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Sodium in PDB 3lk6: Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis

Protein crystallography data

The structure of Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis, PDB code: 3lk6 was solved by M.Krug, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.99 / 2.88
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.315, 99.149, 139.861, 90.11, 90.05, 89.94
R / Rfree (%) 17.1 / 20.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis (pdb code 3lk6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis, PDB code: 3lk6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3lk6

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Sodium binding site 1 out of 4 in the Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na647

b:63.0
occ:1.00
OD1 A:ASP107 3.1 75.8 1.0
OG1 A:THR106 3.1 59.8 1.0
CG A:ASP107 3.4 75.7 1.0
CA A:GLY168 3.6 36.0 1.0
O A:LEU167 3.7 50.4 1.0
CD A:LYS410 3.7 69.9 1.0
OD2 A:ASP107 3.7 76.7 1.0
CB A:THR106 3.8 43.0 1.0
N A:ASP107 4.0 59.5 1.0
O A:VAL103 4.0 52.6 1.0
CE A:LYS410 4.2 70.2 1.0
CB A:ASP107 4.3 69.4 1.0
N A:GLY168 4.3 43.2 1.0
C A:LEU167 4.3 53.6 1.0
CA A:ASP107 4.4 68.1 1.0
C A:THR106 4.5 52.4 1.0
C A:GLY168 4.7 46.7 1.0
O A:GLY168 4.8 59.7 1.0
CA A:THR106 4.8 45.5 1.0
CG1 A:VAL103 4.8 53.6 1.0
C A:VAL103 4.9 41.3 1.0
NZ A:LYS410 5.0 69.2 1.0
CG2 A:THR106 5.0 28.2 1.0

Sodium binding site 2 out of 4 in 3lk6

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Sodium binding site 2 out of 4 in the Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na651

b:51.7
occ:1.00
OG1 B:THR106 3.2 60.1 1.0
OD1 B:ASP107 3.2 77.8 1.0
CA B:GLY168 3.5 33.6 1.0
CG B:ASP107 3.6 77.4 1.0
O B:LEU167 3.6 52.5 1.0
CD B:LYS410 3.6 70.0 1.0
OD2 B:ASP107 3.8 76.7 1.0
CB B:THR106 3.9 42.5 1.0
O B:VAL103 4.0 50.9 1.0
N B:ASP107 4.1 58.4 1.0
CE B:LYS410 4.1 71.8 1.0
N B:GLY168 4.2 40.6 1.0
C B:LEU167 4.2 54.1 1.0
CB B:ASP107 4.4 69.8 1.0
CA B:ASP107 4.5 66.6 1.0
C B:THR106 4.6 54.9 1.0
C B:GLY168 4.6 45.0 1.0
O B:GLY168 4.7 57.9 1.0
CG1 B:VAL103 4.8 54.3 1.0
CA B:THR106 4.9 46.8 1.0
C B:VAL103 5.0 41.0 1.0
NZ B:LYS410 5.0 70.0 1.0

Sodium binding site 3 out of 4 in 3lk6

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Sodium binding site 3 out of 4 in the Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na648

b:69.2
occ:1.00
OD1 C:ASP107 3.1 78.5 1.0
OG1 C:THR106 3.2 60.1 1.0
CG C:ASP107 3.5 76.3 1.0
CA C:GLY168 3.6 34.8 1.0
CD C:LYS410 3.7 70.9 1.0
O C:LEU167 3.7 49.7 1.0
OD2 C:ASP107 3.7 75.1 1.0
CB C:THR106 3.9 44.5 1.0
N C:ASP107 4.0 59.9 1.0
O C:VAL103 4.0 53.4 1.0
CE C:LYS410 4.1 71.5 1.0
CB C:ASP107 4.3 68.7 1.0
N C:GLY168 4.3 39.1 1.0
C C:LEU167 4.4 52.9 1.0
CA C:ASP107 4.4 68.4 1.0
C C:THR106 4.5 54.6 1.0
C C:GLY168 4.7 45.1 1.0
O C:GLY168 4.7 59.6 1.0
CA C:THR106 4.8 47.1 1.0
CG1 C:VAL103 4.8 53.1 1.0
NZ C:LYS410 4.9 70.0 1.0
C C:VAL103 5.0 42.1 1.0

Sodium binding site 4 out of 4 in 3lk6

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Sodium binding site 4 out of 4 in the Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na647

b:71.9
occ:1.00
OD1 D:ASP107 3.1 77.5 1.0
OG1 D:THR106 3.2 58.1 1.0
CG D:ASP107 3.5 74.9 1.0
CA D:GLY168 3.6 35.5 1.0
O D:LEU167 3.7 49.3 1.0
CD D:LYS410 3.7 70.2 1.0
OD2 D:ASP107 3.8 74.0 1.0
CB D:THR106 3.9 43.1 1.0
N D:ASP107 4.0 59.3 1.0
O D:VAL103 4.0 53.1 1.0
CE D:LYS410 4.2 71.6 1.0
N D:GLY168 4.3 41.1 1.0
CB D:ASP107 4.3 68.5 1.0
C D:LEU167 4.3 52.7 1.0
CA D:ASP107 4.4 67.7 1.0
C D:THR106 4.5 53.6 1.0
C D:GLY168 4.7 47.1 1.0
O D:GLY168 4.7 59.5 1.0
CA D:THR106 4.8 45.1 1.0
CG1 D:VAL103 4.8 53.9 1.0
NZ D:LYS410 5.0 68.5 1.0
C D:VAL103 5.0 40.8 1.0
CG2 D:THR106 5.0 27.1 1.0

Reference:

M.Krug, S.Fischer, K.Diederichs, W.Boos, C.Mayer. Beta-N-Hexosaminidase N318D Mutant (YBBD_N318D) From Bacillus Subtilis To Be Published.
Page generated: Tue Dec 15 06:16:51 2020

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