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Sodium in PDB 4m53: Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp

Protein crystallography data

The structure of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp, PDB code: 4m53 was solved by O.S.Nikonov, E.A.Stolboushkina, V.I.Arkhipova, A.M.Lazopulo, S.M.Lazopulo, 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) 19.70 / 2.00
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 186.891, 186.891, 186.891, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.4

Other elements in 4m53:

The structure of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

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 Gdpcp (pdb code 4m53). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp, PDB code: 4m53:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 4m53

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Sodium binding site 1 out of 9 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp


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 Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na528

b:26.7
occ:0.88
 O A:HOH685 2.4 26.7 1.0
OG1 A:THR54 2.4 17.6 0.9
O A:HOH658 2.5 22.3 0.8
O A:HOH655 2.6 23.3 1.0
O A:THR70 2.7 29.2 1.0
O A:HOH1103 3.0 50.9 1.0
O A:HOH1037 3.2 50.0 1.0
CB A:THR54 3.3 19.7 0.9
CB A:THR70 3.7 24.8 1.0
C A:THR70 3.8 30.6 1.0
O2 A:FMT521 3.9 36.5 0.5
OG1 A:THR70 4.0 26.5 1.0
O A:THR30 4.0 17.8 0.9
CA A:THR54 4.0 16.7 0.9
N A:ASN55 4.3 19.1 0.9
CA A:THR70 4.3 27.3 1.0
O A:ASN55 4.4 16.9 0.9
C A:THR30 4.6 18.5 0.9
CA A:THR30 4.6 15.8 0.9
CG2 A:THR54 4.6 11.3 0.9
O1 A:FMT514 4.6 39.8 0.7
C A:THR54 4.6 17.4 0.9
O A:ILE29 4.7 20.3 1.0
O A:HOH895 4.7 49.2 1.0
O1 A:FMT517 4.8 31.7 0.7
CG2 A:THR70 4.8 19.4 1.0
C A:FMT521 4.8 34.0 0.5
O A:GLU53 4.9 14.1 0.9
O1 A:FMT521 4.9 24.9 0.7
O2 A:FMT514 4.9 30.2 0.8
N A:GLU71 5.0 21.0 0.9

Sodium binding site 2 out of 9 in 4m53

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Sodium binding site 2 out of 9 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp


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 Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na529

b:22.3
occ:0.72
 O A:VAL323 2.4 19.9 0.9
O A:HOH661 2.5 26.8 0.9
O A:HOH623 2.5 14.8 0.9
O A:HOH1163 2.6 26.0 0.9
O A:HOH682 2.6 29.3 1.0
O A:HOH905 2.6 34.6 0.8
C A:VAL323 3.3 17.1 0.9
O2 A:FMT512 4.0 17.4 0.8
CA A:PRO324 4.0 16.2 0.9
N A:PRO324 4.0 19.0 0.9
N A:VAL323 4.1 17.6 0.9
N A:VAL325 4.2 15.9 1.0
O A:HOH678 4.2 17.6 0.9
O A:HOH665 4.3 20.4 0.9
CA A:VAL323 4.3 13.9 0.9
C A:PRO324 4.5 21.2 0.9
CG2 A:VAL325 4.6 13.8 1.0
O A:HOH1164 4.7 39.2 1.0
O A:HOH836 4.9 22.8 0.8
CB A:VAL325 5.0 19.5 1.0

Sodium binding site 3 out of 9 in 4m53

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Sodium binding site 3 out of 9 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp


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 Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na530

b:26.7
occ:0.68
 O A:MET111 2.3 16.8 0.9
O A:HOH611 2.4 15.9 0.9
O A:HOH648 2.5 23.3 0.9
O A:HOH735 2.5 29.5 0.8
O A:HOH693 2.6 24.9 0.7
O A:HOH818 2.7 25.2 0.8
NA A:NA536 2.9 25.3 0.5
O A:HOH935 3.1 49.5 1.0
C A:MET111 3.5 15.7 0.9
O A:HOH899 4.1 39.6 0.9
N A:ASP112 4.3 13.8 0.9
O A:HOH1038 4.3 54.9 1.0
CA A:ASP112 4.3 16.2 0.9
N A:MET111 4.3 14.6 0.9
O A:ALA109 4.4 15.2 0.9
OD1 A:ASP112 4.5 15.8 0.9
CA A:MET111 4.5 14.9 0.9
O A:HOH838 4.5 31.9 1.0
O A:HOH697 4.6 23.7 1.0
O A:HOH998 4.6 50.8 1.0
O A:HOH708 4.7 21.7 0.7
CG2 A:VAL141 4.8 16.7 0.9
O A:ALA108 4.8 11.3 0.9
O A:HOH724 4.8 22.9 0.9
C A:LEU110 4.9 18.4 1.0
O A:HOH860 4.9 37.9 0.8
C A:ALA109 5.0 16.6 0.9

Sodium binding site 4 out of 9 in 4m53

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Sodium binding site 4 out of 9 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp


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 Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na531

b:32.5
occ:0.59
 O A:HOH1193 2.3 33.9 0.8
O A:HOH743 2.4 27.1 0.8
O A:HOH859 2.4 33.9 0.9
O A:HOH851 2.5 41.7 0.8
O A:HOH746 2.6 25.0 0.8
O A:HOH877 2.6 39.6 0.9
NA A:NA534 3.3 34.6 0.5
NA A:NA535 3.6 25.0 0.8
O A:HOH906 3.8 44.5 0.8
O A:HOH762 3.9 29.2 1.0
O A:HOH775 4.1 32.6 0.8
O A:HOH952 4.3 45.6 0.9
O A:HOH712 4.4 21.6 0.9
O A:HOH1157 4.6 51.2 0.9
O A:HOH1002 4.6 43.2 0.9

Sodium binding site 5 out of 9 in 4m53

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Sodium binding site 5 out of 9 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na532

b:24.0
occ:0.83
 O A:TYR68 2.3 21.1 0.9
OD2 A:ASP192 2.4 21.8 0.9
O A:GLU66 2.4 16.7 0.9
O A:HOH737 2.5 34.6 1.0
O A:HOH854 3.4 50.7 0.9
C A:GLU66 3.4 17.1 0.9
C A:TYR68 3.4 26.2 0.9
CG A:ASP192 3.6 43.9 0.9
CA A:GLU66 3.9 20.3 0.9
CG1 A:VAL69 3.9 18.6 0.9
N A:TYR68 4.1 21.5 0.9
O A:HOH908 4.2 34.8 0.8
N A:VAL69 4.3 18.9 0.9
CA A:VAL69 4.3 20.2 0.9
CA A:TYR68 4.4 18.9 0.9
CB A:ASP192 4.4 22.3 0.9
O A:PRO65 4.4 19.7 0.9
C A:ALA67 4.5 22.9 0.8
N A:ALA67 4.5 17.1 0.8
OD1 A:ASP192 4.5 32.4 0.9
O A:HOH728 4.6 29.7 1.0
CB A:GLU66 4.7 25.0 0.9
CB A:VAL69 4.8 24.5 0.9
OG A:SER76 4.8 33.0 0.8
O A:ALA67 4.9 18.6 0.8
CA A:ALA67 4.9 28.4 0.8

Sodium binding site 6 out of 9 in 4m53

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Sodium binding site 6 out of 9 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na533

b:12.8
occ:0.90
 O A:HOH1199 2.3 21.3 0.9
OD1 A:ASN328 2.3 15.1 1.0
O A:HOH1200 2.4 13.9 0.9
CG A:ASN328 3.4 13.9 1.0
CB A:TRP327 3.6 10.6 0.9
ND2 A:ASN328 3.8 12.7 1.0
O A:HOH635 4.1 21.6 1.0
C A:TRP327 4.4 9.1 0.9
O A:TRP327 4.4 14.4 0.9
CG A:TRP327 4.5 16.0 0.9
CA A:TRP327 4.6 12.1 0.9
CB A:ASN328 4.6 17.1 1.0
N A:ASN328 4.7 14.1 1.0
O1 A:FMT518 4.7 15.1 0.7

Sodium binding site 7 out of 9 in 4m53

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Sodium binding site 7 out of 9 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na534

b:34.6
occ:0.45
 O A:HOH851 2.2 41.7 0.8
O A:HOH1244 2.3 54.8 1.0
O A:HOH888 2.3 49.1 0.8
O A:HOH906 2.4 44.5 0.8
O A:HOH1002 2.6 43.2 0.9
O A:HOH877 2.9 39.6 0.9
NA A:NA531 3.3 32.5 0.6
O A:HOH1193 3.8 33.9 0.8
O A:HOH743 4.0 27.1 0.8
O1 A:FMT511 4.3 25.1 0.7
O A:HOH762 4.3 29.2 1.0
NH2 A:ARG338 4.4 46.9 0.9
O A:HOH756 4.4 28.7 0.9
O A:HOH952 4.6 45.6 0.9
O A:HOH975 4.6 58.5 0.9
O A:HOH1172 4.9 44.0 0.9

Sodium binding site 8 out of 9 in 4m53

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Sodium binding site 8 out of 9 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na535

b:25.0
occ:0.76
 O A:HOH1193 2.5 33.9 0.8
O A:LYS171 2.5 19.9 0.9
O A:HOH775 2.6 32.6 0.8
O A:GLN168 2.6 18.0 0.9
O A:PHE169 2.7 15.0 0.9
O A:HOH746 2.8 25.0 0.8
C A:PHE169 3.3 17.5 0.9
NA A:NA531 3.6 32.5 0.6
C A:LYS171 3.6 19.3 0.9
N A:LYS171 3.7 20.3 0.9
O A:HOH762 3.7 29.2 1.0
CA A:PHE169 3.7 16.9 0.9
C A:GLN168 3.7 20.6 0.9
O A:HOH859 3.8 33.9 0.9
O A:HOH871 4.0 29.3 0.9
CA A:LYS171 4.0 24.3 0.9
N A:THR170 4.2 12.4 0.9
C A:THR170 4.2 26.5 0.9
N A:PHE169 4.2 14.1 0.9
O A:HOH952 4.3 45.6 0.9
CB A:LYS171 4.3 21.4 0.9
O A:HOH712 4.4 21.6 0.9
CG2 A:THR173 4.5 23.0 0.9
CA A:THR170 4.6 16.4 0.9
O A:HOH877 4.6 39.6 0.9
O A:THR170 4.8 18.9 0.9
O A:HOH900 4.8 39.1 0.8
N A:GLY172 4.8 19.6 0.8

Sodium binding site 9 out of 9 in 4m53

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Sodium binding site 9 out of 9 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na536

b:25.3
occ:0.50
 O A:HOH838 2.3 31.9 1.0
O A:HOH708 2.4 21.7 0.7
O A:HOH693 2.4 24.9 0.7
O A:HOH735 2.4 29.5 0.8
O A:HOH648 2.5 23.3 0.9
O A:HOH860 2.7 37.9 0.8
NA A:NA530 2.9 26.7 0.7
O A:HOH1038 3.9 54.9 1.0
O A:HOH697 4.1 23.7 1.0
O A:HOH724 4.3 22.9 0.9
O A:HOH995 4.3 36.2 0.7
O A:HOH753 4.5 27.0 0.8
O A:HOH913 4.5 36.5 0.8
O A:ILE243 4.6 22.2 0.9
O A:HOH611 4.6 15.9 0.9
O A:HOH998 4.7 50.8 1.0
OD1 A:ASP112 4.8 15.8 0.9
CB A:ILE243 4.8 17.4 0.9
O A:HOH818 4.8 25.2 0.8
O A:HOH899 4.9 39.6 0.9
O A:HOH935 4.9 49.5 1.0
O A:MET111 4.9 16.8 0.9
O A:ALA109 4.9 15.2 0.9
CG2 A:ILE243 5.0 15.5 0.9

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: Mon Oct 7 16:55:49 2024

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