Sodium in PDB 6r8t: Crystal Structure of AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp

Protein crystallography data

The structure of Crystal Structure of AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp, PDB code: 6r8t was solved by O.Kravchenko, V.Arkhipova, A.Gabdulkhakov, E.Stolboushkina, O.Nikonov, M.Garber, S.Nikonov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.39 / 2.10
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 186.585, 186.585, 186.585, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.6

Other elements in 6r8t:

The structure of Crystal Structure of AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp (pdb code 6r8t). 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 AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp, PDB code: 6r8t:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6r8t

Go back to Sodium Binding Sites List in 6r8t
Sodium binding site 1 out of 3 in the Crystal Structure of AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp


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 AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na526

b:24.7
occ:1.00
O A:HOH1078 2.4 36.8 1.0
O A:HOH970 2.5 33.7 1.0
O A:LYS171 2.6 19.7 1.0
O A:GLN168 2.6 16.7 1.0
O A:PHE169 2.7 12.1 1.0
C A:PHE169 3.3 14.8 1.0
C A:LYS171 3.6 20.9 1.0
C A:GLN168 3.7 14.8 1.0
N A:LYS171 3.7 16.1 1.0
CA A:PHE169 3.7 15.5 1.0
O A:HOH1215 3.7 33.2 1.0
O A:HOH972 3.8 26.8 1.0
O A:HOH890 4.0 22.9 1.0
CA A:LYS171 4.0 18.5 1.0
N A:PHE169 4.2 14.2 1.0
N A:THR170 4.2 11.3 1.0
C A:THR170 4.2 18.0 1.0
CB A:LYS171 4.3 21.7 1.0
O A:HOH907 4.3 23.8 1.0
O A:HOH1049 4.4 46.0 1.0
CG2 A:THR173 4.6 16.9 1.0
O A:HOH1075 4.6 42.6 1.0
CA A:THR170 4.6 13.3 1.0
N A:GLY172 4.8 20.2 1.0
O A:THR170 4.8 15.6 1.0
CA A:GLN168 5.0 13.7 1.0

Sodium binding site 2 out of 3 in 6r8t

Go back to Sodium Binding Sites List in 6r8t
Sodium binding site 2 out of 3 in the Crystal Structure of AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp


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 AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na527

b:33.1
occ:1.00
O A:MET111 2.3 17.3 1.0
O A:HOH776 2.5 16.6 1.0
O A:HOH1208 2.5 23.8 1.0
O A:HOH909 2.6 19.0 1.0
O A:HOH1032 2.7 23.8 1.0
O A:HOH781 2.7 28.1 1.0
O A:HOH1207 2.8 26.9 1.0
O A:HOH923 3.2 33.1 1.0
C A:MET111 3.4 14.4 1.0
O A:HOH1150 4.1 36.1 1.0
N A:ASP112 4.2 11.5 1.0
CA A:ASP112 4.2 13.6 1.0
O A:HOH1223 4.3 50.5 1.0
N A:MET111 4.4 12.9 1.0
O A:HOH1198 4.4 36.5 1.0
OD1 A:ASP112 4.4 15.3 1.0
CA A:MET111 4.4 14.9 1.0
O A:HOH630 4.5 55.9 1.0
O A:HOH1200 4.5 34.3 1.0
O A:ALA109 4.6 16.7 1.0
O A:HOH908 4.6 25.8 1.0
O A:HOH873 4.7 21.4 1.0
O A:HOH1175 4.8 30.2 1.0
CG2 A:VAL141 4.8 11.7 1.0
O A:ALA108 4.8 11.8 1.0
C A:LEU110 4.9 17.7 1.0
O A:HOH852 5.0 19.7 1.0
C A:ASP112 5.0 14.1 1.0

Sodium binding site 3 out of 3 in 6r8t

Go back to Sodium Binding Sites List in 6r8t
Sodium binding site 3 out of 3 in the Crystal Structure of AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp


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 AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na528

b:11.8
occ:1.00
O A:VAL151 2.3 11.4 1.0
O A:VAL154 2.3 10.9 1.0
O A:HOH1101 2.4 13.6 1.0
C A:VAL151 3.3 11.6 1.0
C A:VAL154 3.5 9.6 1.0
C A:SER155 4.0 15.6 1.0
CB A:VAL151 4.0 14.9 1.0
CA A:VAL151 4.1 10.8 1.0
N A:LYS156 4.2 11.8 1.0
O A:SER155 4.2 15.4 1.0
N A:ASP152 4.2 9.6 1.0
CA A:SER155 4.3 16.3 1.0
N A:VAL154 4.3 10.4 1.0
N A:SER155 4.4 11.1 1.0
CA A:ASP152 4.4 13.7 1.0
CG2 A:VAL154 4.5 10.4 1.0
CG2 A:VAL151 4.5 12.9 1.0
CA A:VAL154 4.5 13.7 1.0
C A:ASP152 4.6 13.7 1.0
CA A:LYS156 4.7 16.7 1.0
O A:HOH1187 4.8 15.2 1.0
O A:ASP152 4.9 13.2 1.0

Reference:

O.Nikonov, O.Kravchenko, E.Stolboushkina, N.Nevskaya, M.Garber, S.Nikonov. Crystal Structure of AIF2GAMMA Subunit I181T From Archaeon Sulfolobus Solfataricus Complexed with Gdpcp To Be Published.
Page generated: Tue Dec 15 12:52:13 2020

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