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Sodium in PDB 7bop: Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form

Protein crystallography data

The structure of Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form, PDB code: 7bop was solved by D.Hira, T.Onoue, T.Oka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.82 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 154.504, 273.006, 186.279, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.1

Other elements in 7bop:

The structure of Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form (pdb code 7bop). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form, PDB code: 7bop:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 7bop

Go back to Sodium Binding Sites List in 7bop
Sodium binding site 1 out of 7 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:36.9
occ:1.00
 O A:ASN66 2.2 33.9 1.0
O A:ALA63 2.2 39.5 1.0
O A:HOH797 2.3 42.8 1.0
O A:HOH733 2.4 33.9 1.0
C A:ASN66 3.5 33.2 1.0
C A:ALA63 3.5 39.4 1.0
O A:HOH782 4.0 44.4 1.0
N A:ASN66 4.0 34.3 1.0
O A:HOH510 4.2 36.7 1.0
N A:TYR68 4.2 33.2 1.0
C A:ASP64 4.2 43.9 1.0
CA A:ASP64 4.3 44.5 1.0
O A:HOH831 4.3 53.4 1.0
N A:ASP64 4.3 38.7 1.0
CA A:ASN66 4.4 33.9 1.0
N A:ASP67 4.4 31.9 1.0
O A:ASP64 4.4 45.0 1.0
CA A:ALA63 4.5 37.9 1.0
CA A:ASP67 4.5 32.6 1.0
N A:ASP65 4.6 40.4 1.0
C A:ASP67 4.9 32.2 1.0
CB A:ALA63 5.0 38.5 1.0

Sodium binding site 2 out of 7 in 7bop

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Sodium binding site 2 out of 7 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:31.1
occ:1.00
 O A:THR166 2.2 31.1 1.0
O A:LYS169 2.3 29.6 1.0
O A:TYR172 2.3 32.3 1.0
O A:HOH760 2.4 29.9 1.0
C A:TYR172 3.4 33.0 1.0
C A:THR166 3.4 32.8 1.0
C A:LYS169 3.4 29.5 1.0
N A:TYR172 3.7 32.7 1.0
N A:LYS169 3.9 29.4 1.0
CA A:TYR172 3.9 32.9 1.0
CA A:THR166 4.1 31.5 1.0
CA A:LYS169 4.1 30.1 1.0
CB A:TYR172 4.2 32.7 1.0
O A:LEU165 4.3 30.4 1.0
C A:GLU167 4.4 33.2 1.0
N A:GLU167 4.4 34.0 1.0
O A:GLU167 4.4 31.5 1.0
N A:ILE170 4.5 30.0 1.0
N A:GLN171 4.5 30.1 1.0
O A:HOH813 4.5 45.1 1.0
CB A:LYS169 4.5 30.1 1.0
N A:SER173 4.6 32.6 1.0
C A:GLN168 4.6 30.3 1.0
CG2 A:THR166 4.7 32.1 1.0
C A:ILE170 4.7 31.3 1.0
CA A:GLU167 4.7 34.9 0.5
CA A:GLU167 4.7 34.7 0.5
N A:GLN168 4.8 31.7 1.0
CA A:ILE170 4.8 31.2 1.0
CD1 A:TYR172 4.8 34.7 1.0
C A:GLN171 4.9 32.8 1.0

