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Sodium in PDB 4m4s: Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi)

Protein crystallography data

The structure of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi), PDB code: 4m4s was solved by O.S.Nikonov, E.A.Stolboushkina, V.I.Arkhipova, A.G.Gabdulkhakov, A.D.Nikulin, M.B.Garber, S.V.Nikonov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.73 / 2.25
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 142.860, 142.860, 218.410, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 18.2

Other elements in 4m4s:

The structure of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi) (pdb code 4m4s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi), PDB code: 4m4s:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4m4s

Go back to Sodium Binding Sites List in 4m4s
Sodium binding site 1 out of 4 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na533

b:46.0
occ:0.87
O A:GLU66 2.5 35.9 1.0
O A:HOH922 2.5 55.6 1.0
O A:TYR68 2.6 37.4 0.9
OG A:SER76 2.7 58.6 0.9
O A:HOH921 2.9 50.1 1.0
C A:GLU66 3.4 39.2 0.8
CB A:SER76 3.7 53.5 0.8
C A:TYR68 3.7 36.0 1.0
CG1 A:VAL69 3.7 35.6 1.0
CA A:GLU66 3.9 33.0 1.0
CB A:ASP192 4.4 31.5 1.0
CB A:GLU66 4.4 47.3 1.0
N A:TYR68 4.4 38.3 1.0
CA A:VAL69 4.5 36.1 0.9
C A:SER76 4.5 64.8 0.5
N A:ALA67 4.6 41.2 1.0
N A:VAL69 4.6 33.4 0.9
O A:SER76 4.6 60.0 1.0
C A:ALA67 4.6 41.7 0.7
O A:HOH741 4.7 44.0 1.0
CA A:TYR68 4.7 38.2 0.9
OD2 A:ASP192 4.7 50.0 1.0
CA A:SER76 4.7 61.4 1.0
CB A:VAL69 4.8 42.2 1.0
O A:PRO65 4.8 36.4 1.0
N A:CYS77 4.9 63.0 1.0
CA A:ALA67 5.0 38.6 1.0
O A:ALA67 5.0 36.7 1.0

Sodium binding site 2 out of 4 in 4m4s

Go back to Sodium Binding Sites List in 4m4s
Sodium binding site 2 out of 4 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na534

b:30.1
occ:0.81
O A:VAL151 2.3 26.8 0.9
O A:HOH657 2.4 34.4 1.0
O A:VAL154 2.5 25.9 1.0
C A:VAL151 3.4 29.6 0.9
O A:HOH697 3.6 36.2 0.9
C A:VAL154 3.7 27.5 0.9
N A:ASP152 4.3 25.1 1.0
CA A:VAL151 4.3 27.8 0.9
CB A:VAL151 4.3 24.5 1.0
CA A:ASP152 4.4 25.2 0.9
N A:VAL154 4.4 22.6 0.9
CG2 A:VAL154 4.4 25.7 1.0
C A:SER155 4.5 27.3 0.9
C A:ASP152 4.6 26.1 1.0
CA A:SER155 4.6 29.8 0.9
N A:SER155 4.6 29.7 0.9
CA A:VAL154 4.6 23.4 1.0
O A:SER155 4.6 24.7 1.0
O A:ASP152 4.8 28.2 0.8
N A:LYS156 4.9 24.3 1.0
CG2 A:VAL151 5.0 27.3 1.0

Sodium binding site 3 out of 4 in 4m4s

Go back to Sodium Binding Sites List in 4m4s
Sodium binding site 3 out of 4 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na535

b:40.4
occ:0.74
O A:HOH613 2.3 30.1 1.0
O A:HOH720 2.3 43.7 0.9
O A:HOH779 2.4 52.6 1.0
O A:MET111 2.4 25.7 0.9
O A:HOH1004 2.5 55.5 1.0
O A:HOH675 2.6 36.6 1.0
O A:HOH1017 3.1 39.5 0.6
O A:HOH1005 3.2 56.1 1.0
C A:MET111 3.6 28.1 0.8
O A:HOH761 4.0 49.1 1.0
CA A:ASP112 4.4 28.2 0.9
OD1 A:ASP112 4.4 28.8 0.9
N A:ASP112 4.4 23.0 1.0
O A:HOH879 4.4 52.3 1.0
O A:ALA109 4.4 28.2 0.9
N A:MET111 4.5 31.8 0.9
CG2 A:VAL141 4.6 28.4 1.0
CA A:MET111 4.6 27.6 0.9
O A:HOH789 4.7 41.7 1.0
O A:HOH767 4.7 42.9 0.8
O A:HOH686 4.8 35.0 1.0
O A:ALA108 4.9 24.8 1.0
O A:HOH799 4.9 60.9 1.0
C A:LEU110 4.9 27.5 1.0

Sodium binding site 4 out of 4 in 4m4s

Go back to Sodium Binding Sites List in 4m4s
Sodium binding site 4 out of 4 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion Mimic AIF2GAMMA*Gdp*Pi Complex (A Formate Ion Substitutes For Pi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na536

b:32.6
occ:0.89
O A:HOH683 2.4 40.0 1.0
O A:HOH653 2.4 28.2 0.9
OG1 A:THR54 2.4 26.6 0.9
O A:HOH638 2.4 25.9 0.9
O A:HOH630 2.4 32.1 1.0
O A:THR70 2.4 37.4 0.9
CB A:THR54 3.4 30.8 0.9
C A:THR70 3.6 39.3 0.9
CB A:THR70 4.0 30.4 0.8
CA A:THR54 4.0 25.3 1.0
OG1 A:THR70 4.1 31.8 0.9
O A:THR30 4.2 28.4 0.9
O1 A:FMT512 4.2 39.2 0.9
N A:ASN55 4.3 25.2 0.9
C A:FMT512 4.4 41.6 0.6
CA A:THR70 4.4 32.4 1.0
O A:ASN55 4.4 28.3 0.9
O A:ILE29 4.6 24.2 1.0
C A:THR54 4.6 26.2 0.8
N A:GLU71 4.7 36.6 1.0
CG2 A:THR54 4.7 22.1 1.0
O2 A:FMT522 4.7 40.4 0.9
CA A:THR30 4.7 24.6 0.8
C A:THR30 4.7 27.9 0.8
O A:GLU53 4.7 24.3 0.9
O A:HOH836 4.7 44.4 1.0
CB A:GLU71 4.8 44.8 1.0
CA A:GLU71 4.9 39.9 1.0
O1 A:FMT522 4.9 59.7 1.0

Reference:

O.Nikonov, E.Stolboushkina, V.Arkhipova, O.Kravchenko, S.Nikonov, M.Garber. Conformational Transitions in the Gamma Subunit of the Archaeal Translation Initiation Factor 2 Acta Crystallogr.,Sect.D V. 70 658 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004713032240
Page generated: Tue Dec 15 06:53:10 2020

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