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Sodium in PDB 6se8: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q

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

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

Protein crystallography data

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q, PDB code: 6se8 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) 46.56 / 1.84
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.859, 136.859, 127.082, 90.00, 90.00, 120.00
R / Rfree (%) 13.5 / 16.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q (pdb code 6se8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q, PDB code: 6se8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6se8

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Sodium binding site 1 out of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1117

b:32.4
occ:1.00
 OD2 A:ASP584 2.3 30.6 1.0
O A:PHE581 2.4 30.5 1.0
O A:HOH1541 2.4 44.9 1.0
OD2 A:ASP207 2.4 33.4 1.0
O A:HOH1640 2.5 34.1 1.0
CG A:ASP207 3.3 35.6 1.0
CG A:ASP584 3.3 28.9 1.0
CD1 A:PHE581 3.4 39.7 0.5
C A:PHE581 3.4 30.0 1.0
OD1 A:ASP207 3.5 29.8 1.0
CE1 A:PHE581 3.8 47.7 0.5
OH A:TYR108 3.8 30.2 1.0
NE1 A:TRP548 3.9 25.1 1.0
OD1 A:ASP584 4.0 28.7 1.0
O A:HOH1298 4.0 36.7 1.0
CG A:PHE581 4.0 38.3 0.5
CA A:VAL582 4.2 28.8 1.0
N A:VAL582 4.2 32.5 1.0
CB A:ASP584 4.3 28.4 1.0
OE1 A:GLU549 4.4 25.7 1.0
CB A:PHE581 4.4 29.2 0.5
CB A:PHE581 4.4 29.3 0.5
CA A:PHE581 4.4 29.1 0.5
CA A:PHE581 4.4 29.1 0.5
NE2 A:HIS520 4.5 26.5 1.0
CB A:ASP207 4.6 29.4 1.0
CZ A:PHE581 4.6 55.0 0.5
CE2 A:TRP548 4.7 22.8 1.0
CD1 A:TRP548 4.8 26.0 1.0
O A:ASP207 4.8 28.4 1.0
CD2 A:PHE581 4.8 35.0 0.5
C A:VAL582 4.9 33.1 1.0
O A:HOH1605 4.9 39.4 1.0
CZ A:TYR108 4.9 29.2 1.0
CZ2 A:TRP548 4.9 25.1 1.0

Sodium binding site 2 out of 6 in 6se8

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Sodium binding site 2 out of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1118

b:29.7
occ:1.00
 O A:HOH1871 2.3 38.8 1.0
O A:LEU542 2.4 26.7 1.0
O A:PHE536 2.4 28.7 1.0
O A:HOH1881 2.4 40.0 1.0
O A:TYR539 2.6 28.2 1.0
C A:LEU542 3.5 28.1 1.0
C A:TYR539 3.5 26.8 1.0
C A:PHE536 3.5 28.9 1.0
O A:PRO540 3.9 28.1 1.0
CA A:PRO540 3.9 27.2 1.0
C A:PRO540 4.0 25.3 1.0
CB A:LEU542 4.1 24.4 1.0
CA A:LEU542 4.1 23.5 1.0
N A:LEU542 4.1 24.4 1.0
N A:PRO540 4.1 27.6 1.0
CA A:PHE536 4.2 26.9 1.0
NE A:ARG325 4.4 39.6 1.0
CD A:ARG325 4.4 37.2 1.0
N A:TYR539 4.4 26.5 1.0
CA A:TYR539 4.6 28.0 1.0
N A:GLU537 4.6 29.2 1.0
N A:MET543 4.6 24.6 1.0
CD1 A:LEU327 4.7 27.6 1.0
CA A:GLU537 4.8 31.2 1.0
C A:GLU537 4.8 33.7 1.0
N A:ARG541 4.9 26.8 1.0
O A:LEU535 4.9 26.2 1.0
CB A:PHE536 4.9 24.9 1.0
CA A:MET543 5.0 23.6 1.0
O A:GLU537 5.0 38.3 1.0

Sodium binding site 3 out of 6 in 6se8

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Sodium binding site 3 out of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1119

b:39.2
occ:1.00
 OD2 A:ASP651 2.3 32.9 1.0
O A:HOH1904 2.3 44.0 1.0
O A:HOH1764 2.4 29.7 1.0
O A:HOH1884 2.5 41.0 1.0
O A:HOH2019 2.5 44.9 1.0
CG A:ASP651 3.4 32.5 1.0
CA A:ASP651 4.0 30.0 1.0
CB A:ASP651 4.0 29.7 1.0
N A:VAL652 4.0 29.3 1.0
O A:HOH1438 4.2 31.2 1.0
O A:VAL652 4.3 29.9 1.0
O A:HOH1809 4.3 48.1 1.0
O A:HOH1447 4.4 29.9 1.0
O A:HOH1914 4.4 38.5 1.0
OD1 A:ASP651 4.4 35.4 1.0
C A:ASP651 4.5 33.9 1.0
O A:HOH1248 4.6 50.6 1.0
C A:VAL652 4.8 30.7 1.0
O A:HOH1842 4.9 44.3 1.0

