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Sodium in PDB 2ux9: Crystal Structure of the T. Thermophilus Dodecin R65A Mutant

Protein crystallography data

The structure of Crystal Structure of the T. Thermophilus Dodecin R65A Mutant, PDB code: 2ux9 was solved by B.Meissner, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.88 / 1.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.585, 67.585, 169.188, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the T. Thermophilus Dodecin R65A Mutant (pdb code 2ux9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the T. Thermophilus Dodecin R65A Mutant, PDB code: 2ux9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2ux9

Go back to Sodium Binding Sites List in 2ux9
Sodium binding site 1 out of 4 in the Crystal Structure of the T. Thermophilus Dodecin R65A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the T. Thermophilus Dodecin R65A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1068

b:63.5
occ:1.00
O A:HOH2062 2.3 32.5 1.0
O1P A:FMN1069 2.3 18.6 1.0
P A:FMN1069 3.3 19.4 1.0
O3P A:FMN1069 3.4 21.4 1.0
O2P A:FMN1069 3.9 21.1 1.0
CB A:ALA65 3.9 15.2 1.0
ND1 A:HIS35 4.0 20.0 1.0
NZ A:LYS3 4.1 29.5 1.0
CB A:HIS35 4.1 14.6 1.0
CG A:HIS35 4.3 17.4 1.0
OD2 A:ASP37 4.4 15.8 1.0
OD1 A:ASP37 4.4 15.0 1.0
O5' A:FMN1069 4.7 20.9 1.0
CA A:HIS35 4.9 14.3 1.0
CG A:ASP37 4.9 14.7 1.0
CE1 A:HIS35 4.9 19.2 1.0

Sodium binding site 2 out of 4 in 2ux9

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Sodium binding site 2 out of 4 in the Crystal Structure of the T. Thermophilus Dodecin R65A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the T. Thermophilus Dodecin R65A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1071

b:34.1
occ:1.00
O C:HOH2063 1.7 33.8 1.0
O C:HOH2062 1.9 34.3 1.0
OE2 C:GLU55 2.3 23.9 1.0
CD C:GLU55 2.9 21.3 1.0
OE1 C:GLU55 3.0 24.8 1.0
O C:HOH2013 3.3 40.0 1.0
O C:HOH2005 3.5 50.5 1.0
OG1 C:THR13 3.8 14.2 1.0
O C:HOH2015 3.9 30.7 1.0
CG C:GLU55 4.2 18.8 1.0
CG C:GLU15 4.5 18.9 1.0
CB C:THR13 4.9 12.9 1.0
N C:GLU15 4.9 15.2 1.0
CA C:SER14 4.9 14.1 1.0

Sodium binding site 3 out of 4 in 2ux9

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Sodium binding site 3 out of 4 in the Crystal Structure of the T. Thermophilus Dodecin R65A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the T. Thermophilus Dodecin R65A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1072

b:63.6
occ:1.00
O1P C:FMN1073 2.1 21.1 1.0
O C:HOH2044 2.3 58.0 1.0
O C:HOH2079 2.4 46.8 1.0
O C:HOH2077 2.9 43.3 1.0
O3P C:FMN1073 3.0 25.1 1.0
P C:FMN1073 3.1 23.6 1.0
OD1 C:ASP37 3.6 16.5 1.0
ND1 C:HIS35 3.8 20.7 1.0
OD2 C:ASP37 3.9 16.7 1.0
O2P C:FMN1073 4.0 24.6 1.0
NZ C:LYS3 4.2 30.9 1.0
CG C:ASP37 4.2 15.2 1.0
CB C:HIS35 4.2 13.1 1.0
O5' C:FMN1073 4.2 23.4 1.0
CB C:ALA65 4.3 13.8 1.0
CG C:HIS35 4.4 15.9 1.0
CA C:HIS35 4.8 12.8 1.0
CE1 C:HIS35 4.8 22.3 1.0
O C:HIS35 4.9 13.2 1.0

Sodium binding site 4 out of 4 in 2ux9

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Sodium binding site 4 out of 4 in the Crystal Structure of the T. Thermophilus Dodecin R65A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the T. Thermophilus Dodecin R65A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1072

b:55.0
occ:1.00
O F:HOH2050 2.1 32.5 1.0
O1P E:FMN1070 2.2 16.9 1.0
O F:HOH2007 2.2 40.3 1.0
P E:FMN1070 3.2 18.6 1.0
O3P E:FMN1070 3.2 21.7 1.0
O2P E:FMN1070 3.9 22.0 1.0
ND1 F:HIS35 4.0 20.0 1.0
CB F:HIS35 4.1 13.7 1.0
CB F:ALA65 4.1 12.8 1.0
NZ F:LYS3 4.1 23.2 0.5
OD1 F:ASP37 4.1 15.1 1.0
OD2 F:ASP37 4.2 15.6 1.0
O F:HOH2048 4.4 34.8 1.0
CG F:HIS35 4.4 15.5 1.0
O5' E:FMN1070 4.5 18.4 1.0
O F:HOH2072 4.6 33.5 1.0
CG F:ASP37 4.6 13.6 1.0
CA F:HIS35 4.8 13.1 1.0

Reference:

B.Meissner, E.Schleicher, S.Weber, L.-O.Essen. The Dodecin From Thermus Thermophilus, A Bifunctional Cofactor Storage Protein. J.Biol.Chem. V. 282 33142 2007.
ISSN: ISSN 0021-9258
PubMed: 17855371
DOI: 10.1074/JBC.M704951200
Page generated: Tue Dec 15 05:56:11 2020

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