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

Protein crystallography data

The structure of Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Apo Form, PDB code: 7boo 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) 45.99 / 1.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 154.719, 274.296, 185.974, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Apo Form (pdb code 7boo). 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, Apo Form, PDB code: 7boo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 7boo

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Sodium binding site 1 out of 7 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Apo 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:32.3
occ:1.00
 O A:ASN66 2.2 28.0 1.0
O A:HOH776 2.3 38.4 1.0
O A:HOH732 2.3 29.8 1.0
O A:ALA63 2.4 34.1 1.0
C A:ASN66 3.4 28.3 1.0
C A:ALA63 3.6 34.8 1.0
O A:HOH747 3.9 42.5 1.0
N A:ASN66 4.0 29.2 1.0
N A:TYR68 4.2 28.7 1.0
O A:HOH523 4.2 32.7 1.0
CA A:ASP64 4.3 38.2 0.5
CA A:ASP64 4.3 37.8 0.5
C A:ASP64 4.3 38.8 1.0
CA A:ASN66 4.3 28.9 1.0
N A:ASP67 4.4 27.1 1.0
N A:ASP64 4.4 35.5 1.0
CA A:ASP67 4.5 28.0 1.0
O A:ASP64 4.5 41.2 1.0
CA A:ALA63 4.6 33.7 1.0
N A:ASP65 4.7 37.6 1.0
C A:ASP67 4.8 27.9 1.0

Sodium binding site 2 out of 7 in 7boo

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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, Apo 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:26.6
occ:1.00
 O A:THR166 2.3 26.3 1.0
O A:LYS169 2.3 23.9 1.0
O A:HOH751 2.3 23.9 1.0
O A:TYR172 2.5 28.0 1.0
C A:THR166 3.4 28.3 1.0
C A:LYS169 3.5 25.0 1.0
C A:TYR172 3.5 29.1 1.0
N A:TYR172 3.8 28.0 1.0
N A:LYS169 3.9 24.4 1.0
CA A:TYR172 4.0 28.9 1.0
CA A:THR166 4.1 27.3 1.0
CA A:LYS169 4.2 25.3 1.0
CB A:TYR172 4.3 28.5 1.0
O A:LEU165 4.3 25.8 1.0
C A:GLU167 4.4 28.7 1.0
O A:GLU167 4.4 26.1 1.0
N A:GLU167 4.5 28.9 1.0
N A:GLN171 4.5 26.6 1.0
N A:ILE170 4.5 25.1 1.0
C A:GLN168 4.6 26.3 1.0
CB A:LYS169 4.6 24.6 1.0
N A:GLN168 4.7 27.4 1.0
CA A:GLU167 4.7 29.6 0.5
N A:SER173 4.7 28.3 1.0
C A:ILE170 4.7 27.2 1.0
O A:HOH786 4.7 41.9 1.0
CG2 A:THR166 4.7 28.4 1.0
CA A:GLU167 4.7 29.8 0.5
CA A:ILE170 4.8 26.5 1.0
C A:GLN171 4.9 29.5 1.0

Sodium binding site 3 out of 7 in 7boo

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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, Apo 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:26.3
occ:1.00
 O B:THR166 2.3 23.9 1.0
O B:LYS169 2.3 25.7 1.0
O A:HOH647 2.3 25.4 1.0
O B:HOH741 2.3 26.4 1.0
O B:TYR172 2.4 27.7 1.0
C B:THR166 3.4 26.4 1.0
C B:LYS169 3.5 26.4 1.0
C B:TYR172 3.5 28.3 1.0
N B:TYR172 3.8 28.7 1.0
N B:LYS169 3.9 25.1 1.0
CA B:TYR172 4.0 28.0 1.0
CA B:THR166 4.1 25.8 1.0
CA B:LYS169 4.2 26.1 1.0
O B:LEU165 4.2 27.1 1.0
CB A:PRO364 4.3 29.1 1.0
CB B:TYR172 4.3 28.4 1.0
N A:PRO364 4.3 27.9 1.0
O A:HOH592 4.3 27.6 1.0
CD A:PRO364 4.3 27.8 1.0
C B:GLU167 4.4 28.0 1.0
O B:GLU167 4.4 26.8 1.0
OD1 A:ASN362 4.4 24.6 1.0
CA A:PRO364 4.4 28.6 1.0
N B:GLU167 4.4 26.1 1.0
N B:GLN171 4.5 26.8 1.0
N B:ILE170 4.5 26.2 1.0
C B:GLN168 4.6 25.8 1.0
CB B:LYS169 4.6 25.5 1.0
O B:HOH778 4.7 49.0 1.0
N B:SER173 4.7 29.3 1.0
N B:GLN168 4.7 25.2 1.0
CG A:PRO364 4.7 28.4 1.0
CA B:GLU167 4.7 29.9 1.0
CG2 B:THR166 4.7 27.0 1.0
C B:ILE170 4.7 27.8 1.0
C A:SER363 4.8 27.7 1.0
CA B:ILE170 4.8 26.9 1.0
C B:GLN171 4.9 29.2 1.0

