Atomistry » Sodium » PDB 6zl3-7c67 » 7bop
Atomistry »
  Sodium »
    PDB 6zl3-7c67 »
      7bop »

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

Go back to Sodium Binding Sites List in 7bop
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

Go back to Sodium Binding Sites List in 7bop
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

Go back to Sodium Binding Sites List in 7bop
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

Go back to Sodium Binding Sites List in 7bop
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 Dec 15 17:27:38 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy