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Sodium in PDB 8wfu: Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)

Protein crystallography data

The structure of Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2), PDB code: 8wfu 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) 49.81 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.213, 72.739, 97.385, 92.48, 91.43, 95.22
R / Rfree (%) 16 / 20.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2) (pdb code 8wfu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2), PDB code: 8wfu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 8wfu

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Sodium binding site 1 out of 10 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:21.4
occ:1.00
 O A:GLY49 2.7 14.8 1.0
O A:TYR17 2.7 12.2 1.0
O A:HOH628 2.8 15.9 1.0
N A:GLY21 3.0 13.8 1.0
C A:TYR17 3.4 15.6 1.0
CA A:GLY21 3.6 14.3 1.0
C A:GLY49 3.6 16.9 1.0
CA A:TYR17 3.6 15.2 1.0
CD1 A:TYR17 3.8 14.6 1.0
CA A:GLY49 3.8 14.7 1.0
CB A:ALA52 3.9 10.4 1.0
N A:GLU20 3.9 11.0 1.0
O A:SER16 3.9 18.9 1.0
C A:GLU20 4.1 15.2 1.0
CE1 A:TYR17 4.1 12.6 1.0
O A:GLY21 4.2 16.4 1.0
CG A:TYR17 4.2 17.3 1.0
C A:GLY21 4.3 18.2 1.0
CA A:GLU20 4.4 17.0 1.0
CB A:GLU20 4.5 14.4 1.0
N A:GLN18 4.5 10.7 1.0
CB A:TYR17 4.5 13.3 1.0
N A:VAL19 4.6 16.1 1.0
C A:VAL19 4.6 12.1 1.0
N A:TYR17 4.7 15.9 1.0
C A:SER16 4.7 17.2 1.0
CZ A:TYR17 4.8 14.3 1.0
CD2 A:TYR17 4.8 14.5 1.0
C A:GLN18 4.8 14.0 1.0
N A:ASP50 4.9 16.0 1.0
O A:HOH714 4.9 15.6 1.0

Sodium binding site 2 out of 10 in 8wfu

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Sodium binding site 2 out of 10 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:26.9
occ:1.00
 O A:SER37 2.8 22.4 0.3
ND2 A:ASN48 2.8 23.9 1.0
O A:SER37 2.9 22.5 0.7
O A:SER46 2.9 16.8 1.0
O A:HOH941 3.1 32.1 1.0
C A:SER37 3.5 19.6 0.3
C A:SER37 3.5 19.6 0.7
CB A:ASN48 3.6 18.0 1.0
CG A:ASN48 3.7 20.4 1.0
C A:SER46 3.8 16.7 1.0
O A:HIS47 3.8 16.9 1.0
OG A:SER37 3.8 20.7 0.7
CG A:ARG38 3.9 17.1 1.0
O A:HOH912 3.9 45.5 1.0
CA A:ARG38 4.0 20.4 1.0
N A:ARG38 4.0 18.7 1.0
CB A:SER37 4.1 13.8 0.7
CB A:SER37 4.1 14.9 0.3
C A:HIS47 4.2 17.9 1.0
CB A:SER46 4.3 22.0 1.0
O A:HOH868 4.3 29.9 1.0
CA A:SER46 4.3 17.3 1.0
CA A:SER37 4.4 16.3 0.3
CA A:SER37 4.4 16.1 0.7
N A:ASN48 4.5 15.3 1.0
CB A:ARG38 4.6 21.5 1.0
CA A:ASN48 4.6 18.6 1.0
N A:HIS47 4.7 15.8 1.0
OD1 A:ASN48 4.9 17.4 1.0
NH1 A:ARG38 4.9 27.8 1.0
CA A:HIS47 4.9 16.5 1.0

Sodium binding site 3 out of 10 in 8wfu

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Sodium binding site 3 out of 10 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:28.4
occ:1.00
 N A:LEU286 2.8 18.0 1.0
O A:HOH896 2.8 34.4 1.0
O A:HOH606 3.0 36.0 1.0
CB A:LEU286 3.4 17.6 1.0
CA A:LYS285 3.5 26.4 1.0
CD A:LYS285 3.6 31.9 1.0
C A:LYS285 3.6 24.4 1.0
CA A:LEU286 3.6 18.4 1.0
CE1 A:PHE253 3.7 21.9 1.0
O A:GLN284 3.7 20.5 1.0
CG A:LEU286 3.7 20.8 1.0
CD1 A:PHE253 3.8 24.5 1.0
CE A:LYS285 3.9 35.4 1.0
SD A:MET345 4.0 29.9 1.0
O A:LEU286 4.1 25.4 1.0
C A:LEU286 4.3 23.8 1.0
CG A:LYS285 4.4 30.8 1.0
CD1 A:LEU286 4.4 15.4 1.0
C A:GLN284 4.4 29.6 1.0
N A:LYS285 4.4 23.2 1.0
CB A:LYS285 4.5 25.6 1.0
NZ A:LYS285 4.6 37.0 1.0
O A:LYS285 4.8 23.4 1.0
CZ A:PHE253 4.9 21.5 1.0
CD2 A:LEU286 5.0 12.7 1.0
O A:LEU252 5.0 23.3 1.0
CE A:MET345 5.0 20.3 1.0

Sodium binding site 4 out of 10 in 8wfu

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Sodium binding site 4 out of 10 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)


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 Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:17.6
occ:1.00
 O B:GLY49 2.7 13.5 1.0
N B:GLY21 2.8 11.8 1.0
O B:TYR17 2.8 9.1 1.0
O B:HOH665 2.9 13.2 1.0
CA B:GLY21 3.4 12.6 1.0
C B:TYR17 3.5 14.9 1.0
CA B:TYR17 3.7 10.7 1.0
C B:GLY49 3.7 14.6 1.0
O B:SER16 3.8 15.4 1.0
N B:GLU20 3.8 12.6 1.0
C B:GLU20 3.9 15.9 1.0
CB B:ALA52 3.9 11.7 1.0
CA B:GLY49 4.0 10.0 1.0
CD1 B:TYR17 4.0 14.1 1.0
O B:GLY21 4.0 17.5 1.0
C B:GLY21 4.1 17.3 1.0
CA B:GLU20 4.2 14.9 1.0
CB B:GLU20 4.3 13.1 1.0
CG B:TYR17 4.3 15.7 1.0
CE1 B:TYR17 4.4 15.2 1.0
C B:VAL19 4.5 13.4 1.0
O B:HOH784 4.6 17.9 1.0
CB B:TYR17 4.6 11.4 1.0
N B:GLN18 4.6 13.1 1.0
N B:VAL19 4.6 14.6 1.0
C B:SER16 4.6 15.4 1.0
N B:TYR17 4.7 10.5 1.0
N B:ASP50 4.9 11.6 1.0
C B:GLN18 4.9 16.4 1.0
CD2 B:TYR17 4.9 12.2 1.0
O B:GLU20 5.0 19.0 1.0

Sodium binding site 5 out of 10 in 8wfu

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Sodium binding site 5 out of 10 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)


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 Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:34.6
occ:1.00
 O B:SER37 2.7 20.5 0.9
O B:SER37 2.8 20.4 0.1
O B:SER46 2.8 17.9 1.0
ND2 B:ASN48 3.1 18.7 1.0
C B:SER37 3.6 19.3 0.9
C B:SER37 3.6 19.1 0.1
C B:SER46 3.7 19.6 1.0
CB B:ASN48 3.8 12.5 1.0
O B:HIS47 3.9 11.6 1.0
CG B:ASN48 3.9 15.4 1.0
OG B:SER37 3.9 15.8 0.9
CB B:SER37 4.1 17.2 0.1
CB B:SER37 4.1 17.0 0.9
CB B:SER46 4.2 19.3 1.0
C B:HIS47 4.3 12.6 1.0
CA B:SER46 4.3 13.6 1.0
NH1 B:ARG38 4.3 25.3 1.0
N B:ARG38 4.4 17.7 1.0
CA B:SER37 4.4 16.8 0.9
CA B:SER37 4.4 16.7 0.1
CA B:ARG38 4.5 17.5 1.0
CG B:ARG38 4.6 26.7 1.0
N B:ASN48 4.7 13.5 1.0
N B:HIS47 4.7 14.8 1.0
CZ B:ARG38 4.7 29.9 1.0
CA B:ASN48 4.8 15.9 1.0
CD B:ARG38 4.8 26.1 1.0
O B:HOH662 4.9 24.5 1.0
NE B:ARG38 4.9 25.4 1.0
CA B:HIS47 4.9 15.2 1.0