Sodium binding site 3 out of 7 in 7bop

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Sodium binding site 3 out of 7 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:32.5
occ:1.00
 O B:LYS169 2.2 31.0 1.0
O B:THR166 2.2 30.9 1.0
O B:TYR172 2.3 32.5 1.0
O B:HOH763 2.4 30.6 1.0
O A:HOH635 2.5 31.8 1.0
C B:THR166 3.4 32.7 1.0
C B:TYR172 3.4 34.6 1.0
C B:LYS169 3.4 31.8 1.0
N B:TYR172 3.7 33.6 1.0
N B:LYS169 3.9 30.2 1.0
CA B:TYR172 3.9 33.5 1.0
CA B:THR166 4.0 31.8 1.0
CA B:LYS169 4.1 30.9 1.0
CB B:TYR172 4.2 33.6 1.0
O B:LEU165 4.3 30.6 1.0
CB A:PRO364 4.3 35.1 1.0
O B:HOH616 4.3 32.1 1.0
N A:PRO364 4.3 33.5 1.0
CD A:PRO364 4.4 33.2 1.0
N B:GLU167 4.4 32.5 1.0
C B:GLU167 4.4 32.3 1.0
O B:GLU167 4.4 32.4 1.0
OD1 A:ASN362 4.4 30.1 1.0
N B:ILE170 4.5 30.8 1.0
CA A:PRO364 4.5 33.9 1.0
N B:GLN171 4.5 32.0 1.0
O B:HOH808 4.5 49.1 1.0
N B:SER173 4.5 35.2 1.0
CB B:LYS169 4.6 29.9 1.0
C B:GLN168 4.6 30.1 1.0
CG A:PRO364 4.7 34.5 1.0
C B:ILE170 4.7 32.0 1.0
CG2 B:THR166 4.7 32.8 1.0
CA B:GLU167 4.7 36.1 1.0
N B:GLN168 4.7 30.1 1.0
CA B:ILE170 4.8 31.6 1.0
C B:GLN171 4.9 33.9 1.0
C A:SER363 4.9 32.7 1.0
CD2 B:TYR172 4.9 36.9 1.0

Sodium binding site 4 out of 7 in 7bop

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Sodium binding site 4 out of 7 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:41.4
occ:1.00
 O B:HOH796 2.2 43.9 1.0
O B:ASN66 2.2 36.1 1.0
O B:ALA63 2.3 37.5 1.0
O B:HOH748 2.3 36.3 1.0
O B:HOH811 2.5 56.8 1.0
C B:ASN66 3.4 34.0 1.0
C B:ALA63 3.5 37.9 1.0
N B:ASN66 4.0 35.9 1.0
C B:ASP64 4.1 43.4 1.0
O B:HOH828 4.1 61.1 1.0
CA B:ASP64 4.2 44.5 1.0
N B:TYR68 4.2 34.3 1.0
O B:ASP64 4.2 45.8 1.0
CA B:ASP67 4.2 34.7 1.0
N B:ASP67 4.2 33.9 1.0
N B:ASP64 4.2 39.9 1.0
CA B:ASN66 4.4 35.3 1.0
O B:HOH514 4.4 34.5 1.0
N B:ASP65 4.5 42.0 1.0
CA B:ALA63 4.5 36.7 1.0
C B:ASP67 4.8 34.9 1.0
O B:HOH632 5.0 50.7 1.0
C B:ASP65 5.0 38.6 1.0

Sodium binding site 5 out of 7 in 7bop

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Sodium binding site 5 out of 7 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:49.8
occ:1.00
 O C:ALA63 2.2 47.9 1.0
O C:ASN66 2.3 42.4 1.0
O C:HOH729 2.3 45.0 1.0
O C:HOH787 2.4 57.2 1.0
O C:HOH778 2.5 56.2 1.0
C C:ALA63 3.5 46.6 1.0
C C:ASN66 3.5 40.9 1.0
O C:ASP64 3.7 61.2 1.0
C C:ASP64 3.9 55.2 1.0
N C:ASN66 4.0 42.7 1.0
O C:HOH811 4.1 64.7 1.0
O C:HOH545 4.2 38.3 1.0
CA C:ASP64 4.2 56.3 1.0
N C:TYR68 4.2 38.5 1.0
N C:ASP64 4.2 50.3 1.0
N C:ASP67 4.4 42.0 1.0
CA C:ASP67 4.4 42.0 1.0
CA C:ASN66 4.4 42.0 1.0
N C:ASP65 4.5 53.0 1.0
CA C:ALA63 4.5 43.3 1.0
O C:HOH824 4.6 55.0 1.0
C C:ASP67 4.9 39.3 1.0
C C:ASP65 5.0 46.6 1.0
CB C:TYR68 5.0 39.2 1.0

