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Sodium in PDB 1yq2: Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)

Enzymatic activity of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)

All present enzymatic activity of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1):
3.2.1.23;

Protein crystallography data

The structure of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1), PDB code: 1yq2 was solved by T.Skalova, J.Dohnalek, V.Spiwok, P.Lipovova, E.Vondrackova, H.Petrokova, H.Strnad, B.Kralova, J.Hasek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 140.091, 205.698, 140.458, 90.00, 102.34, 90.00
R / Rfree (%) 15.7 / 19.5

Other elements in 1yq2:

The structure of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) (pdb code 1yq2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1), PDB code: 1yq2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 1yq2

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Sodium binding site 1 out of 12 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na7501

b:38.3
occ:1.00
 OD2 A:ASP588 2.1 25.4 1.0
OD2 A:ASP201 2.4 20.2 1.0
O A:HOH9788 2.5 42.4 1.0
O A:HOH9751 2.5 33.8 1.0
O A:PHE585 2.5 17.8 1.0
CG A:ASP588 3.2 22.0 1.0
CG A:ASP201 3.2 19.3 1.0
OD1 A:ASP201 3.4 21.7 1.0
NE1 A:TRP552 3.6 13.7 1.0
C A:PHE585 3.6 18.0 1.0
OH A:TYR98 3.7 18.2 1.0
OD1 A:ASP588 3.9 25.9 1.0
CB A:ASP588 4.2 18.9 1.0
O A:HOH9589 4.3 21.7 1.0
OE1 A:GLU553 4.3 20.0 1.0
CE2 A:TRP552 4.4 13.5 1.0
CB A:PHE585 4.4 18.8 1.0
N A:VAL586 4.4 17.4 1.0
CA A:VAL586 4.5 17.7 1.0
CZ2 A:TRP552 4.5 12.7 1.0
CA A:PHE585 4.5 18.1 1.0
CD1 A:TRP552 4.6 11.1 1.0
CB A:ASP201 4.6 16.7 1.0
NE2 A:HIS524 4.6 15.7 1.0
CZ A:TYR98 4.8 16.1 1.0
O A:HOH2097 4.9 48.0 1.0

Sodium binding site 2 out of 12 in 1yq2

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Sodium binding site 2 out of 12 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na7511

b:30.7
occ:1.00
 O A:GLN200 2.7 13.8 1.0
OG1 A:THR99 2.8 16.9 1.0
O A:ASN100 2.9 20.2 1.0
OD1 A:ASP199 2.9 14.5 1.0
O A:THR99 2.9 16.5 1.0
O A:HOH9678 3.0 26.8 1.0
O A:ASP199 3.5 13.4 1.0
C A:THR99 3.5 17.7 1.0
C A:GLN200 3.6 14.0 1.0
C A:ASP199 3.7 13.5 1.0
C A:ASN100 3.7 19.3 1.0
CG A:ASP199 3.8 15.8 1.0
CZ2 A:TRP204 3.9 14.4 1.0
NE1 A:TRP204 3.9 14.9 1.0
CB A:THR99 4.0 17.4 1.0
CE2 A:TRP204 4.1 14.7 1.0
N A:ASN100 4.2 18.3 1.0
CA A:ASP199 4.2 13.2 1.0
O A:GLN102 4.3 15.9 1.0
N A:GLN200 4.3 13.4 1.0
CA A:ASN100 4.3 18.8 1.0
CA A:THR99 4.3 16.8 1.0
N A:ASP201 4.3 15.6 1.0
CA A:ASP201 4.3 16.0 1.0
OD2 A:ASP199 4.6 12.2 1.0
CA A:GLN200 4.6 13.8 1.0
N A:GLN202 4.6 15.4 1.0
O A:HOH9204 4.6 22.4 1.0
O A:GLN202 4.6 14.8 1.0
N A:VAL101 4.7 18.2 1.0
CB A:ASP199 4.7 13.2 1.0
N A:THR99 4.7 16.9 1.0
O A:HOH9360 4.7 33.9 1.0
O A:VAL101 4.9 19.6 1.0
CH2 A:TRP204 4.9 15.4 1.0
C A:VAL101 4.9 18.9 1.0
CD1 A:TRP204 4.9 15.5 1.0

