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Sodium in PDB 6zjq: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose

Enzymatic activity of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose

All present enzymatic activity of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose:
3.2.1.23;

Protein crystallography data

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose, PDB code: 6zjq was solved by M.Rutkiewicz, A.Bujacz, G.Bujacz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.72 / 1.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.608, 138.608, 127.656, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 19.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose (pdb code 6zjq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose, PDB code: 6zjq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6zjq

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Sodium binding site 1 out of 5 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1101

b:27.7
occ:1.00
 OD2 A:ASP207 2.3 25.9 1.0
OD2 A:ASP584 2.4 26.3 1.0
O6 A:GAL1106 2.4 27.7 1.0
O A:PHE581 2.4 27.4 1.0
O A:HOH1647 2.5 27.7 1.0
CG A:ASP207 3.2 28.7 1.0
CG A:ASP584 3.4 27.7 1.0
C6 A:GAL1106 3.6 29.0 1.0
C A:PHE581 3.6 26.9 1.0
OD1 A:ASP207 3.6 26.0 1.0
CD2 A:PHE581 3.6 47.8 1.0
NE1 A:TRP548 3.9 24.1 1.0
OH A:TYR108 4.0 26.7 1.0
O4 A:GAL1106 4.1 27.7 1.0
C4 A:GAL1106 4.1 27.7 1.0
OD1 A:ASP584 4.1 24.7 1.0
CE2 A:PHE581 4.2 50.1 1.0
CA A:VAL582 4.3 27.1 1.0
N A:VAL582 4.4 27.0 1.0
CB A:ASP584 4.4 24.8 1.0
C5 A:GAL1106 4.4 27.7 1.0
CG A:PHE581 4.4 31.8 1.0
CB A:ASP207 4.5 25.9 1.0
OE2 A:GLU549 4.5 23.6 1.0
NE2 A:HIS520 4.5 23.4 1.0
CB A:PHE581 4.5 29.0 1.0
CA A:PHE581 4.6 25.0 1.0
CE2 A:TRP548 4.7 23.4 1.0
CD1 A:TRP548 4.8 23.5 1.0
O A:ASP207 4.9 25.7 1.0
CZ2 A:TRP548 4.9 23.2 1.0

Sodium binding site 2 out of 5 in 6zjq

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Sodium binding site 2 out of 5 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1102

b:29.1
occ:1.00
 O A:HOH1662 2.2 44.0 1.0
O A:PHE536 2.4 30.2 1.0
O A:LEU542 2.4 24.4 1.0
O A:HOH1671 2.5 45.0 1.0
O A:TYR539 2.5 26.9 1.0
C A:TYR539 3.5 27.6 1.0
C A:LEU542 3.5 22.8 1.0
C A:PHE536 3.6 31.4 1.0
CA A:PRO540 3.9 28.9 1.0
O A:PRO540 4.0 25.4 1.0
CB A:LEU542 4.1 23.0 1.0
C A:PRO540 4.1 24.4 1.0
N A:LEU542 4.1 23.9 1.0
CA A:LEU542 4.1 22.9 1.0
N A:PRO540 4.1 25.4 1.0
CA A:PHE536 4.3 25.6 1.0
N A:TYR539 4.4 27.8 1.0
NE A:ARG325 4.4 48.2 1.0
CD A:ARG325 4.5 38.0 1.0
CA A:TYR539 4.5 25.5 1.0
N A:GLU537 4.6 26.4 1.0
N A:MET543 4.7 24.8 1.0
CD1 A:LEU327 4.7 31.2 1.0
CA A:GLU537 4.8 28.3 1.0
O A:HOH1746 4.8 67.4 1.0
C A:GLU537 4.9 30.5 1.0
N A:ARG541 4.9 25.4 1.0
O A:LEU535 4.9 27.6 1.0
CB A:PHE536 4.9 24.5 1.0