Sodium binding site 6 out of 7 in 7bop

Go back to Sodium Binding Sites List in 7bop
Sodium binding site 6 out of 7 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:30.8
occ:1.00
 O D:THR166 2.2 31.4 1.0
O D:LYS169 2.3 31.6 1.0
O D:TYR172 2.3 32.3 1.0
O D:HOH740 2.4 30.1 1.0
O D:HOH652 2.5 32.3 1.0
C D:THR166 3.4 32.2 1.0
C D:LYS169 3.4 31.3 1.0
C D:TYR172 3.4 32.9 1.0
N D:TYR172 3.7 31.8 1.0
N D:LYS169 3.9 30.0 1.0
CA D:TYR172 4.0 32.7 1.0
CA D:THR166 4.1 31.7 1.0
CA D:LYS169 4.1 30.4 1.0
CB D:TYR172 4.2 33.0 1.0
O D:LEU165 4.3 31.6 1.0
O D:GLU167 4.4 32.4 1.0
O D:HOH777 4.4 40.6 1.0
C D:GLU167 4.4 32.5 1.0
N D:GLU167 4.5 32.4 1.0
N D:ILE170 4.5 29.6 1.0
N D:GLN171 4.5 31.7 1.0
N D:SER173 4.6 34.6 1.0
CB D:LYS169 4.6 30.6 1.0
CG2 D:THR166 4.6 33.6 1.0
C D:GLN168 4.7 30.8 1.0
CA D:GLU167 4.7 34.5 0.5
C D:ILE170 4.7 31.3 1.0
CA D:GLU167 4.7 33.4 0.5
CA D:ILE170 4.8 31.1 1.0
N D:GLN168 4.8 32.2 1.0
CD1 D:TYR172 4.9 34.9 1.0
C D:GLN171 4.9 33.5 1.0
CB D:THR166 5.0 32.6 1.0

Sodium binding site 7 out of 7 in 7bop

Go back to Sodium Binding Sites List in 7bop
Sodium binding site 7 out of 7 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na404

b:51.7
occ:1.00
 O D:HOH762 2.2 48.8 1.0
O D:ASN66 2.2 46.5 1.0
O D:ALA63 2.2 48.3 1.0
O D:HOH700 2.3 46.4 1.0
C D:ASN66 3.4 45.3 1.0
C D:ALA63 3.4 49.0 1.0
O D:HOH795 3.7 53.6 1.0
O D:ASP64 3.8 52.3 1.0
C D:ASP64 3.8 50.1 1.0
N D:ASN66 3.9 47.2 1.0
CA D:ASP64 4.0 51.9 0.5
CA D:ASP64 4.0 51.1 0.5
N D:ASP64 4.2 49.7 1.0
CA D:ASN66 4.3 46.5 1.0
N D:ASP67 4.3 48.2 1.0
N D:TYR68 4.4 44.6 1.0
N D:ASP65 4.4 52.3 1.0
CA D:ASP67 4.4 47.3 1.0
O D:HOH572 4.5 49.8 1.0
CA D:ALA63 4.6 44.7 1.0
O D:HOH573 4.7 61.3 1.0
C D:ASP65 4.8 47.9 1.0
C D:ASP67 4.9 46.8 1.0

Reference:

D.Hira, T.Onoue, T.Oka. Structural Basis For the Core-Mannan Biosynthesis of Cell Wall Fungal-Type Galactomannan in Aspergillus Fumigatus . J.Biol.Chem. V. 295 15407 2020.
ISSN: ESSN 1083-351X
PubMed: 32873705
DOI: 10.1074/JBC.RA120.013742
Page generated: Tue Oct 8 16:15:07 2024

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