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Sodium in PDB 6sea: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode

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

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

Protein crystallography data

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode, PDB code: 6sea 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) 46.89 / 1.87
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.613, 138.613, 127.347, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 20.5

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

Sodium binding site 1 out of 4 in 6sea

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Sodium binding site 1 out of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode


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 Lactose Bound in Deep Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1102

b:45.5
occ:1.00
 OD2 A:ASP584 2.3 40.1 1.0
O A:PHE581 2.4 49.4 1.0
O A:HOH1572 2.4 40.6 1.0
OD2 A:ASP207 2.4 40.0 1.0
O6 A:LAT1101 2.6 50.5 1.0
CG A:ASP584 3.3 42.1 1.0
CG A:ASP207 3.3 42.1 1.0
C A:PHE581 3.5 49.0 1.0
OD1 A:ASP207 3.7 41.4 1.0
C6 A:LAT1101 3.8 48.9 1.0
CD2 A:PHE581 3.8 53.5 1.0
NE1 A:TRP548 3.9 38.7 1.0
OD1 A:ASP584 3.9 39.5 1.0
OH A:TYR108 3.9 39.1 1.0
CA A:VAL582 4.1 44.2 1.0
O4 A:LAT1101 4.1 41.5 1.0
N A:VAL582 4.2 44.1 1.0
CB A:ASP584 4.2 40.9 1.0
OE2 A:GLU549 4.3 35.8 1.0
C4 A:LAT1101 4.3 45.0 1.0
CB A:ASP207 4.5 36.1 1.0
CB A:PHE581 4.5 48.0 1.0
CA A:PHE581 4.5 48.4 1.0
C5 A:LAT1101 4.6 48.3 1.0
CG A:PHE581 4.6 50.0 1.0
CE2 A:PHE581 4.6 53.6 1.0
NE2 A:HIS520 4.7 38.6 1.0
CE2 A:TRP548 4.8 35.1 1.0
O A:ASP207 4.8 35.5 1.0
C A:VAL582 4.8 44.4 1.0
CD1 A:TRP548 4.9 36.6 1.0
CZ2 A:TRP548 4.9 35.1 1.0

Sodium binding site 2 out of 4 in 6sea

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Sodium binding site 2 out of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode


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 Lactose Bound in Deep Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1103

b:56.4
occ:1.00
 OE1 A:GLN951 2.6 51.0 1.0
OE1 A:GLU916 2.7 45.8 1.0
N A:ALA763 2.9 45.3 1.0
O A:HOH1330 3.4 43.9 1.0
CB A:TRP762 3.4 48.3 1.0
CD A:GLN951 3.5 51.7 1.0
CA A:TRP762 3.5 47.4 1.0
CB A:ALA763 3.6 46.8 1.0
C A:TRP762 3.7 45.0 1.0
NH1 A:ARG947 3.7 47.9 1.0
CG A:GLN951 3.7 52.1 1.0
CA A:ALA763 3.8 46.4 1.0
CD A:GLU916 3.8 46.1 1.0
CD2 A:LEU954 3.8 47.7 1.0
NH2 A:ARG947 3.9 46.8 1.0
CB A:GLU916 3.9 45.2 1.0
CA A:GLU916 4.1 45.4 1.0
CZ A:ARG947 4.1 45.9 1.0
CB A:GLN951 4.3 50.1 1.0
NH2 A:ARG863 4.3 44.3 1.0
CG A:GLU916 4.4 45.0 1.0
CG A:TRP762 4.6 48.8 1.0
O A:ALA763 4.6 44.2 1.0
NE2 A:GLN951 4.7 52.8 1.0
N A:GLU916 4.7 46.5 1.0
C A:ALA763 4.7 43.9 1.0
CA A:GLN951 4.8 51.6 1.0
OE2 A:GLU916 4.9 45.6 1.0
O A:TRP762 4.9 44.5 1.0
N A:TRP762 4.9 47.4 1.0
CG A:LEU954 5.0 48.7 1.0

Sodium binding site 3 out of 4 in 6sea

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Sodium binding site 3 out of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode


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 Lactose Bound in Deep Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1104

b:43.5
occ:1.00
 O A:PRO914 2.5 48.9 1.0
O A:ALA957 2.6 52.9 1.0
O A:LEU954 2.7 49.9 1.0
O A:ASP955 2.8 52.1 1.0
O A:HOH1444 3.0 43.5 1.0
O A:HOH1759 3.1 48.6 1.0
C A:ASP955 3.3 53.3 1.0
NH2 A:ARG913 3.3 42.5 1.0
CA A:ASP955 3.5 51.3 1.0
C A:PRO914 3.6 48.5 1.0
C A:ALA957 3.7 51.9 1.0
C A:LEU954 3.7 49.1 1.0
N A:ALA957 3.9 51.8 1.0
N A:ASP955 4.1 50.4 1.0
OD1 A:ASP955 4.3 48.9 1.0
CA A:ALA957 4.3 52.2 1.0
N A:ALA956 4.3 52.5 1.0
CA A:PRO914 4.4 49.8 1.0
CB A:PRO914 4.4 50.0 1.0
C A:ALA956 4.4 52.4 1.0
CZ A:ARG913 4.4 43.3 1.0
N A:GLN915 4.5 44.1 1.0
N A:PRO914 4.5 47.5 1.0
CG A:ARG913 4.5 44.8 1.0
CB A:ALA957 4.6 51.1 1.0
CA A:GLN915 4.7 43.7 1.0
CD A:PRO914 4.8 48.0 1.0
N A:ALA958 4.9 53.8 1.0
O A:HOH1669 4.9 50.3 1.0
CB A:ASP955 4.9 49.1 1.0
CA A:ALA956 4.9 52.8 1.0
CD A:ARG913 4.9 44.1 1.0
O A:ALA956 4.9 52.0 1.0
C A:ARG913 5.0 44.8 1.0

Sodium binding site 4 out of 4 in 6sea

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Sodium binding site 4 out of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode


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 Lactose Bound in Deep Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1105

b:43.8
occ:1.00
 O A:GLN206 2.6 39.5 1.0
O A:HOH1475 2.8 44.7 1.0
OD1 A:ASP205 2.8 40.2 1.0
O A:ASN110 2.9 41.0 1.0
O A:THR109 3.0 43.2 1.0
OG1 A:THR109 3.1 44.6 1.0
C A:GLN206 3.6 38.2 1.0
CZ2 A:TRP210 3.6 42.4 1.0
O A:ASP205 3.7 40.4 1.0
NE1 A:TRP210 3.7 42.9 1.0
C A:THR109 3.7 43.0 1.0
CE2 A:TRP210 3.8 42.9 1.0
C A:ASN110 3.8 42.2 1.0
C A:ASP205 3.8 40.9 1.0
CG A:ASP205 3.9 40.0 1.0
CA A:ASP205 4.2 38.2 1.0
CB A:THR109 4.3 43.7 1.0
N A:GLN206 4.3 39.5 1.0
N A:ASN110 4.3 44.3 1.0
N A:ASP207 4.3 38.3 1.0
CA A:ASN110 4.4 44.3 1.0
CA A:ASP207 4.4 37.1 1.0
O A:MET208 4.4 39.9 1.0
O A:GLN112 4.4 43.4 1.0
CA A:THR109 4.5 42.8 1.0
N A:MET208 4.5 36.8 1.0
O A:HOH1642 4.5 38.6 1.0
CA A:GLN206 4.6 41.0 1.0
CH2 A:TRP210 4.6 41.1 1.0
OD2 A:ASP205 4.6 39.5 1.0
CD1 A:TRP210 4.7 43.4 1.0
CB A:ASP205 4.7 38.8 1.0
O A:HOH1421 4.7 38.5 1.0
N A:VAL111 4.8 43.7 1.0
O A:VAL111 4.8 42.0 1.0
N A:THR109 4.8 42.8 1.0
CD2 A:TRP210 4.9 43.1 1.0
C A:VAL111 5.0 45.1 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 Oct 8 13:26:20 2024

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