Sodium binding site 3 out of 12 in 1yq2

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Sodium binding site 3 out of 12 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na7502

b:44.2
occ:1.00
 OD2 B:ASP588 2.3 27.4 1.0
OD2 B:ASP201 2.4 21.3 1.0
O B:PHE585 2.6 15.0 1.0
O B:HOH9824 2.8 40.5 1.0
O B:HOH9825 2.8 37.3 1.0
CG B:ASP201 3.2 20.1 1.0
CG B:ASP588 3.3 21.0 1.0
OD1 B:ASP201 3.3 20.7 1.0
NE1 B:TRP552 3.6 12.6 1.0
C B:PHE585 3.6 15.3 1.0
OH B:TYR98 3.7 15.8 1.0
OD1 B:ASP588 3.9 23.5 1.0
O B:HOH9744 4.2 20.8 1.0
CB B:ASP588 4.3 18.8 1.0
CE2 B:TRP552 4.4 11.0 1.0
CB B:PHE585 4.4 16.4 1.0
OE1 B:GLU553 4.4 20.7 1.0
N B:VAL586 4.5 15.1 1.0
CA B:PHE585 4.5 15.2 1.0
CZ2 B:TRP552 4.5 11.2 1.0
CD1 B:TRP552 4.5 10.5 1.0
NE2 B:HIS524 4.6 13.5 1.0
CA B:VAL586 4.6 15.5 1.0
CB B:ASP201 4.6 16.6 1.0
O B:HOH9228 4.6 25.1 1.0
CZ B:TYR98 4.9 14.0 1.0
CD2 B:PHE585 4.9 22.6 1.0
O B:ASP201 5.0 16.5 1.0

Sodium binding site 4 out of 12 in 1yq2

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Sodium binding site 4 out of 12 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na7512

b:32.8
occ:1.00
 O B:GLN200 2.8 16.0 1.0
O B:ASN100 2.9 16.4 1.0
OD1 B:ASP199 2.9 9.0 1.0
O B:THR99 3.0 15.2 1.0
OG1 B:THR99 3.0 14.9 1.0
O B:ASP199 3.4 11.7 1.0
O B:HOH9778 3.5 31.8 1.0
C B:THR99 3.6 14.8 1.0
C B:GLN200 3.7 14.8 1.0
C B:ASN100 3.7 16.7 1.0
C B:ASP199 3.7 12.1 1.0
CZ2 B:TRP204 3.8 13.1 1.0
CG B:ASP199 3.8 13.3 1.0
NE1 B:TRP204 3.9 14.3 1.0
CE2 B:TRP204 4.1 11.7 1.0
CB B:THR99 4.1 14.6 1.0
N B:ASN100 4.2 15.5 1.0
CA B:ASP199 4.2 11.1 1.0
O B:GLN102 4.2 15.0 1.0
CA B:ASN100 4.3 16.1 1.0
N B:GLN200 4.3 12.6 1.0
N B:ASP201 4.3 15.7 1.0
CA B:ASP201 4.4 16.7 1.0
CA B:THR99 4.4 14.4 1.0
OD2 B:ASP199 4.5 13.2 1.0
O B:HOH9615 4.6 20.3 1.0
N B:VAL101 4.6 16.1 1.0
CA B:GLN200 4.6 13.8 1.0
O B:GLN202 4.6 14.0 1.0
CB B:ASP199 4.6 11.8 1.0
N B:GLN202 4.7 15.0 1.0
O B:VAL101 4.8 16.2 1.0
C B:VAL101 4.8 16.6 1.0
O B:HOH9337 4.8 30.1 1.0
N B:THR99 4.8 13.7 1.0
CH2 B:TRP204 4.8 12.3 1.0
CA B:VAL101 4.9 16.2 1.0

Sodium binding site 5 out of 12 in 1yq2

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Sodium binding site 5 out of 12 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na7503

b:41.6
occ:1.00
 OD2 C:ASP201 2.4 18.8 1.0
O C:HOH9524 2.4 32.2 1.0
O C:PHE585 2.4 16.4 1.0
OD2 C:ASP588 2.4 27.3 1.0
O C:HOH9818 2.6 46.0 1.0
CG C:ASP201 3.1 16.9 1.0
OD1 C:ASP201 3.2 19.1 1.0
OH C:TYR98 3.4 14.2 1.0
C C:PHE585 3.4 15.8 1.0
CG C:ASP588 3.5 20.3 1.0
NE1 C:TRP552 3.9 12.3 1.0
CB C:PHE585 4.1 16.2 1.0
CA C:PHE585 4.2 15.5 1.0
OD1 C:ASP588 4.2 22.6 1.0
O C:HOH9262 4.3 19.0 1.0
N C:VAL586 4.3 14.6 1.0
CB C:ASP588 4.4 18.0 1.0
CA C:VAL586 4.5 14.2 1.0
CB C:ASP201 4.6 12.9 1.0
CZ C:TYR98 4.6 13.2 1.0
NE2 C:HIS524 4.7 15.1 1.0
OE1 C:GLU553 4.7 20.2 1.0
CE2 C:TRP552 4.7 12.6 1.0
CD2 C:PHE585 4.8 21.6 1.0
CZ2 C:TRP552 4.9 13.4 1.0
CD1 C:TRP552 4.9 11.6 1.0
OD1 C:ASN100 4.9 19.0 1.0
CG C:PHE585 5.0 19.4 1.0
CG C:ASN100 5.0 18.2 1.0

Sodium binding site 6 out of 12 in 1yq2

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Sodium binding site 6 out of 12 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na7513

b:29.0
occ:1.00
 O C:GLN200 2.8 10.8 1.0
OG1 C:THR99 2.9 12.0 1.0
OD1 C:ASP199 2.9 11.5 1.0
O C:ASN100 2.9 15.7 1.0
O C:THR99 3.0 12.8 1.0
O C:HOH9708 3.2 31.9 1.0
O C:ASP199 3.5 11.0 1.0
C C:THR99 3.6 12.9 1.0
C C:GLN200 3.6 10.4 1.0
C C:ASN100 3.7 15.2 1.0
C C:ASP199 3.7 10.8 1.0
CZ2 C:TRP204 3.8 8.7 1.0
CG C:ASP199 3.8 12.5 1.0
NE1 C:TRP204 3.9 11.5 1.0
CB C:THR99 4.0 12.6 1.0
CE2 C:TRP204 4.1 11.3 1.0
N C:ASN100 4.1 13.3 1.0
O C:GLN102 4.2 13.7 1.0
CA C:ASP199 4.2 10.2 1.0
N C:GLN200 4.3 10.4 1.0
CA C:ASN100 4.3 15.3 1.0
N C:ASP201 4.3 11.9 1.0
CA C:THR99 4.3 11.3 1.0
CA C:ASP201 4.4 12.6 1.0
OD2 C:ASP199 4.5 13.2 1.0
CA C:GLN200 4.6 10.5 1.0
O C:HOH9136 4.6 19.5 1.0
N C:VAL101 4.6 14.6 1.0
CB C:ASP199 4.6 10.7 1.0
O C:GLN202 4.6 13.4 1.0
N C:GLN202 4.7 12.3 1.0
N C:THR99 4.8 11.5 1.0
CH2 C:TRP204 4.8 11.4 1.0
C C:VAL101 4.8 15.3 1.0
O C:VAL101 4.9 14.9 1.0
CA C:VAL101 4.9 15.2 1.0
O C:HOH9261 4.9 25.2 1.0