Sodium binding site 4 out of 7 in 7boo

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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, Apo 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:42.0
occ:1.00
 O B:HOH772 2.2 40.9 1.0
O B:HOH733 2.3 32.0 1.0
O B:ALA63 2.4 32.2 1.0
O B:ASN66 2.4 31.0 1.0
C B:ASN66 3.5 30.4 1.0
C B:ALA63 3.6 34.0 1.0
N B:ASN66 4.1 31.1 1.0
C B:ASP64 4.1 37.8 1.0
CA B:ASP64 4.2 38.9 1.0
N B:TYR68 4.2 30.2 1.0
O B:ASP64 4.3 38.3 1.0
CA B:ASP67 4.3 30.9 1.0
O B:HOH673 4.3 52.0 1.0
N B:ASP67 4.3 30.2 1.0
N B:ASP64 4.4 35.7 1.0
CA B:ASN66 4.5 31.5 1.0
O B:HOH522 4.5 29.9 1.0
N B:ASP65 4.5 35.9 1.0
CA B:ALA63 4.7 32.2 1.0
O B:HOH792 4.8 55.1 1.0
C B:ASP67 4.8 30.5 1.0

Sodium binding site 5 out of 7 in 7boo

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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, Apo 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:45.8
occ:1.00
 O C:HOH737 2.2 39.7 1.0
O C:HOH758 2.3 47.0 1.0
O C:ASN66 2.4 34.4 1.0
O C:HOH750 2.4 51.5 1.0
O C:ALA63 2.4 40.7 1.0
C C:ASN66 3.6 34.8 1.0
C C:ALA63 3.6 40.4 1.0
O C:ASP64 3.7 53.2 1.0
C C:ASP64 3.9 49.4 1.0
N C:ASN66 4.1 37.1 1.0
CA C:ASP64 4.2 49.4 1.0
O C:HOH520 4.2 32.6 1.0
N C:TYR68 4.3 32.1 1.0
N C:ASP64 4.3 44.0 1.0
CA C:ASP67 4.4 35.7 1.0
N C:ASP67 4.5 34.5 1.0
N C:ASP65 4.5 46.5 1.0
CA C:ASN66 4.5 35.6 1.0
CA C:ALA63 4.7 36.7 1.0
C C:ASP67 4.9 32.5 1.0

Sodium binding site 6 out of 7 in 7boo

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Sodium binding site 6 out of 7 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Apo 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:25.7
occ:1.00
 O D:THR166 2.3 27.8 1.0
O D:HOH732 2.3 27.5 1.0
O D:LYS169 2.3 25.3 1.0
O D:TYR172 2.5 27.2 1.0
C D:THR166 3.4 28.5 1.0
C D:LYS169 3.5 26.3 1.0
C D:TYR172 3.6 29.1 1.0
N D:TYR172 3.8 28.1 1.0
N D:LYS169 3.9 24.5 1.0
CA D:TYR172 4.1 28.8 1.0
CA D:THR166 4.1 29.2 1.0
CA D:LYS169 4.2 24.8 1.0
O D:LEU165 4.3 29.4 1.0
CB D:TYR172 4.3 29.3 1.0
O D:GLU167 4.4 27.6 1.0
C D:GLU167 4.4 29.2 1.0
N D:GLU167 4.4 28.9 1.0
O D:HOH766 4.5 40.3 1.0
N D:GLN171 4.5 27.1 1.0
N D:ILE170 4.5 25.7 1.0
C D:GLN168 4.6 25.5 1.0
CB D:LYS169 4.6 24.1 1.0
C D:ILE170 4.7 27.5 1.0
CA D:GLU167 4.7 29.8 0.5
CG2 D:THR166 4.7 29.5 1.0
N D:GLN168 4.7 27.2 1.0
CA D:GLU167 4.7 29.7 0.5
N D:SER173 4.7 30.1 1.0
CA D:ILE170 4.8 27.1 1.0
C D:GLN171 4.9 29.8 1.0

Sodium binding site 7 out of 7 in 7boo

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Sodium binding site 7 out of 7 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Apo 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:50.0
occ:1.00
 O D:HOH711 2.3 43.1 1.0
O D:HOH757 2.3 44.6 1.0
O D:ASN66 2.3 41.5 1.0
O D:ALA63 2.4 44.5 1.0
C D:ASN66 3.5 40.8 1.0
C D:ALA63 3.6 46.2 1.0
O D:HOH775 3.7 51.8 1.0
O D:ASP64 3.8 48.3 1.0
N D:ASN66 4.0 42.8 1.0
C D:ASP64 4.0 46.6 1.0
CA D:ASP64 4.2 46.7 0.5
CA D:ASP64 4.2 48.3 0.5
N D:ASP64 4.3 46.0 1.0
CA D:ASN66 4.4 41.5 1.0
N D:ASP67 4.4 42.9 1.0
CA D:ASP67 4.4 42.6 1.0
N D:TYR68 4.5 40.5 1.0
O D:HOH617 4.6 42.9 1.0
N D:ASP65 4.6 49.7 1.0
CA D:ALA63 4.7 41.6 1.0
C D:ASP65 4.9 44.0 1.0
C D:ASP67 5.0 42.8 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 Dec 15 17:27:23 2020

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