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Magnesium in PDB 4m0l: Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp

Protein crystallography data

The structure of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp, PDB code: 4m0l was solved by O.S.Nikonov, E.A.Stolboushkina, V.I.Arkhipova, A.G.Gabdulkhakov, A.D.Nikulin, A.M.Lazopulo, S.M.Lazopulo, 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) 19.81 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.050, 106.550, 156.300, 90.00, 90.63, 90.00
R / Rfree (%) 23.4 / 28.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp (pdb code 4m0l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp, PDB code: 4m0l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4m0l

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Magnesium binding site 1 out of 7 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:24.7
occ:0.74
 O A:HOH644 2.1 32.7 0.8
O A:HOH646 2.1 32.9 0.5
O3B A:GDP501 2.1 26.9 0.8
O A:HOH645 2.1 34.0 0.9
O A:HOH632 2.1 32.4 0.8
OG1 A:THR23 2.1 27.4 0.8
CB A:THR23 3.4 26.6 0.8
PB A:GDP501 3.5 35.8 0.8
O A:ALA94 3.9 49.3 0.7
O2B A:GDP501 4.1 33.1 0.8
O2A A:GDP501 4.1 26.6 0.8
OD2 A:ASP93 4.2 37.5 0.7
N A:THR23 4.3 35.1 0.8
CG2 A:THR23 4.3 30.4 0.8
O1B A:GDP501 4.4 34.4 0.8
CA A:THR23 4.4 33.3 0.8
O3A A:GDP501 4.6 36.3 0.8
OD1 A:ASP93 4.6 48.7 0.7
CA A:PRO95 4.7 48.3 0.8
PA A:GDP501 4.7 30.2 0.8
C A:ALA94 4.8 48.0 0.7
CG A:ASP93 4.8 39.9 0.7
O1A A:GDP501 4.9 32.7 0.8

Magnesium binding site 2 out of 7 in 4m0l

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Magnesium binding site 2 out of 7 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:25.7
occ:0.74
 O3B B:GDP501 2.1 33.8 0.7
OG1 B:THR23 2.2 30.7 0.8
O B:HOH622 2.2 32.0 0.8
O B:HOH625 2.3 27.6 0.8
O B:HOH645 2.4 28.6 0.6
CB B:THR23 3.3 39.1 0.8
PB B:GDP501 3.4 32.8 0.7
O2A B:GDP501 3.8 28.7 0.7
O2B B:GDP501 3.9 32.1 0.7
N B:THR23 4.1 34.4 0.8
OD2 B:ASP93 4.1 33.8 0.8
O B:ALA94 4.3 35.4 0.8
CA B:THR23 4.3 37.1 0.8
CG2 B:THR23 4.3 34.4 0.8
OD1 B:ASP93 4.3 45.9 0.8
O1B B:GDP501 4.3 38.6 0.7
O3A B:GDP501 4.4 29.9 0.7
PA B:GDP501 4.4 29.6 0.7
O1A B:GDP501 4.6 30.6 0.7
CG B:ASP93 4.7 37.8 0.8
O B:PRO95 4.8 44.1 0.7
CA B:PRO95 4.9 37.8 0.7
CE B:LYS22 4.9 30.3 0.8
NZ B:LYS22 5.0 31.9 0.8

Magnesium binding site 3 out of 7 in 4m0l

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Magnesium binding site 3 out of 7 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:26.0
occ:0.70
 O C:HOH665 2.1 48.8 0.7
OG1 C:THR23 2.1 28.5 0.8
O C:HOH634 2.1 33.2 0.5
O C:HOH655 2.1 35.8 0.8
O1B C:GDP501 2.2 32.8 0.8
O C:HOH643 2.2 33.5 0.8
CB C:THR23 3.2 30.6 0.8
O2A C:GDP501 3.3 31.2 0.8
PB C:GDP501 3.5 28.8 0.8
O C:ALA94 3.9 34.9 0.8
O3B C:GDP501 4.0 31.2 0.8
N C:THR23 4.1 28.8 0.8
CG2 C:THR23 4.2 34.8 0.8
CA C:THR23 4.2 27.6 0.8
OD2 C:ASP93 4.3 40.9 1.0
OD1 C:ASP93 4.3 40.4 1.0
PA C:GDP501 4.4 26.1 0.8
O3A C:GDP501 4.4 18.3 0.8
O2B C:GDP501 4.5 25.7 0.8
CA C:PRO95 4.7 35.0 0.8
CG C:ASP93 4.7 42.1 1.0
C C:ALA94 4.9 36.2 0.8

Magnesium binding site 4 out of 7 in 4m0l

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Magnesium binding site 4 out of 7 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:30.0
occ:1.00
 O C:HOH630 2.3 48.1 1.0
OG1 C:THR54 2.4 34.8 1.0
OE2 C:GLU71 2.5 44.7 0.7
O C:HOH607 2.9 29.9 0.9
O C:THR70 3.0 41.2 0.7
CD C:GLU71 3.4 43.8 0.7
CB C:THR70 3.6 34.1 0.7
CB C:THR54 3.8 36.9 1.0
OG1 C:THR70 3.8 37.3 0.7
C C:THR70 3.9 36.8 0.7
OE1 C:GLU71 3.9 49.4 0.7
O C:THR30 4.1 40.1 0.7
CA C:THR70 4.4 37.9 0.7
CA C:THR54 4.4 34.5 1.0
CG C:GLU71 4.4 44.3 0.7
N C:ASN55 4.5 32.5 0.7
O C:ASN55 4.8 33.0 0.7
CG2 C:THR70 4.8 29.4 0.7
O C:ILE29 4.8 40.1 0.8
CG2 C:THR54 4.8 35.4 1.0
C C:THR30 4.9 38.3 0.7
N C:GLU71 4.9 38.3 0.7
C C:THR54 5.0 39.7 1.0

Magnesium binding site 5 out of 7 in 4m0l

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Magnesium binding site 5 out of 7 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:33.8
occ:0.67
 O1B D:GDP501 2.1 29.1 0.7
O D:HOH632 2.2 33.6 0.7
OG1 D:THR23 2.2 32.2 0.8
O D:HOH617 2.2 25.9 0.9
O D:HOH631 2.3 29.4 1.0
O2A D:GDP501 3.1 36.5 0.7
CB D:THR23 3.3 35.0 0.8
PB D:GDP501 3.4 29.7 0.7
O3B D:GDP501 3.6 34.0 0.7
CG2 D:THR23 4.1 35.7 0.8
OD2 D:ASP93 4.2 33.6 0.7
O3A D:GDP501 4.3 32.6 0.7
PA D:GDP501 4.3 33.5 0.7
N D:THR23 4.4 29.6 0.8
OG D:SER35 4.4 55.9 0.7
CA D:THR23 4.4 33.9 0.8
O2B D:GDP501 4.5 29.2 0.7
O D:ALA94 4.8 34.9 0.8
OD1 D:ASP93 4.8 38.9 0.7
CG D:ASP93 4.9 34.0 0.7

Magnesium binding site 6 out of 7 in 4m0l

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Magnesium binding site 6 out of 7 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:46.7
occ:0.73
 O E:HOH621 2.2 53.0 0.7
O E:HOH638 2.2 43.9 1.0
OG1 E:THR23 2.3 49.5 0.9
O E:HOH636 2.4 44.4 0.9
O2B E:GDP501 2.5 50.5 0.8
O E:HOH637 2.7 55.4 1.0
O2A E:GDP501 3.0 60.4 0.8
O1B E:GDP501 3.0 51.8 0.8
CB E:THR23 3.2 52.8 0.9
PB E:GDP501 3.3 48.7 0.8
PA E:GDP501 4.0 56.0 0.8
CG2 E:THR23 4.1 55.4 0.9
O3A E:GDP501 4.2 55.5 0.8
OD2 E:ASP93 4.2 48.2 0.8
O E:ALA94 4.3 54.1 0.8
N E:THR23 4.4 54.9 0.9
O E:HOH608 4.4 60.9 0.8
CA E:THR23 4.4 57.9 0.9
O1A E:GDP501 4.5 52.2 0.8
O3B E:GDP501 4.6 41.3 0.8
OD1 E:ASP93 4.8 56.7 0.8
CA E:PRO95 4.9 44.3 0.7
CG E:ASP93 4.9 57.1 0.8

Magnesium binding site 7 out of 7 in 4m0l

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Magnesium binding site 7 out of 7 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:58.2
occ:1.00
 OG1 F:THR23 2.2 56.3 0.8
O1B F:GDP501 2.2 40.2 0.8
O F:HOH615 2.2 52.1 1.0
O F:HOH619 2.2 56.1 1.0
O F:HOH606 2.7 49.0 1.0
CB F:THR23 3.2 47.8 0.8
PB F:GDP501 3.3 40.8 0.8
O3B F:GDP501 3.3 48.1 0.8
O2A F:GDP501 3.9 45.0 0.8
CG2 F:THR23 4.2 51.9 0.8
N F:THR23 4.2 52.2 0.8
O3A F:GDP501 4.3 45.4 0.8
OD2 F:ASP93 4.3 57.0 0.8
CA F:THR23 4.3 48.2 0.8
OD1 F:ASP93 4.3 47.0 0.8
PA F:GDP501 4.3 39.4 0.8
O1A F:GDP501 4.3 47.5 0.8
O2B F:GDP501 4.4 36.0 0.8
O F:ALA94 4.5 61.3 0.8
CG F:ASP93 4.7 55.6 0.8

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 Dec 14 19:11:15 2020

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