Sodium binding site 3 out of 5 in 6zjq

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Sodium binding site 3 out of 5 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1103

b:48.9
occ:1.00
 O A:HOH1740 2.3 70.0 1.0
O A:HOH1679 2.4 33.4 1.0
OD1 A:ASP651 2.4 36.3 1.0
CG A:ASP651 3.5 37.2 1.0
CA A:ASP651 4.0 36.7 1.0
O A:HOH1488 4.1 31.4 1.0
CB A:ASP651 4.1 37.7 1.0
N A:VAL652 4.1 35.1 1.0
O A:HOH1710 4.1 70.2 1.0
O A:HOH1402 4.2 29.1 1.0
O A:HOH1718 4.3 56.8 1.0
O A:VAL652 4.4 33.6 1.0
OD2 A:ASP651 4.5 38.0 1.0
C A:ASP651 4.5 36.2 1.0
O A:HOH1587 5.0 54.0 1.0

Sodium binding site 4 out of 5 in 6zjq

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Sodium binding site 4 out of 5 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1104

b:31.5
occ:1.00
 O A:PRO914 2.4 27.9 1.0
O A:ALA957 2.5 31.4 1.0
O A:LEU954 2.5 30.8 1.0
O A:ASP955 2.5 35.0 1.0
O A:HOH1372 2.7 46.6 1.0
O A:HOH1499 3.1 29.0 1.0
C A:ASP955 3.2 36.6 1.0
NH1 A:ARG913 3.4 26.4 1.0
C A:PRO914 3.5 26.1 1.0
CA A:ASP955 3.5 30.0 1.0
C A:ALA957 3.6 28.3 1.0
C A:LEU954 3.6 30.2 1.0
N A:ALA957 3.8 29.6 1.0
N A:ASP955 4.0 30.3 1.0
CA A:ALA957 4.1 31.2 1.0
O A:HOH1503 4.2 67.5 1.0
N A:ALA956 4.2 32.1 1.0
C A:ALA956 4.2 32.0 1.0
CA A:PRO914 4.3 26.9 1.0
CB A:PRO914 4.3 27.5 1.0
N A:GLN915 4.4 25.8 1.0
CB A:ALA957 4.4 30.4 1.0
N A:PRO914 4.4 27.2 1.0
OD1 A:ASP955 4.5 35.5 1.0
CZ A:ARG913 4.5 25.4 1.0
CG A:ARG913 4.6 31.5 1.0
CA A:GLN915 4.6 28.3 1.0
CD A:PRO914 4.7 28.0 1.0
N A:ALA958 4.7 31.4 1.0
CA A:ALA956 4.7 34.2 1.0
O A:ALA956 4.8 34.1 1.0
CB A:ASP955 4.9 30.6 1.0
CA A:LEU954 4.9 32.0 1.0
C A:ARG913 5.0 26.9 1.0

Sodium binding site 5 out of 5 in 6zjq

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Sodium binding site 5 out of 5 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1105

b:64.6
occ:1.00
 OE1 A:GLN882 2.3 63.4 1.0
O A:HOH1374 2.4 64.1 1.0
O A:HOH1498 2.5 72.6 1.0
O A:GLY892 2.5 29.2 1.0
O A:ALA895 2.6 50.5 1.0
CD A:GLN882 3.4 54.8 1.0
C A:GLY892 3.6 28.6 1.0
C A:ALA895 3.7 31.7 1.0
O A:GLN893 3.9 30.8 1.0
NE2 A:GLN882 4.0 43.8 1.0
CA A:GLN893 4.1 29.3 1.0
C A:GLN893 4.1 30.0 1.0
N A:ALA895 4.2 30.4 1.0
CB A:ALA895 4.2 33.1 1.0
N A:GLN893 4.2 29.0 1.0
CA A:ALA895 4.3 33.3 1.0
CG A:GLN882 4.4 43.2 1.0
CA A:GLY892 4.6 28.8 1.0
CB A:GLN882 4.7 39.1 1.0
N A:ARG896 4.8 32.6 1.0
O A:HOH1642 4.8 52.1 1.0
N A:GLY894 4.9 29.8 1.0

Reference:

M.Rutkiewicz, M.Wanarska, A.Bujacz. Mapping the Transglycosylation Relevant Sites of Cold-Adapted Beta-D-Galactosidase Fromarthrobactersp. 32CB. Int J Mol Sci V. 21 2020.
ISSN: ESSN 1422-0067
PubMed: 32731412
DOI: 10.3390/IJMS21155354
Page generated: Tue Oct 8 15:33:09 2024

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