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Sodium in PDB 6zjs: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Galactose

Enzymatic activity of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Galactose

All present enzymatic activity of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Galactose:
3.2.1.23;

Protein crystallography data

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Galactose, PDB code: 6zjs 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) 46.94 / 1.50
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.378, 138.378, 127.807, 90.00, 90.00, 120.00
R / Rfree (%) 14.3 / 16.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Galactose (pdb code 6zjs). 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 E441Q in Complex with Galactose, PDB code: 6zjs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6zjs

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Sodium binding site 1 out of 5 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q 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 E441Q in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1108

b:24.5
occ:1.00
 OD2 A:ASP207 2.3 25.0 1.0
OD2 A:ASP584 2.3 21.2 1.0
O A:PHE581 2.3 24.5 1.0
O6 A:GAL1102 2.4 47.5 1.0
O A:HOH1653 2.4 27.1 1.0
CG A:ASP207 3.2 27.5 1.0
CG A:ASP584 3.3 21.3 1.0
C6 A:GAL1102 3.3 48.7 1.0
C A:PHE581 3.4 24.1 1.0
OD1 A:ASP207 3.6 24.9 1.0
OH A:TYR108 3.8 25.5 1.0
NE1 A:TRP548 3.9 21.6 1.0
OD1 A:ASP584 4.0 21.6 1.0
O4 A:GAL1102 4.0 47.8 1.0
CA A:VAL582 4.2 23.0 1.0
N A:VAL582 4.2 22.8 1.0
CB A:ASP584 4.3 21.5 1.0
CB A:PHE581 4.3 24.1 1.0
OE2 A:GLU549 4.3 21.6 1.0
C4 A:GAL1102 4.4 49.3 1.0
CA A:PHE581 4.4 23.1 1.0
C5 A:GAL1102 4.4 48.6 1.0
CB A:ASP207 4.5 24.9 1.0
NE2 A:HIS520 4.6 20.8 1.0
CE2 A:TRP548 4.7 20.5 1.0
CD1 A:TRP548 4.8 20.3 1.0
CD1 A:PHE581 4.8 25.9 1.0
O A:ASP207 4.8 24.0 1.0
C A:VAL582 4.9 21.9 1.0
CZ2 A:TRP548 4.9 21.6 1.0
CZ A:TYR108 4.9 23.6 1.0

Sodium binding site 2 out of 5 in 6zjs

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Sodium binding site 2 out of 5 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q 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 E441Q in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1109

b:26.6
occ:1.00
 O A:HOH1780 2.3 36.2 1.0
O A:PHE536 2.3 25.6 1.0
O A:HOH1784 2.4 36.0 1.0
O A:LEU542 2.4 24.1 1.0
O A:TYR539 2.5 23.5 1.0
C A:LEU542 3.5 23.1 1.0
C A:TYR539 3.5 24.4 1.0
C A:PHE536 3.5 24.6 1.0
CA A:PRO540 3.9 24.8 1.0
O A:PRO540 4.0 22.7 1.0
CB A:LEU542 4.1 19.8 1.0
C A:PRO540 4.1 22.9 1.0
N A:LEU542 4.1 20.4 1.0
CA A:LEU542 4.1 20.8 1.0
N A:PRO540 4.1 22.9 1.0
CA A:PHE536 4.2 21.4 1.0
N A:TYR539 4.4 22.6 1.0
NE A:ARG325 4.4 34.9 1.0
CD A:ARG325 4.6 32.8 1.0
CA A:TYR539 4.6 23.1 1.0
N A:GLU537 4.6 23.1 1.0
N A:MET543 4.6 19.9 1.0
CD1 A:LEU327 4.7 28.0 1.0
CA A:GLU537 4.8 25.1 1.0
C A:GLU537 4.9 31.6 1.0
N A:ARG541 4.9 22.1 1.0
O A:LEU535 4.9 23.5 1.0
CB A:PHE536 5.0 23.3 1.0
O A:HOH1834 5.0 62.9 1.0
CA A:MET543 5.0 19.3 1.0