Sodium binding site 7 out of 12 in 1yq2

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Sodium binding site 7 out of 12 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na7504

b:39.6
occ:1.00
 OD2 D:ASP201 2.3 19.7 1.0
OD2 D:ASP588 2.3 23.2 1.0
O D:PHE585 2.5 14.9 1.0
O D:HOH9827 2.5 40.7 1.0
O D:HOH9559 2.5 34.4 1.0
CG D:ASP201 3.1 18.3 1.0
OD1 D:ASP201 3.2 22.1 1.0
CG D:ASP588 3.3 20.4 1.0
C D:PHE585 3.5 14.1 1.0
OH D:TYR98 3.6 13.9 1.0
NE1 D:TRP552 3.7 13.1 1.0
OD1 D:ASP588 4.0 23.9 1.0
O D:HOH9408 4.2 19.5 1.0
N D:VAL586 4.3 13.6 1.0
CA D:VAL586 4.3 14.6 1.0
CB D:ASP588 4.4 18.2 1.0
CB D:PHE585 4.4 15.1 1.0
CA D:PHE585 4.5 14.6 1.0
OE1 D:GLU553 4.5 21.1 1.0
CB D:ASP201 4.5 15.4 1.0
CE2 D:TRP552 4.5 11.7 1.0
CZ2 D:TRP552 4.6 12.9 1.0
CD1 D:TRP552 4.7 10.9 1.0
CZ D:TYR98 4.7 11.6 1.0
O D:ASP201 4.8 14.9 1.0
NE2 D:HIS524 4.8 10.9 1.0

Sodium binding site 8 out of 12 in 1yq2

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Sodium binding site 8 out of 12 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na7514

b:30.6
occ:1.00
 O D:GLN200 2.7 12.9 1.0
OG1 D:THR99 2.9 13.3 1.0
OD1 D:ASP199 2.9 12.5 1.0
O D:ASN100 3.0 14.3 1.0
O D:HOH9624 3.0 24.8 1.0
O D:THR99 3.0 12.4 1.0
O D:ASP199 3.5 11.3 1.0
C D:THR99 3.6 12.9 1.0
C D:GLN200 3.7 11.8 1.0
C D:ASP199 3.8 11.0 1.0
C D:ASN100 3.8 14.5 1.0
NE1 D:TRP204 3.8 11.9 1.0
CZ2 D:TRP204 3.8 11.4 1.0
CG D:ASP199 3.9 13.8 1.0
CB D:THR99 4.0 12.7 1.0
CE2 D:TRP204 4.0 12.8 1.0
CA D:ASP199 4.2 10.5 1.0
N D:ASN100 4.2 13.1 1.0
O D:GLN102 4.2 13.1 1.0
CA D:THR99 4.3 12.1 1.0
CA D:ASN100 4.3 13.8 1.0
N D:GLN200 4.4 10.8 1.0
N D:ASP201 4.4 12.9 1.0
CA D:ASP201 4.4 14.1 1.0
O D:GLN202 4.5 13.3 1.0
OD2 D:ASP199 4.6 13.1 1.0
CA D:GLN200 4.6 11.6 1.0
CB D:ASP199 4.7 10.3 1.0
O D:HOH9375 4.7 27.9 1.0
N D:GLN202 4.7 12.8 1.0
N D:VAL101 4.7 14.7 1.0
O D:HOH9291 4.7 20.4 1.0
N D:THR99 4.7 12.5 1.0
O D:VAL101 4.8 16.4 1.0
C D:VAL101 4.8 15.3 1.0
CD1 D:TRP204 4.8 12.7 1.0
CH2 D:TRP204 4.9 13.5 1.0
CA D:VAL101 5.0 15.6 1.0

