Atomistry » Sodium » PDB 7b7h-7bov » 7boo
Atomistry »
  Sodium »
    PDB 7b7h-7bov »
      7boo »

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

Go back to Sodium Binding Sites List in 7boo
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

Go back to Sodium Binding Sites List in 7boo
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

Go back to Sodium Binding Sites List in 7boo
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

Go back to Sodium Binding Sites List in 7boo
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

Go back to Sodium Binding Sites List in 7boo
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

Go back to Sodium Binding Sites List in 7boo
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

Go back to Sodium Binding Sites List in 7boo
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 Oct 8 16:14:58 2024

Last articles

Cl in 5QF7
Cl in 5QED
Cl in 5QFA
Cl in 5QEW
Cl in 5QEJ
Cl in 5QEV
Cl in 5QES
Cl in 5QEU
Cl in 5QDH
Cl in 5QEB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy