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Sodium in PDB 4uys: X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae

Protein crystallography data

The structure of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae, PDB code: 4uys was solved by T.Kraushaar, M.Veelders, S.Brueckner, D.Rhinow, H.U.Moesch, L.O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.51 / 1.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 52.720, 101.550, 33.870, 90.00, 90.00, 90.00
R / Rfree (%) 14.683 / 16.968

Other elements in 4uys:

The structure of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae (pdb code 4uys). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae, PDB code: 4uys:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4uys

Go back to Sodium Binding Sites List in 4uys
Sodium binding site 1 out of 7 in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1207

b:31.0
occ:1.00
 O A:HOH2006 2.4 26.4 1.0
O A:HOH2284 2.8 32.5 1.0
N A:ASP73 2.9 10.1 1.0
OD1 A:ASP73 3.2 13.5 1.0
O A:HOH2122 3.4 13.7 1.0
OE2 A:GLU33 3.6 22.8 1.0
CZ2 A:TRP70 3.6 12.3 1.0
CA A:GLN72 3.8 9.5 1.0
CA A:ASP73 3.8 9.2 1.0
C A:GLN72 3.8 9.7 1.0
O A:HOH2120 3.8 22.4 1.0
CB A:GLN72 3.9 11.3 1.0
CH2 A:TRP70 3.9 12.7 1.0
O A:HOH2024 3.9 59.3 0.5
CG A:ASP73 4.1 11.9 1.0
O A:HOH2005 4.2 23.4 1.0
CD A:GLU33 4.5 17.8 1.0
CB A:ASP73 4.6 9.7 1.0
CG A:GLU33 4.7 15.1 1.0
CE2 A:TRP70 4.7 9.7 1.0
O A:HOH2024 4.7 20.4 0.5
O A:HOH2118 4.8 18.4 0.5
O A:HOH2023 4.9 60.0 1.0
C A:ASP73 5.0 8.9 1.0
O A:GLN72 5.0 9.5 1.0

Sodium binding site 2 out of 7 in 4uys

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Sodium binding site 2 out of 7 in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1208

b:39.7
occ:1.00
 OD2 A:ASP73 2.8 19.9 1.0
O A:HOH2123 3.0 13.3 1.0
CB A:ASP73 3.5 9.7 1.0
CG A:ASP73 3.6 11.9 1.0
O A:HOH2115 3.6 22.3 1.0
O A:HOH2056 4.0 31.1 1.0
OG1 A:THR75 4.2 10.7 1.0
O A:HOH2208 4.3 23.5 1.0
O A:HOH2121 4.4 16.0 1.0
O A:HOH2126 4.4 19.9 0.5
NE2 A:GLN72 4.6 34.1 1.0
OD1 A:ASP73 4.8 13.5 1.0
CA A:ASP73 5.0 9.2 1.0

Sodium binding site 3 out of 7 in 4uys

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Sodium binding site 3 out of 7 in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1209

b:18.9
occ:1.00
 N A:ASN46 3.1 12.3 1.0
C A:CYS44 3.3 11.0 1.0
CA A:CYS44 3.4 10.4 1.0
O A:HOH2285 3.4 23.9 1.0
N A:PRO45 3.6 11.4 1.0
CB A:ASN46 3.6 16.9 1.0
O A:CYS44 3.6 11.1 1.0
CA A:ASN46 3.7 13.6 1.0
N A:LEU47 3.8 11.8 1.0
CB A:CYS44 3.8 9.9 1.0
CD A:PRO45 3.9 12.4 1.0
C A:ASN46 4.0 12.9 1.0
C A:PRO45 4.2 13.0 1.0
ND2 A:ASN46 4.2 26.9 1.0
CG A:LEU47 4.3 10.5 1.0
CG A:ASN46 4.3 19.2 1.0
CA A:PRO45 4.5 12.8 1.0
O A:HOH2270 4.6 24.1 1.0
N A:CYS44 4.7 9.6 1.0
CG A:PRO45 4.7 13.8 1.0
CA A:LEU47 4.8 10.9 1.0
CD2 A:LEU47 4.9 12.5 1.0
O A:ASN46 4.9 16.1 1.0
CB A:LEU47 4.9 10.6 1.0
O A:GLY43 5.0 12.2 1.0

Sodium binding site 4 out of 7 in 4uys

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Sodium binding site 4 out of 7 in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1210

b:25.1
occ:1.00
 O A:HOH2257 2.7 41.4 1.0
O A:HOH2236 2.8 18.2 1.0
OD1 A:ASP174 2.8 13.0 1.0
OE2 A:GLU153 3.2 20.8 1.0
C A:PHE173 3.6 8.4 1.0
N A:PHE173 3.6 8.9 1.0
CG A:ASP174 3.6 12.4 1.0
CA A:PHE173 3.7 8.7 1.0
O A:PHE173 3.7 9.9 1.0
CG A:GLN151 3.8 8.4 1.0
OG A:SER172 3.8 12.0 0.5
N A:ASP174 3.9 8.4 1.0
NE2 A:GLN151 4.0 13.9 1.0
C A:SER172 4.0 8.7 0.5
CD A:GLN151 4.0 10.4 1.0
OD2 A:ASP174 4.1 15.2 1.0
C A:SER172 4.1 9.7 0.5
CD A:GLU153 4.2 14.9 1.0
O A:SER172 4.3 9.9 0.5
O A:PHE152 4.6 9.5 1.0
CB A:ASP174 4.6 10.4 1.0
OE1 A:GLU153 4.6 16.9 1.0
O A:SER172 4.7 8.9 0.5
CB A:SER172 4.7 12.8 0.5
O A:HOH2258 4.7 35.3 1.0
CA A:ASP174 4.7 8.9 1.0
CA A:SER172 4.8 10.6 0.5
CA A:SER172 4.8 10.2 0.5
OE1 A:GLN151 4.9 11.5 1.0
CB A:SER172 4.9 11.7 0.5
CB A:GLN151 4.9 8.0 1.0

Sodium binding site 5 out of 7 in 4uys

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Sodium binding site 5 out of 7 in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1211

b:39.4
occ:1.00
 N A:SER140 3.2 14.3 1.0
OG A:SER140 3.5 27.0 1.0
CB A:ASN139 3.6 13.1 1.0
CB A:SER140 3.7 19.6 1.0
CA A:ASN139 3.9 12.0 1.0
C A:ASN139 4.0 11.5 1.0
O A:HOH2223 4.0 34.2 1.0
CA A:SER140 4.0 15.7 1.0
CG A:ASN139 4.7 12.5 1.0

Sodium binding site 6 out of 7 in 4uys

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Sodium binding site 6 out of 7 in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1212

b:42.9
occ:1.00
 O A:HOH2106 2.4 24.5 1.0
OG1 A:THR79 2.7 10.5 1.0
OG A:SER67 3.1 13.1 0.3
NE2 A:GLN77 3.1 16.9 1.0
OG A:SER67 3.5 13.6 0.3
O A:HOH2107 3.5 30.0 1.0
CB A:SER67 3.8 7.8 0.3
CB A:SER67 3.8 10.0 0.3
CG A:GLN77 3.8 10.9 1.0
CB A:THR79 3.9 9.0 1.0
CG2 A:THR129 3.9 11.1 1.0
CD A:GLN77 4.0 14.1 1.0
N A:THR79 4.0 8.1 1.0
C A:ILE78 4.1 8.0 1.0
O A:GLN77 4.2 8.9 1.0
O A:SER67 4.3 7.1 0.3
CB A:SER67 4.3 10.6 0.3
C A:GLN77 4.4 7.9 1.0
O A:ILE78 4.4 8.6 1.0
OG1 A:THR129 4.5 11.2 1.0
CA A:THR79 4.5 8.1 1.0
CA A:ILE78 4.5 8.0 1.0
OG A:SER67 4.6 10.5 0.3
O A:SER67 4.6 8.9 0.3
CB A:GLN77 4.6 9.2 1.0
N A:ILE78 4.6 7.6 1.0
O A:SER67 4.6 8.3 0.3
C A:SER67 4.6 8.4 0.3
C A:SER67 4.7 8.8 0.3
C A:SER67 4.7 8.2 0.3
OG A:SER69 4.8 11.9 1.0
CB A:THR129 4.9 10.1 1.0
CA A:SER67 4.9 8.0 0.3
O A:HOH2010 4.9 24.1 1.0
CA A:SER67 4.9 8.9 0.3

Sodium binding site 7 out of 7 in 4uys

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Sodium binding site 7 out of 7 in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO11 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1213

b:35.9
occ:1.00
 O A:HOH2287 2.6 30.0 1.0
O A:ILE120 2.7 15.1 1.0
O A:HOH2286 3.6 30.0 1.0
C A:ILE120 3.6 12.6 1.0
O A:TYR118 3.7 16.7 1.0
CB A:TYR118 3.7 14.6 1.0
C A:TYR118 3.7 12.6 1.0
CE1 A:TYR111 3.8 12.6 1.0
CA A:TYR118 4.0 11.5 1.0
CD2 A:LEU90 4.0 13.7 1.0
CD1 A:TYR111 4.1 11.1 1.0
CA A:ASP121 4.1 14.2 1.0
N A:ILE120 4.2 11.4 1.0
N A:ASP121 4.3 11.6 1.0
N A:LEU119 4.4 12.0 1.0
CB A:ASP121 4.4 19.7 1.0
CA A:ILE120 4.6 11.6 1.0
CG A:TYR118 4.8 15.0 1.0
C A:LEU119 4.8 13.8 1.0
CD1 A:TYR118 4.9 17.4 1.0
CZ A:TYR111 5.0 13.2 1.0

Reference:

T.Kraushaar, S.Bruckner, M.Veelders, D.Rhinow, F.Schreiner, R.Birke, A.Pagenstecher, H.Mosch, L.Essen. Interactions By the Fungal FLO11 Adhesin Depend on A Fibronectin Type III-Like Adhesin Domain Girdled By Aromatic Bands. Structure V. 23 1005 2015.
ISSN: ISSN 0969-2126
PubMed: 25960408
DOI: 10.1016/J.STR.2015.03.021
Page generated: Mon Oct 7 18:47:52 2024

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