Sodium binding site 9 out of 12 in 1yq2

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Sodium binding site 9 out of 12 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na7505

b:38.5
occ:1.00
 OD2 E:ASP588 2.3 24.2 1.0
OD2 E:ASP201 2.4 19.9 1.0
O E:PHE585 2.5 13.8 1.0
O E:HOH9802 2.6 37.5 1.0
O E:HOH9803 3.1 46.4 1.0
CG E:ASP201 3.2 18.7 1.0
OD1 E:ASP201 3.3 21.5 1.0
CG E:ASP588 3.4 18.7 1.0
C E:PHE585 3.5 14.6 1.0
OH E:TYR98 3.5 12.1 1.0
NE1 E:TRP552 3.9 10.2 1.0
CB E:PHE585 4.1 15.1 1.0
OD1 E:ASP588 4.1 23.5 1.0
CA E:PHE585 4.3 14.1 1.0
CB E:ASP588 4.3 15.6 1.0
N E:VAL586 4.3 13.8 1.0
O E:HOH9658 4.5 25.1 1.0
NE2 E:HIS524 4.5 14.8 1.0
CA E:VAL586 4.5 14.5 1.0
OE1 E:GLU553 4.6 20.3 1.0
CB E:ASP201 4.7 15.4 1.0
CE2 E:TRP552 4.7 10.0 1.0
CZ E:TYR98 4.7 10.7 1.0
CD2 E:PHE585 4.8 19.5 1.0
CD1 E:TRP552 4.8 11.4 1.0
CZ2 E:TRP552 4.8 13.0 1.0
CG E:PHE585 5.0 15.8 1.0

Sodium binding site 10 out of 12 in 1yq2

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Sodium binding site 10 out of 12 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na7515

b:31.9
occ:1.00
 O E:GLN200 2.8 13.7 1.0
OG1 E:THR99 2.8 11.9 1.0
OD1 E:ASP199 2.9 14.1 1.0
O E:ASN100 2.9 16.2 1.0
O E:THR99 2.9 11.9 1.0
O E:HOH9743 3.1 30.6 1.0
O E:ASP199 3.5 10.9 1.0
C E:THR99 3.5 12.4 1.0
C E:GLN200 3.7 13.1 1.0
C E:ASN100 3.7 14.7 1.0
NE1 E:TRP204 3.8 11.1 1.0
C E:ASP199 3.8 11.4 1.0
CZ2 E:TRP204 3.8 9.3 1.0
CG E:ASP199 3.9 13.6 1.0
CB E:THR99 4.0 11.3 1.0
CE2 E:TRP204 4.0 10.2 1.0
O E:GLN102 4.1 14.4 1.0
N E:ASN100 4.2 12.6 1.0
CA E:ASP199 4.2 11.2 1.0
CA E:THR99 4.3 11.4 1.0
CA E:ASN100 4.3 14.3 1.0
N E:GLN200 4.3 10.7 1.0
N E:ASP201 4.4 13.8 1.0
CA E:ASP201 4.4 14.5 1.0
OD2 E:ASP199 4.6 14.1 1.0
O E:GLN202 4.6 11.4 1.0
N E:GLN202 4.6 11.8 1.0
N E:VAL101 4.7 13.9 1.0
CA E:GLN200 4.7 12.2 1.0
CB E:ASP199 4.7 11.2 1.0
O E:HOH9450 4.7 20.0 1.0
O E:VAL101 4.7 13.4 1.0
N E:THR99 4.7 12.0 1.0
C E:VAL101 4.8 13.6 1.0
CH2 E:TRP204 4.9 9.6 1.0
CD1 E:TRP204 4.9 10.5 1.0
O E:HOH9224 4.9 29.2 1.0
CA E:VAL101 4.9 13.6 1.0

Reference:

T.Skalova, J.Dohnalek, V.Spiwok, P.Lipovova, E.Vondrackova, H.Petrokova, J.Duskova, H.Strnad, B.Kralova, J.Hasek. Cold-Active Beta-Galactosidase From Arthrobacter Sp. C2-2 Forms Compact 660KDA Hexamers: Crystal Structure at 1.9A Resolution J.Mol.Biol. V. 353 282 2005.
ISSN: ISSN 0022-2836
PubMed: 16171818
DOI: 10.1016/J.JMB.2005.08.028
Page generated: Mon Oct 7 01:17:53 2024

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