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Magnesium 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:

Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2yoi

Go back to Magnesium Binding Sites List in 2yoi
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg1110

b:30.3
occ:1.00
 HG1 A:THR29 2.2 20.1 1.0
O A:HOH2143 2.6 19.9 1.0
O A:HOH2137 2.6 11.3 0.6
OG1 A:THR29 2.6 16.8 1.0
O A:HOH2222 2.7 37.3 1.0
O A:HOH2080 3.2 10.2 0.9
HG22 A:THR29 3.5 17.6 1.0
HG21 A:THR29 3.6 17.6 1.0
CB A:THR29 3.8 13.4 1.0
CG2 A:THR29 3.8 14.7 1.0
HD1 A:TRP30 3.8 11.8 1.0
HB3 B:PRO63 3.9 16.4 1.0
HG3 B:PRO63 3.9 17.2 1.0
HB2 A:ASP60 4.0 13.1 1.0
H A:THR29 4.1 10.8 1.0
O A:HOH2084 4.1 23.2 0.9
OD2 A:ASP60 4.2 13.4 1.0
HB A:THR29 4.3 16.1 1.0
O A:HOH2141 4.3 39.0 0.8
OD1 B:ASP60 4.3 22.9 0.7
OE2 A:GLU61 4.5 21.6 0.5
O A:HOH2039 4.5 36.3 1.0
CB B:PRO63 4.5 13.7 1.0
HB2 B:PRO63 4.6 16.4 1.0
HB3 A:ASP60 4.6 13.1 1.0
HA B:ASP60 4.6 25.4 0.7
HA B:ASP60 4.6 25.4 0.3
CB A:ASP60 4.6 10.9 1.0
CG B:PRO63 4.7 14.3 1.0
CD1 A:TRP30 4.7 9.8 1.0
HG23 A:THR29 4.8 17.6 1.0
OD2 A:ASP58 4.8 15.8 1.0
N A:THR29 4.8 9.0 1.0
CA A:THR29 4.8 11.3 1.0
CG A:ASP60 4.9 10.5 1.0

Magnesium binding site 2 out of 2 in 2yoi

Go back to Magnesium Binding Sites List in 2yoi
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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:Mg1112

b:19.8
occ:1.00
 O A:HOH2225 2.2 21.5 0.8
O A:HOH2224 2.2 13.7 0.5
O A:HOH2116 2.4 23.1 1.0
O A:HOH2136 3.9 13.7 0.5
HZ2 A:LYS56 4.0 22.8 1.0
OE2 A:GLU42 4.1 20.0 1.0
HZ1 A:LYS56 4.2 22.8 1.0
O A:HOH2008 4.3 15.2 0.9
O A:HOH2117 4.3 11.0 0.6
O A:HOH2002 4.4 36.7 0.8
O A:HOH2001 4.4 29.0 0.8
OE1 A:GLU42 4.4 20.2 1.0
CD A:GLU42 4.5 18.1 1.0
O A:HOH2007 4.5 18.5 0.9
O A:HOH2115 4.5 25.4 0.9
NZ A:LYS56 4.6 19.0 1.0
O A:HOH2118 4.8 16.1 0.5

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: Sun Aug 10 16:46:50 2025

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