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Sodium in PDB 4lgn: The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase

Protein crystallography data

The structure of The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase, PDB code: 4lgn was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.41 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.761, 78.686, 143.952, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 19.6

Other elements in 4lgn:

The structure of The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase also contains other interesting chemical elements:

Potassium (K) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase (pdb code 4lgn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase, PDB code: 4lgn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4lgn

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Sodium binding site 1 out of 6 in the The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na827

b:24.9
occ:1.00
 O A:SER667 2.3 19.4 1.0
O A:HOH1740 2.4 44.9 1.0
O A:HOH1652 2.4 33.8 1.0
O A:ALA664 2.5 13.9 1.0
OG A:SER663 2.6 13.8 1.0
O A:HOH1428 3.1 39.5 1.0
C A:SER667 3.5 22.3 1.0
C A:ALA664 3.5 15.8 1.0
CB A:SER663 3.5 12.5 1.0
N A:SER667 3.7 25.7 1.0
O A:SER663 3.8 11.7 1.0
C A:SER663 3.9 11.9 1.0
N A:GLY666 4.1 26.6 1.0
O A:HOH1605 4.1 33.1 1.0
O A:HOH1708 4.1 22.4 0.5
CA A:SER667 4.2 21.9 1.0
CA A:PRO665 4.2 22.2 1.0
N A:PRO665 4.2 18.6 1.0
N A:ALA664 4.3 12.6 1.0
CA A:SER663 4.3 11.4 1.0
O A:HOH1524 4.4 35.4 1.0
C A:PRO665 4.4 23.9 1.0
CA A:ALA664 4.6 14.1 1.0
N A:SER668 4.6 19.6 1.0
O A:HOH1153 4.7 19.5 1.0
C A:GLY666 4.7 30.9 1.0
CB A:SER667 4.7 23.4 1.0
CA A:SER668 4.8 23.1 1.0
CA A:GLY666 4.9 30.4 1.0

Sodium binding site 2 out of 6 in 4lgn

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Sodium binding site 2 out of 6 in the The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na828

b:27.0
occ:1.00
 O A:HOH1186 2.5 16.4 1.0
O A:HOH1288 2.5 20.7 1.0
OD2 A:ASP38 2.6 5.9 1.0
O A:HOH914 2.6 5.5 1.0
CG A:ASP38 3.4 6.2 1.0
OD1 A:ASP38 3.5 6.1 1.0
O A:HOH1433 3.8 12.0 0.5
NH1 A:ARG126 3.8 7.8 1.0
CB A:PHE19 3.9 6.4 1.0
OH A:TYR266 4.1 12.3 1.0
O A:HOH1203 4.1 18.8 1.0
O A:HOH1559 4.4 28.9 1.0
OD1 A:ASN122 4.4 7.8 1.0
CD2 A:PHE19 4.5 5.7 1.0
N A:PHE19 4.6 6.8 1.0
O A:HOH1434 4.7 37.3 1.0
O A:HOH1176 4.7 7.8 1.0
O A:HOH1433 4.7 10.0 0.5
CG A:PHE19 4.8 5.7 1.0
CB A:ASP38 4.8 6.1 1.0
CZ A:ARG126 4.8 7.4 1.0
NE A:ARG126 4.8 7.7 1.0
O A:HOH1437 4.9 21.8 0.5
CA A:PHE19 5.0 6.5 1.0

Sodium binding site 3 out of 6 in 4lgn

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Sodium binding site 3 out of 6 in the The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na829

b:32.3
occ:1.00
 O A:HOH1795 2.5 36.0 1.0
O A:HOH1551 2.5 35.1 1.0
O A:ILE320 2.5 7.3 1.0
O A:TYR298 2.8 8.2 1.0
O A:HOH955 3.0 2.9 0.5
O A:GLY268 3.1 10.0 1.0
C A:ILE320 3.7 8.0 1.0
CG2 A:ILE320 4.0 7.8 1.0
C A:TYR298 4.0 9.9 1.0
C A:GLY268 4.0 9.9 1.0
CA A:SER269 4.2 10.1 1.0
CD2 A:TYR298 4.2 10.7 1.0
CB A:SER269 4.4 10.7 1.0
O A:HOH1576 4.4 6.1 0.5
N A:ILE320 4.4 7.8 1.0
CA A:PHE299 4.4 7.8 1.0
O1 A:EDO814 4.5 27.6 1.0
N A:SER269 4.5 10.3 1.0
CA A:ILE320 4.6 7.7 1.0
N A:SER321 4.6 7.6 1.0
N A:PHE299 4.7 8.4 1.0
CB A:PHE299 4.8 7.6 1.0
CA A:SER321 4.8 8.4 1.0
CB A:TYR298 4.9 11.0 1.0
CD1 A:TRP322 4.9 13.6 1.0
CB A:ILE320 4.9 8.1 1.0
CE2 A:TYR298 4.9 10.1 1.0