Sodium binding site 3 out of 5 in 6zjs

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Sodium binding site 3 out of 5 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q 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 E441Q in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1110

b:43.3
occ:1.00
 O A:HOH1206 2.3 0.6 1.0
O A:HOH1731 2.4 30.8 1.0
OD1 A:ASP651 2.5 32.2 1.0
CG A:ASP651 3.5 28.9 1.0
CA A:ASP651 4.0 28.9 1.0
O A:HOH1359 4.1 29.7 1.0
CB A:ASP651 4.1 29.6 1.0
O A:HOH1324 4.2 30.5 1.0
N A:VAL652 4.2 29.2 1.0
O A:VAL652 4.5 28.3 1.0
O A:HOH1817 4.5 52.6 1.0
OD2 A:ASP651 4.5 31.3 1.0
C A:ASP651 4.5 33.1 1.0
O A:HOH1551 4.8 47.9 1.0

Sodium binding site 4 out of 5 in 6zjs

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Sodium binding site 4 out of 5 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q 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 E441Q in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1111

b:30.7
occ:1.00
 O A:PRO914 2.3 24.8 1.0
O A:ALA957 2.5 29.5 1.0
O A:LEU954 2.5 26.7 1.0
O A:ASP955 2.6 30.2 1.0
O A:HOH1553 2.8 40.0 1.0
O A:HOH1513 3.1 26.9 1.0
C A:ASP955 3.2 29.0 1.0
C A:PRO914 3.4 23.3 1.0
NH1 A:ARG913 3.5 24.2 1.0
CA A:ASP955 3.6 24.1 1.0
C A:ALA957 3.6 31.1 1.0
C A:LEU954 3.6 25.8 1.0
N A:ALA957 3.8 27.6 1.0
N A:ASP955 4.1 25.6 1.0
CA A:ALA957 4.1 28.0 1.0
N A:ALA956 4.2 27.2 1.0
CA A:PRO914 4.3 24.8 1.0
C A:ALA956 4.3 27.0 1.0
CB A:PRO914 4.3 24.5 1.0
N A:GLN915 4.4 21.8 1.0
N A:PRO914 4.4 23.2 1.0
CB A:ALA957 4.4 29.5 1.0
OD1 A:ASP955 4.5 30.2 1.0
CZ A:ARG913 4.5 23.4 1.0
CA A:GLN915 4.6 23.9 1.0
CG A:ARG913 4.6 25.1 1.0
CD A:PRO914 4.7 25.2 1.0
N A:ALA958 4.7 29.1 1.0
CA A:ALA956 4.8 29.4 1.0
CA A:LEU954 4.9 24.2 1.0
O A:ALA956 4.9 29.8 1.0
CB A:ASP955 4.9 25.2 1.0
C A:ARG913 5.0 24.1 1.0

Sodium binding site 5 out of 5 in 6zjs

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Sodium binding site 5 out of 5 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q 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 E441Q in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1112

b:47.7
occ:1.00
 OE1 A:GLN882 2.4 49.4 1.0
O A:ALA895 2.4 36.1 1.0
O A:HOH1671 2.4 62.6 1.0
O A:HOH1832 2.5 62.5 1.0
O A:GLY892 2.5 24.6 1.0
O A:HOH1329 2.6 46.6 1.0
O A:HOH1811 3.1 63.0 1.0
CD A:GLN882 3.4 47.4 1.0
C A:ALA895 3.5 29.2 1.0
C A:GLY892 3.6 23.9 1.0
O A:GLN893 3.8 26.4 1.0
NE2 A:GLN882 4.0 34.4 1.0
C A:GLN893 4.1 25.2 1.0
N A:ALA895 4.1 24.7 1.0
CA A:GLN893 4.1 24.1 1.0
CB A:ALA895 4.1 27.8 1.0
CA A:ALA895 4.1 25.9 1.0
N A:GLN893 4.3 24.8 1.0
CG A:GLN882 4.5 31.0 1.0
CB A:GLN882 4.5 35.0 1.0
CA A:GLY892 4.6 23.2 1.0
N A:ARG896 4.7 29.1 1.0
O A:HOH1916 4.8 64.5 1.0
N A:GLY894 4.8 25.5 1.0
CA A:ARG896 5.0 28.7 1.0
O A:HOH1726 5.0 44.1 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 15:34:25 2024

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