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Sodium in PDB 5mse: Gfp Nuclear Transport Receptor Mimic 3B8

Protein crystallography data

The structure of Gfp Nuclear Transport Receptor Mimic 3B8, PDB code: 5mse was solved by T.Huyton, D.Gorlich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.86 / 1.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.401, 73.398, 93.927, 90.00, 93.73, 90.00
R / Rfree (%) 17.4 / 20.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Gfp Nuclear Transport Receptor Mimic 3B8 (pdb code 5mse). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Gfp Nuclear Transport Receptor Mimic 3B8, PDB code: 5mse:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5mse

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Sodium binding site 1 out of 8 in the Gfp Nuclear Transport Receptor Mimic 3B8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gfp Nuclear Transport Receptor Mimic 3B8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:27.2
occ:1.00
 NA A:NA302 2.8 21.6 1.0
NE2 A:HIS169 3.0 19.1 1.0
CE1 A:HIS181 3.5 14.7 1.0
NE2 A:HIS181 3.5 15.1 1.0
OG1 A:THR167 3.6 15.9 1.0
CE1 A:HIS169 3.6 20.1 1.0
O A:THR59 3.7 15.8 1.0
OG1 A:THR62 3.7 16.6 1.0
CZ A:PHE100 3.8 15.7 1.0
CE1 A:PHE100 3.9 15.7 1.0
CB A:ALA179 3.9 17.2 1.0
O A:HOH427 4.0 15.7 1.0
CD2 A:HIS169 4.2 19.1 1.0
C A:THR59 4.3 13.9 1.0
CA A:THR59 4.3 13.5 1.0
O A:HOH420 4.4 82.9 1.0
CG2 A:ILE98 4.4 16.6 1.0
O A:PRO58 4.4 16.1 1.0
CG2 A:THR62 4.5 16.1 1.0
CB A:THR167 4.6 16.9 1.0
CB A:THR62 4.7 15.3 1.0
ND1 A:HIS181 4.7 15.6 1.0
CG2 A:THR167 4.8 17.9 1.0
CD2 A:HIS181 4.8 15.6 1.0
CD1 A:ILE98 4.8 18.1 1.0
ND1 A:HIS169 4.8 17.5 1.0
CE2 A:PHE100 5.0 16.1 1.0

Sodium binding site 2 out of 8 in 5mse

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Sodium binding site 2 out of 8 in the Gfp Nuclear Transport Receptor Mimic 3B8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gfp Nuclear Transport Receptor Mimic 3B8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:21.6
occ:1.00
 O A:PRO58 2.7 16.1 1.0
NA A:NA301 2.8 27.2 1.0
O A:HOH420 3.0 82.9 1.0
N A:THR62 3.0 14.7 1.0
N A:VAL61 3.3 15.2 1.0
OG1 A:THR62 3.3 16.6 1.0
O A:THR59 3.5 15.8 1.0
CG2 A:THR62 3.5 16.1 1.0
C A:THR59 3.5 13.9 1.0
O A:HOH427 3.6 15.7 1.0
CB A:VAL61 3.7 15.9 1.0
CZ A:PHE145 3.8 17.3 1.0
CA A:VAL61 3.8 15.3 1.0
CB A:THR62 3.8 15.3 1.0
CE1 A:HIS169 3.8 20.1 1.0
C A:PRO58 3.9 13.4 1.0
C A:VAL61 3.9 15.9 1.0
CE1 A:PHE145 3.9 17.1 1.0
N A:LEU60 3.9 13.4 1.0
CA A:THR59 3.9 13.5 1.0
CA A:THR62 4.0 14.5 1.0
C A:LEU60 4.0 14.6 1.0
NE2 A:HIS169 4.3 19.1 1.0
N A:THR59 4.4 13.9 1.0
CA A:LEU60 4.4 14.5 1.0
CG2 A:VAL61 4.7 15.8 1.0
CG1 A:VAL61 4.7 16.4 1.0
O A:LEU60 4.8 14.9 1.0
NE2 A:HIS181 4.8 15.1 1.0
CE2 A:PHE145 5.0 18.2 1.0
ND1 A:HIS169 5.0 17.5 1.0
N A:THR63 5.0 15.6 1.0

