.5
occ:1.00
 CE1 D:PHE265 3.1 41.3 1.0
CD1 D:PHE265 3.7 42.9 1.0
CZ D:PHE265 3.9 40.5 1.0
N D:GLY269 4.1 59.6 1.0
CA D:GLY269 4.1 54.8 1.0
CE2 D:TYR208 4.2 48.3 1.0
OH D:TYR216 4.3 52.8 1.0
OH D:TYR208 4.3 48.7 1.0
C D:ASP268 4.4 57.0 1.0
CB D:ASP268 4.4 62.0 1.0
CE2 D:PHE271 4.5 39.1 1.0
O D:PHE265 4.6 49.0 1.0
CZ D:TYR208 4.6 48.4 1.0
O D:ASP268 4.6 57.2 1.0
OD2 D:ASP268 4.7 64.8 1.0
CG D:PHE265 4.8 44.4 1.0
CE2 D:PHE265 4.9 40.7 1.0
CG D:ASP268 5.0 64.0 1.0

Sodium binding site 5 out of 12 in 7chl

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Sodium binding site 5 out of 12 in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10


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 Hybrid Arabinose Isomerase Ai-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na502

b:29.5
occ:1.00
 CE2 E:PHE265 3.9 50.9 1.0
CZ E:PHE265 3.9 50.4 1.0
CA E:GLY269 4.3 53.6 1.0
OH E:TYR208 4.3 48.0 1.0
CE2 E:TYR208 4.3 48.2 1.0
N E:GLY269 4.4 54.4 1.0
OH E:TYR216 4.4 72.7 1.0
CD2 E:PHE265 4.5 51.1 1.0
CE1 E:PHE265 4.5 50.1 1.0
CE2 E:PHE271 4.6 49.8 1.0
CZ E:TYR208 4.6 47.5 1.0
O E:PHE265 4.7 51.9 1.0
CB E:ASP268 4.7 58.4 1.0
C E:ASP268 4.8 53.1 1.0

Sodium binding site 6 out of 12 in 7chl

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Sodium binding site 6 out of 12 in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10


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 Hybrid Arabinose Isomerase Ai-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na502

b:39.4
occ:1.00
 CE2 F:PHE265 3.7 53.6 1.0
OD1 F:ASP268 3.7 66.3 1.0
OH F:TYR208 3.9 50.1 1.0
CE2 F:TYR208 3.9 49.8 1.0
CZ F:TYR208 4.1 49.7 1.0
CZ F:PHE265 4.2 53.4 1.0
CD2 F:PHE265 4.3 53.8 1.0
CG F:ASP268 4.5 65.6 1.0
OH F:TYR216 4.6 62.0 1.0
OD2 F:ASP268 4.7 66.9 1.0
CA F:GLY269 4.8 55.8 1.0
CD2 F:TYR208 4.8 49.6 1.0
CE2 F:PHE271 4.9 43.0 1.0
N F:GLY269 5.0 57.6 1.0

Sodium binding site 7 out of 12 in 7chl

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Sodium binding site 7 out of 12 in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10


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 Hybrid Arabinose Isomerase Ai-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na502

b:31.6
occ:1.00
 CE1 G:PHE265 3.3 51.8 1.0
CA G:GLY269 3.8 54.9 1.0
CZ G:PHE265 3.9 51.0 1.0
N G:GLY269 3.9 58.4 1.0
OH G:TYR208 4.0 40.2 1.0
CD1 G:PHE265 4.0 52.0 1.0
CE2 G:PHE271 4.1 40.1 1.0
CE2 G:TYR208 4.1 42.2 1.0
CZ G:TYR208 4.3 41.2 1.0
C G:ASP268 4.4 56.1 1.0
O G:PHE265 4.5 47.4 1.0
CB G:ASP268 4.6 62.5 1.0
O G:ASP268 4.7 56.6 1.0
CZ G:PHE271 4.7 39.8 1.0
OH G:TYR216 4.8 63.0 1.0
CE2 G:PHE265 4.9 50.6 1.0
CG G:PHE265 4.9 51.3 1.0