Sodium binding site 6 out of 10 in 8wfu

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Sodium binding site 6 out of 10 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)


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 Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:28.4
occ:1.00
 O B:HOH794 2.3 32.6 1.0
CE B:MET345 2.9 26.6 1.0
N B:LEU286 2.9 20.4 1.0
CE1 B:PHE253 3.4 20.9 1.0
CB B:LEU286 3.6 15.0 1.0
CD1 B:PHE253 3.6 23.4 1.0
CD B:LYS285 3.6 32.4 1.0
CA B:LYS285 3.7 23.8 1.0
CG B:LEU286 3.7 16.5 1.0
CA B:LEU286 3.8 16.6 1.0
C B:LYS285 3.8 21.4 1.0
O B:GLN284 4.0 22.3 1.0
CG B:LYS285 4.3 27.4 1.0
O B:LEU286 4.3 21.4 1.0
SD B:MET345 4.3 31.6 1.0
C B:LEU286 4.4 23.6 1.0
CD1 B:LEU286 4.4 17.1 1.0
CB B:LYS285 4.6 25.9 1.0
CZ B:PHE253 4.6 20.9 1.0
N B:LYS285 4.6 16.9 1.0
C B:GLN284 4.7 23.8 1.0
O B:LEU252 4.9 21.3 1.0
CE B:LYS285 4.9 45.2 1.0
O B:HOH672 4.9 20.1 1.0
CG B:PHE253 5.0 21.2 1.0
O B:LYS285 5.0 19.1 1.0
NZ B:LYS285 5.0 43.8 1.0
CD2 B:LEU286 5.0 11.4 1.0

Sodium binding site 7 out of 10 in 8wfu

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Sodium binding site 7 out of 10 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)


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 Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:19.7
occ:1.00
 O C:GLY49 2.8 23.0 1.0
O C:HOH693 2.8 22.1 1.0
O C:TYR17 2.8 17.2 1.0
N C:GLY21 2.9 16.9 1.0
C C:TYR17 3.4 23.1 1.0
CA C:GLY21 3.4 21.6 1.0
CA C:TYR17 3.6 17.7 1.0
C C:GLY49 3.7 24.2 1.0
O C:SER16 3.8 17.0 1.0
CB C:ALA52 3.8 21.1 1.0
CD1 C:TYR17 3.9 22.4 1.0
N C:GLU20 3.9 16.4 1.0
C C:GLU20 4.0 18.5 1.0
CA C:GLY49 4.0 21.2 1.0
O C:GLY21 4.1 20.6 1.0
C C:GLY21 4.2 23.1 1.0
CG C:TYR17 4.2 21.9 1.0
CA C:GLU20 4.2 19.3 1.0
CB C:GLU20 4.3 16.0 1.0
CE1 C:TYR17 4.3 21.9 1.0
CB C:TYR17 4.5 15.3 1.0
N C:GLN18 4.6 19.6 1.0
N C:TYR17 4.6 17.4 1.0
C C:VAL19 4.6 21.9 1.0
C C:SER16 4.6 19.0 1.0
O C:HOH772 4.7 17.4 1.0
N C:VAL19 4.7 15.8 1.0
CD2 C:TYR17 4.9 22.0 1.0
C C:GLN18 5.0 19.1 1.0
N C:ASP50 5.0 26.9 1.0

