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Sodium in PDB 2yoi: Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period

Enzymatic activity of Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period

All present enzymatic activity of Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period:
1.8.1.9;

Protein crystallography data

The structure of Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period, PDB code: 2yoi was solved by J.A.Gavira, A.Ingles-Prieto, B.Ibarra-Molero, J.M.Sanchez-Ruiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.583 / 1.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 58.366, 47.772, 73.836, 90.00, 98.49, 90.00
R / Rfree (%) 15.6 / 18.44

Other elements in 2yoi:

The structure of Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period (pdb code 2yoi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period, PDB code: 2yoi:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2yoi

Go back to Sodium Binding Sites List in 2yoi
Sodium binding site 1 out of 3 in the Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period


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 Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1108

b:31.7
occ:1.00
 O A:HOH2064 2.7 16.4 0.8
O A:HOH2051 2.9 13.0 0.6
HA A:ALA18 2.9 18.6 1.0
O A:HOH2220 3.0 34.2 0.8
HG22 A:VAL53 3.1 21.0 1.0
HB3 A:ALA18 3.4 21.3 1.0
HB2 A:ALA18 3.6 21.3 1.0
CA A:ALA18 3.8 15.5 1.0
CB A:ALA18 3.8 17.8 1.0
CG2 A:VAL53 3.9 17.5 1.0
O A:HOH2057 3.9 41.0 0.9
H A:ASP19 4.0 21.7 1.0
HG23 A:VAL53 4.0 21.0 1.0
HG21 A:VAL53 4.2 21.0 1.0
O A:HOH2069 4.3 44.9 1.0
HD2 A:LYS20 4.5 28.8 1.0
H A:LYS20 4.5 18.0 1.0
O A:HOH2023 4.5 22.7 0.6
HG12 A:VAL53 4.5 16.6 1.0
N A:ALA18 4.6 17.9 1.0
N A:ASP19 4.6 18.1 1.0
O A:HOH2059 4.6 21.6 0.9
HB2 A:LYS20 4.7 21.9 1.0
HB1 A:ALA18 4.7 21.3 1.0
C A:ALA18 4.8 19.1 1.0
HG21 A:ILE14 4.8 18.4 1.0
O A:GLU17 4.9 19.9 1.0

Sodium binding site 2 out of 3 in 2yoi

Go back to Sodium Binding Sites List in 2yoi
Sodium binding site 2 out of 3 in the Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period


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 Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1109

b:22.2
occ:1.00
 H A:PHE54 2.2 9.0 1.0
O A:MET1 2.7 16.8 1.0
HD1 A:PHE54 3.0 11.5 1.0
HB2 A:PHE54 3.0 9.1 1.0
HA A:VAL53 3.0 11.8 1.0
O A:HOH2221 3.0 23.9 0.7
O A:HOH2124 3.0 12.8 0.4
N A:PHE54 3.0 7.5 1.0
O A:HOH2003 3.6 41.1 1.0
HG12 A:ILE3 3.6 15.7 0.2
O A:PHE54 3.7 8.2 1.0
CB A:PHE54 3.7 7.6 1.0
HG13 A:ILE3 3.8 16.8 0.8
CD1 A:PHE54 3.8 9.6 1.0
HG11 A:VAL53 3.8 16.6 1.0
CA A:VAL53 3.8 9.8 1.0
CA A:PHE54 3.8 6.6 1.0
HB2 A:MET1 3.8 24.0 0.3
C A:MET1 3.9 11.3 1.0
HB2 A:SER45 3.9 11.6 1.0
C A:VAL53 3.9 9.6 1.0
H1 A:MET1 4.0 22.5 0.7
HD12 A:ILE3 4.0 20.6 0.8
HD13 A:ILE3 4.1 20.6 0.8
H2 A:MET1 4.1 22.5 0.3
O A:HOH2068 4.1 21.6 0.7
HA A:VAL2 4.1 9.8 1.0
O A:VAL52 4.2 13.8 1.0
C A:PHE54 4.2 6.6 1.0
CG A:PHE54 4.2 9.6 1.0
HB3 A:MET1 4.3 22.9 0.7
CD1 A:ILE3 4.4 17.1 0.8
CG1 A:ILE3 4.5 13.0 0.2
HD12 A:ILE3 4.5 18.8 0.2
CG1 A:VAL53 4.5 13.8 1.0
CB A:MET1 4.5 20.0 0.3
HB3 A:MET1 4.5 24.0 0.3
HG13 A:VAL53 4.5 16.6 1.0
H A:ILE3 4.5 8.8 1.0
HB3 A:PHE54 4.5 9.1 1.0
CG1 A:ILE3 4.6 14.0 0.8
CA A:MET1 4.6 14.5 0.3
HG13 A:ILE3 4.6 15.7 0.2
N A:MET1 4.7 18.7 1.0
CB A:VAL53 4.7 12.3 1.0
HA A:PHE54 4.7 8.0 1.0
CA A:MET1 4.7 13.2 0.7
HG23 A:VAL53 4.7 21.0 1.0
N A:VAL2 4.8 11.2 1.0
H1 A:MET1 4.8 22.5 0.3
N A:VAL53 4.8 10.1 1.0
CB A:SER45 4.8 9.6 1.0
CA A:VAL2 4.9 8.2 1.0
HA A:PRO49 4.9 32.4 1.0
C A:VAL52 4.9 11.0 1.0
H3 A:MET1 4.9 22.5 0.7
CD1 A:ILE3 4.9 15.7 0.2
CE1 A:PHE54 4.9 14.1 1.0
CB A:MET1 5.0 19.1 0.7

Sodium binding site 3 out of 3 in 2yoi

Go back to Sodium Binding Sites List in 2yoi
Sodium binding site 3 out of 3 in the Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period


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 Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (Leca) From the Precambrian Period within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1107

b:34.4
occ:1.00
 O B:HOH2198 2.9 6.4 0.3
HG2 B:PRO106 2.9 29.6 1.0
O B:HOH2193 3.0 24.3 0.7
O B:HOH2199 3.0 31.8 1.0
HD2 B:PRO106 3.2 20.3 1.0
CG B:PRO106 3.7 24.6 1.0
CD B:PRO106 3.9 16.9 1.0
HG3 B:PRO106 3.9 29.6 1.0
O B:HOH2121 4.2 17.3 1.0
O B:HOH2194 4.5 11.7 0.5
HD3 B:PRO106 4.6 20.3 1.0
O B:HOH2190 4.7 11.8 0.3
HA B:ALA105 4.7 17.0 1.0
O B:PRO106 4.7 25.2 1.0
O B:HOH2146 4.7 33.6 1.0
N B:PRO106 4.8 19.2 1.0
CB B:PRO106 4.9 25.4 1.0
HB2 B:PRO106 5.0 30.5 1.0

Reference:

A.Ingles-Prieto, B.Ibarra-Molero, A.Delgado-Delgado, R.Perez-Jimenez, J.M.Fernandez, E.A.Gaucher, J.M.Sanchez-Ruiz, J.A.Gavira. Conservation of Protein Structure Over Four Billion Years Structure V. 21 1690 2013.
ISSN: ISSN 0969-2126
PubMed: 23932589
DOI: 10.1016/J.STR.2013.06.020
Page generated: Mon Oct 7 05:27:38 2024

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