Sodium in PDB 8wfw: Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 4)

Protein crystallography data

The structure of Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 4), PDB code: 8wfw was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.58 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.066, 71.211, 99.151, 90, 90, 90
R / Rfree (%) 15.1 / 17.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 4) (pdb code 8wfw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 4), PDB code: 8wfw:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8wfw

Go back to Sodium Binding Sites List in 8wfw
Sodium binding site 1 out of 3 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 4)


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 Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:15.3
occ:1.00
 O A:GLY49 2.7 9.9 1.0
O A:HOH814 2.8 9.2 1.0
O A:TYR17 2.8 7.6 1.0
N A:GLY21 2.9 8.0 1.0
CA A:GLY21 3.4 7.2 1.0
C A:TYR17 3.5 8.7 1.0
C A:GLY49 3.6 8.8 1.0
CA A:TYR17 3.7 8.5 1.0
N A:GLU20 3.8 5.7 1.0
CD1 A:TYR17 3.9 10.0 1.0
O A:SER16 3.9 7.1 1.0
CA A:GLY49 3.9 6.3 1.0
C A:GLU20 4.0 7.8 1.0
CB A:ALA52 4.0 8.9 1.0
O A:GLY21 4.1 8.6 1.0
C A:GLY21 4.2 7.6 1.0
CE1 A:TYR17 4.2 9.1 1.0
CA A:GLU20 4.2 5.7 1.0
CG A:TYR17 4.3 8.1 1.0
CB A:GLU20 4.4 8.2 1.0
C A:VAL19 4.5 6.9 1.0
CB A:TYR17 4.6 7.7 1.0
N A:GLN18 4.7 6.9 1.0
N A:VAL19 4.7 7.0 1.0
C A:SER16 4.7 7.5 1.0
O A:HOH662 4.7 10.7 1.0
N A:TYR17 4.8 7.3 1.0
CZ A:TYR17 4.9 8.3 1.0
N A:ASP50 4.9 9.8 1.0
CD2 A:TYR17 4.9 9.3 1.0
C A:GLN18 4.9 7.2 1.0

Sodium binding site 2 out of 3 in 8wfw

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Sodium binding site 2 out of 3 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 4)


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 Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:20.9
occ:1.00
 O A:HOH1170 2.7 29.6 1.0
O A:SER46 2.7 12.0 1.0
O A:SER37 2.8 11.7 0.6
O A:SER37 2.8 11.7 0.4
ND2 A:ASN48 3.0 11.9 1.0
C A:SER37 3.5 10.7 0.4
C A:SER37 3.5 10.7 0.6
C A:SER46 3.6 12.6 1.0
CB A:ASN48 3.7 10.8 1.0
CG A:ASN48 3.8 13.0 1.0
CA A:ARG38 3.8 10.8 1.0
CG A:ARG38 3.9 10.4 1.0
O A:HIS47 3.9 10.1 1.0
CB A:SER46 3.9 16.7 1.0
N A:ARG38 4.0 10.9 1.0
O A:HOH800 4.1 30.4 1.0
CA A:SER46 4.1 9.2 1.0
OG A:SER37 4.2 10.4 0.6
C A:HIS47 4.2 9.8 1.0
O A:HOH1080 4.3 37.4 1.0
CB A:SER37 4.3 10.8 0.6
CB A:SER37 4.3 10.7 0.4
CB A:ARG38 4.5 14.7 1.0
N A:ASN48 4.5 8.2 1.0
CA A:SER37 4.5 10.0 0.4
CA A:SER37 4.5 10.0 0.6
N A:HIS47 4.6 10.1 1.0
CA A:ASN48 4.7 7.5 1.0
CA A:HIS47 4.9 7.2 1.0
OD1 A:ASN48 5.0 12.4 1.0
O A:HOH713 5.0 28.2 1.0

Sodium binding site 3 out of 3 in 8wfw

Go back to Sodium Binding Sites List in 8wfw
Sodium binding site 3 out of 3 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 4)


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 Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:23.1
occ:1.00
 O A:HOH983 2.7 31.1 1.0
O A:HOH877 2.8 20.2 1.0
N A:LEU286 2.9 10.4 1.0
CE A:MET345 3.2 23.0 1.0
O A:HOH933 3.5 32.4 1.0
CE1 A:PHE253 3.6 12.3 1.0
CA A:LYS285 3.6 9.1 1.0
CB A:LEU286 3.7 7.7 1.0
C A:LYS285 3.7 9.7 1.0
CD A:LYS285 3.8 11.1 1.0
CD1 A:PHE253 3.8 11.0 1.0
CG A:LEU286 3.8 10.0 1.0
CA A:LEU286 3.8 7.8 1.0
O A:GLN284 3.9 12.2 1.0
O A:LEU286 4.2 11.4 1.0
CD1 A:LEU286 4.4 9.6 1.0
CG A:LYS285 4.4 10.6 1.0
C A:LEU286 4.4 9.1 1.0
SD A:MET345 4.5 17.9 1.0
O A:HOH841 4.5 27.1 1.0
O A:HOH756 4.5 30.2 1.0
CE A:LYS285 4.5 21.3 1.0
CB A:LYS285 4.5 11.5 1.0
N A:LYS285 4.5 8.7 1.0
C A:GLN284 4.6 10.3 1.0
NZ A:LYS285 4.7 22.5 1.0
CZ A:PHE253 4.8 11.8 1.0
O A:LEU252 4.8 9.9 1.0
O A:LYS285 4.9 11.5 1.0

Reference:

K.H.Nam, K.H.Nam. N/A N/A.
Page generated: Wed Oct 9 14:17:56 2024

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