Sodium binding site 8 out of 10 in 8wfu

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Sodium binding site 8 out of 10 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:24.5
occ:1.00
 O C:HOH606 2.8 27.0 1.0
N C:LEU286 2.8 15.2 1.0
CE1 C:PHE253 3.4 19.7 1.0
CA C:LYS285 3.5 20.7 1.0
C C:LYS285 3.6 18.4 1.0
CD1 C:PHE253 3.6 16.5 1.0
CB C:LEU286 3.7 15.1 1.0
CG C:LEU286 3.7 18.8 1.0
CA C:LEU286 3.7 17.2 1.0
O C:GLN284 3.8 19.5 1.0
NZ C:LYS285 3.9 39.8 1.0
SD C:MET345 4.0 22.5 1.0
CG C:LYS285 4.2 39.5 1.0
O C:LEU286 4.2 18.2 1.0
CB C:LYS285 4.4 21.0 1.0
C C:LEU286 4.4 15.9 1.0
CE C:MET345 4.5 14.9 1.0
N C:LYS285 4.5 21.9 1.0
CD1 C:LEU286 4.5 11.9 1.0
C C:GLN284 4.5 25.8 1.0
O C:HOH602 4.6 46.1 1.0
O C:HOH715 4.6 31.3 1.0
O C:HOH628 4.6 28.2 1.0
CZ C:PHE253 4.7 17.9 1.0
CD2 C:LEU286 4.8 15.9 1.0
O C:LYS285 4.8 16.6 1.0
CD C:LYS285 4.8 41.5 1.0
O C:LEU252 4.9 18.4 1.0
CG C:PHE253 4.9 20.8 1.0

Sodium binding site 9 out of 10 in 8wfu

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Sodium binding site 9 out of 10 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:22.8
occ:1.00
 O D:GLY49 2.7 21.3 1.0
N D:GLY21 2.7 19.9 1.0
O D:TYR17 2.9 21.6 1.0
O D:HOH739 2.9 21.0 1.0
CA D:GLY21 3.3 19.9 1.0
C D:TYR17 3.5 20.3 1.0
C D:GLY49 3.6 22.9 1.0
N D:GLU20 3.7 17.1 1.0
CA D:TYR17 3.7 19.5 1.0
C D:GLU20 3.8 26.6 1.0
CB D:ALA52 3.9 19.4 1.0
CA D:GLY49 3.9 23.2 1.0
O D:SER16 3.9 21.5 1.0
O D:GLY21 4.0 22.2 1.0
CA D:GLU20 4.1 25.4 1.0
CD1 D:TYR17 4.1 25.8 1.0
C D:GLY21 4.1 27.9 1.0
CB D:GLU20 4.2 20.4 1.0
CG D:TYR17 4.3 24.6 1.0
CE1 D:TYR17 4.5 19.2 1.0
C D:VAL19 4.5 22.8 1.0
N D:GLN18 4.6 18.9 1.0
CB D:TYR17 4.6 14.7 1.0
N D:VAL19 4.7 21.1 1.0
C D:SER16 4.8 16.9 1.0
O D:HOH770 4.8 18.2 1.0
N D:TYR17 4.8 16.7 1.0
C D:GLN18 4.9 24.5 1.0
CD2 D:TYR17 4.9 25.5 1.0
N D:ASP50 4.9 24.6 1.0
O D:GLU20 4.9 21.3 1.0

Sodium binding site 10 out of 10 in 8wfu

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Sodium binding site 10 out of 10 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:27.0
occ:1.00
 O D:HOH607 2.7 25.7 1.0
N D:LEU286 3.0 12.5 1.0
CE1 D:PHE253 3.3 20.9 1.0
CD1 D:PHE253 3.4 19.6 1.0
CA D:LYS285 3.6 19.7 1.0
CB D:LEU286 3.7 12.9 1.0
CG D:LEU286 3.8 14.8 1.0
C D:LYS285 3.8 18.5 1.0
CA D:LEU286 3.8 16.6 1.0
O D:GLN284 3.9 20.8 1.0
SD D:MET345 4.0 25.6 1.0
O D:HOH772 4.3 24.5 1.0
O D:LEU286 4.4 13.0 1.0
CD1 D:LEU286 4.4 17.9 1.0
C D:LEU286 4.5 14.5 1.0
CB D:LYS285 4.5 23.9 1.0
CZ D:PHE253 4.6 17.7 1.0
CE D:MET345 4.6 18.6 1.0
N D:LYS285 4.6 22.6 1.0
C D:GLN284 4.6 19.3 1.0
O D:HOH793 4.7 24.4 1.0
CG D:PHE253 4.8 21.0 1.0
O D:LEU252 4.9 16.3 1.0
O D:HOH647 4.9 28.7 1.0
O D:LYS285 5.0 17.9 1.0

Reference:

K.H.Nam, K.H.Nam. N/A N/A.
Page generated: Wed Oct 9 14:17:57 2024

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