Sodium binding site 4 out of 6 in 6se8

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Sodium binding site 4 out of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1120

b:78.2
occ:1.00
 O A:HOH1292 2.5 33.9 1.0
O A:HOH1799 2.6 53.2 1.0
O A:HOH1833 2.8 39.7 1.0
O A:HOH1728 2.9 53.4 1.0
O A:ALA44 2.9 33.7 1.0
O A:HOH2018 3.4 58.8 1.0
O A:HOH1211 3.5 52.4 1.0
C A:ALA44 3.8 35.6 1.0
O A:HOH1892 3.9 55.6 1.0
OXT A:ACT1101 4.0 58.8 1.0
O A:HOH1671 4.2 45.3 1.0
N A:ALA44 4.2 31.4 1.0
O A:LEU45 4.3 31.3 1.0
CA A:ALA44 4.4 33.4 1.0
CB A:ALA44 4.5 34.1 1.0
O A:HOH1810 4.6 46.4 1.0
NH2 A:ARG422 4.6 33.2 1.0
C A:LEU45 4.7 31.6 1.0
C A:ACT1101 4.7 28.3 1.0
O A:ACT1101 4.8 40.0 1.0
N A:LEU45 4.9 34.6 1.0

Sodium binding site 5 out of 6 in 6se8

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Sodium binding site 5 out of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1121

b:29.6
occ:1.00
 O A:HOH1642 2.3 37.0 1.0
O A:PRO914 2.6 28.9 1.0
O A:ALA957 2.6 32.7 1.0
O A:ASP955 2.7 33.1 1.0
O A:LEU954 2.7 31.0 1.0
O A:HOH1575 3.0 31.2 1.0
NH2 A:ARG913 3.3 27.7 1.0
C A:ASP955 3.3 35.0 1.0
CA A:ASP955 3.6 29.2 1.0
C A:PRO914 3.6 28.0 1.0
C A:ALA957 3.7 31.9 1.0
C A:LEU954 3.8 31.7 1.0
N A:ALA957 3.9 32.9 1.0
O A:HOH1241 4.1 57.9 1.0
N A:ASP955 4.2 31.0 1.0
CA A:ALA957 4.3 35.0 1.0
N A:ALA956 4.3 31.8 1.0
CZ A:ARG913 4.4 30.1 1.0
C A:ALA956 4.4 36.3 1.0
CG A:ARG913 4.4 27.5 1.0
OD1 A:ASP955 4.4 36.5 1.0
CA A:PRO914 4.5 27.2 1.0
CB A:PRO914 4.5 32.1 1.0
O A:HOH1965 4.5 61.5 1.0
N A:PRO914 4.5 28.9 1.0
N A:GLN915 4.5 26.3 1.0
CB A:ALA957 4.6 37.3 1.0
CA A:GLN915 4.7 25.6 1.0
N A:ALA958 4.8 34.1 1.0
CD A:PRO914 4.8 28.3 1.0
CA A:ALA956 4.9 34.8 1.0
CD A:ARG913 4.9 30.3 1.0
CB A:ASP955 4.9 30.1 1.0

Sodium binding site 6 out of 6 in 6se8

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Sodium binding site 6 out of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1122

b:60.2
occ:1.00
 OE1 A:GLN882 2.2 41.7 0.5
O A:ALA895 2.5 39.6 1.0
O A:GLY892 2.6 29.7 1.0
O A:HOH1452 2.6 55.1 1.0
O A:HOH1505 2.7 60.2 1.0
OE1 A:GLN882 3.2 41.2 0.5
CD A:GLN882 3.2 40.6 0.5
C A:ALA895 3.6 29.2 1.0
C A:GLY892 3.6 28.4 1.0
O A:HOH1613 3.8 26.9 0.5
NE2 A:GLN882 3.9 53.4 0.5
CB A:ALA895 4.0 31.4 1.0
CD A:GLN882 4.0 37.5 0.5
CA A:ALA895 4.2 28.7 1.0
N A:ALA895 4.2 28.3 1.0
O A:GLN893 4.2 31.3 1.0
CG A:GLN882 4.3 29.0 0.5
CB A:GLN882 4.3 38.6 0.5
CA A:GLN893 4.3 30.2 1.0
CG A:GLN882 4.3 29.1 0.5
O A:HOH1988 4.3 57.4 1.0
C A:GLN893 4.3 27.9 1.0
N A:GLN893 4.4 28.0 1.0
CB A:GLN882 4.5 30.4 0.5
CA A:GLY892 4.5 28.7 1.0
N A:ARG896 4.7 31.9 1.0
O A:HOH1709 4.9 43.8 1.0

Reference:

M.Rutkiewicz, A.Bujacz, M.Wanarska, A.Wierzbicka-Wos, H.Cieslinski. Active Site Architecture and Reaction Mechanism Determination of Cold Adapted Beta-D-Galactosidase Fromarthrobactersp. 32CB. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 31484304
DOI: 10.3390/IJMS20174301
Page generated: Tue Dec 15 12:59:08 2020

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