Sodium binding site 8 out of 12 in 7chl

Go back to Sodium Binding Sites List in 7chl
Sodium binding site 8 out of 12 in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10


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 Hybrid Arabinose Isomerase Ai-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na502

b:26.5
occ:1.00
 OD2 H:ASP268 3.2 76.0 1.0
CE2 H:TYR208 3.8 43.8 1.0
CE1 H:PHE265 3.8 49.5 1.0
CZ H:PHE265 3.9 49.0 1.0
OH H:TYR208 4.2 43.8 1.0
CA H:GLY269 4.3 60.1 1.0
CZ H:TYR208 4.3 43.4 1.0
CG H:ASP268 4.3 73.7 1.0
CE2 H:PHE271 4.4 46.1 1.0
CD1 H:PHE265 4.5 50.3 1.0
N H:GLY269 4.5 64.4 1.0
CE2 H:PHE265 4.6 49.1 1.0
CD2 H:TYR208 4.6 44.6 1.0
O H:PHE265 4.7 56.2 1.0
CZ H:PHE271 4.8 46.2 1.0
OH H:TYR216 4.8 58.9 1.0
C H:ASP268 4.9 63.5 1.0

Sodium binding site 9 out of 12 in 7chl

Go back to Sodium Binding Sites List in 7chl
Sodium binding site 9 out of 12 in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10


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 Hybrid Arabinose Isomerase Ai-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na502

b:29.4
occ:1.00
 OD2 I:ASP268 3.2 75.5 1.0
CE2 I:TYR208 3.7 37.4 1.0
CG I:ASP268 3.7 72.8 1.0
CE2 I:PHE265 3.8 44.8 1.0
CZ I:PHE265 4.0 44.0 1.0
OD1 I:ASP268 4.0 74.8 1.0
OH I:TYR208 4.2 35.9 1.0
CZ I:TYR208 4.3 36.5 1.0
CE2 I:PHE271 4.3 45.6 1.0
CD2 I:PHE265 4.4 45.4 1.0
CD2 I:TYR208 4.5 38.1 1.0
CB I:ASP268 4.6 67.2 1.0
OH I:TYR216 4.7 63.0 1.0
CE1 I:PHE265 4.7 43.8 1.0
N I:GLY269 4.8 61.2 1.0
CZ I:PHE271 4.9 45.8 1.0
O I:PHE265 4.9 51.8 1.0
CA I:GLY269 4.9 54.1 1.0

Sodium binding site 10 out of 12 in 7chl

Go back to Sodium Binding Sites List in 7chl
Sodium binding site 10 out of 12 in the Crystal Structure of Hybrid Arabinose Isomerase Ai-10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Hybrid Arabinose Isomerase Ai-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na502

b:38.5
occ:1.00
 OD1 J:ASP268 2.8 67.9 1.0
CE1 J:PHE265 3.2 42.2 1.0
CD1 J:PHE265 3.8 43.6 1.0
CZ J:PHE265 3.8 41.6 1.0
CE2 J:TYR208 3.9 43.8 1.0
CG J:ASP268 4.0 67.1 1.0
OH J:TYR208 4.2 43.4 1.0
OH J:TYR216 4.3 52.6 1.0
CA J:GLY269 4.3 56.3 1.0
N J:GLY269 4.4 59.8 1.0
CZ J:TYR208 4.4 43.4 1.0
CE1 J:PHE271 4.5 38.5 1.0
O J:PHE265 4.6 47.2 1.0
CD2 J:TYR208 4.7 44.1 1.0
CG J:PHE265 4.8 44.5 1.0
C J:ASP268 4.8 59.5 1.0
CE2 J:PHE265 4.8 41.7 1.0
CB J:ASP268 4.9 62.8 1.0
OD2 J:ASP268 4.9 69.2 1.0

Reference:

T.P.Cao, I.Dhanasingh, J.Y.Sung, S.M.Shin, D.W.Lee, S.H.Lee. Crystal Structure of Hybrid Arabinose Isomerase Ai-10 To Be Published.
Page generated: Tue Oct 8 16:23:09 2024

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