Sodium binding site 4 out of 6 in 4lgn

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Sodium binding site 4 out of 6 in the The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na830

b:22.5
occ:0.70
 O A:HOH1900 2.3 22.6 0.7
OG1 A:THR590 2.5 8.9 1.0
O A:HOH1874 2.5 20.6 0.7
O A:ASN588 3.2 7.6 1.0
CB A:THR590 3.4 8.2 1.0
O A:SER587 3.5 7.7 1.0
O A:HOH1006 3.8 7.8 1.0
C A:ASN588 4.0 8.8 1.0
O A:HOH1215 4.1 23.8 1.0
N A:THR590 4.1 7.4 1.0
CB A:ASN588 4.1 10.9 1.0
O A:HOH2018 4.1 25.4 0.7
NA A:NA831 4.2 17.1 0.7
O A:HOH1184 4.2 17.5 1.0
OH A:TYR592 4.3 8.9 1.0
CA A:THR590 4.3 7.5 1.0
CG2 A:THR590 4.5 8.8 1.0
C A:SER587 4.6 8.9 1.0
CA A:ASN588 4.6 9.4 1.0
C A:GLY589 4.9 8.5 1.0
N A:GLY589 4.9 8.8 1.0
O A:HOH2013 4.9 3.7 0.7

Sodium binding site 5 out of 6 in 4lgn

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Sodium binding site 5 out of 6 in the The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na831

b:17.1
occ:0.70
 O A:HOH1406 2.2 18.7 0.7
O A:HOH2013 2.3 3.7 0.7
O A:HOH2018 2.5 25.4 0.7
O A:ASN588 2.5 7.6 1.0
O A:HOH1900 2.6 22.6 0.7
C A:ASN588 3.6 8.8 1.0
O A:HOH1471 3.8 12.6 1.0
O A:HOH1006 4.0 7.8 1.0
CB A:ASN588 4.0 10.9 1.0
NA A:NA830 4.2 22.5 0.7
CA A:ASN588 4.3 9.4 1.0
N A:GLY589 4.5 8.8 1.0
CA A:GLY589 4.7 8.7 1.0
O A:HOH1619 4.7 22.2 0.5

Sodium binding site 6 out of 6 in 4lgn

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Sodium binding site 6 out of 6 in the The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na832

b:40.0
occ:1.00
 OD1 A:ASP187 2.3 10.3 1.0
O A:HOH1514 2.5 36.3 1.0
O A:HOH1188 2.7 9.5 0.5
O A:HOH1600 3.1 28.3 1.0
CG A:ASP187 3.5 10.0 1.0
CA A:ASP187 4.0 8.9 1.0
O A:HOH1814 4.1 43.9 1.0
N A:ILE188 4.2 8.1 1.0
O A:SER148 4.2 7.8 1.0
CB A:ASP187 4.2 9.1 1.0
CA A:SER148 4.4 7.6 1.0
CB A:SER148 4.4 7.5 1.0
OD2 A:ASP187 4.4 10.1 1.0
O A:HOH1188 4.5 19.0 0.5
O A:HOH1768 4.5 29.7 1.0
O A:SER186 4.6 9.2 1.0
C A:SER148 4.7 8.3 1.0
C A:ASP187 4.7 8.8 1.0
OG A:SER148 4.9 7.2 1.0
O A:HOH1017 5.0 10.8 1.0

Reference:

M.Alahuhta, W.S.Adney, M.E.Himmel, V.V.Lunin. Structure of Acidothermus Cellulolyticus Family 74 Glycoside Hydrolase at 1.82 Angstrom Resolution. Acta Crystallogr.,Sect.F V. 69 1335 2013.
ISSN: ESSN 1744-3091
PubMed: 24316824
DOI: 10.1107/S1744309113030005
Page generated: Mon Oct 7 16:45:47 2024

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