Sodium binding site 3 out of 8 in 5mse

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Sodium binding site 3 out of 8 in the Gfp Nuclear Transport Receptor Mimic 3B8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gfp Nuclear Transport Receptor Mimic 3B8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:28.4
occ:1.00
 NA C:NA302 2.8 22.5 1.0
NE2 C:HIS169 3.1 20.2 1.0
NE2 C:HIS181 3.5 14.3 1.0
CE1 C:HIS181 3.5 16.3 1.0
OG1 C:THR167 3.6 15.5 1.0
CE1 C:HIS169 3.6 19.5 1.0
OG1 C:THR62 3.7 16.5 1.0
O C:THR59 3.8 14.2 1.0
CZ C:PHE100 3.8 16.4 1.0
CE2 C:PHE100 3.9 16.2 1.0
CB C:ALA179 3.9 16.1 1.0
O C:HOH412 4.1 14.6 1.0
CD2 C:HIS169 4.2 18.5 1.0
C C:THR59 4.3 13.7 1.0
CG2 C:ILE98 4.4 16.8 1.0
CA C:THR59 4.4 13.9 1.0
CG2 C:THR62 4.4 18.4 1.0
O C:PRO58 4.4 16.3 1.0
CB C:THR167 4.6 16.8 1.0
CB C:THR62 4.7 15.9 1.0
ND1 C:HIS181 4.8 14.0 1.0
CG2 C:THR167 4.8 16.9 1.0
CD2 C:HIS181 4.8 14.4 1.0
CD1 C:ILE98 4.8 16.6 1.0
ND1 C:HIS169 4.9 18.8 1.0

Sodium binding site 4 out of 8 in 5mse

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Sodium binding site 4 out of 8 in the Gfp Nuclear Transport Receptor Mimic 3B8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Gfp Nuclear Transport Receptor Mimic 3B8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:22.5
occ:1.00
 O C:PRO58 2.7 16.3 1.0
NA C:NA301 2.8 28.4 1.0
N C:THR62 3.1 14.6 1.0
N C:VAL61 3.3 12.8 1.0
OG1 C:THR62 3.4 16.5 1.0
CG2 C:THR62 3.5 18.4 1.0
O C:THR59 3.5 14.2 1.0
C C:THR59 3.5 13.7 1.0
O C:HOH412 3.5 14.6 1.0
CZ C:PHE145 3.8 17.6 1.0
CB C:THR62 3.8 15.9 1.0
CB C:VAL61 3.8 14.6 1.0
CE1 C:HIS169 3.8 19.5 1.0
CA C:VAL61 3.8 13.5 1.0
C C:PRO58 3.8 13.5 1.0
CE1 C:PHE145 3.9 16.2 1.0
C C:VAL61 3.9 14.9 1.0
N C:LEU60 3.9 12.8 1.0
CA C:THR59 3.9 13.9 1.0
C C:LEU60 4.0 14.0 1.0
CA C:THR62 4.0 15.6 1.0
NE2 C:HIS169 4.2 20.2 1.0
N C:THR59 4.4 14.0 1.0
CA C:LEU60 4.4 12.8 1.0
CG1 C:VAL61 4.7 15.0 1.0
O C:LEU60 4.7 14.6 1.0
CG2 C:VAL61 4.8 15.4 1.0
NE2 C:HIS181 4.8 14.3 1.0
ND1 C:HIS169 5.0 18.8 1.0
CA C:PRO58 5.0 12.9 1.0
N C:THR63 5.0 16.3 1.0
CE2 C:PHE145 5.0 17.3 1.0

Sodium binding site 5 out of 8 in 5mse

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Sodium binding site 5 out of 8 in the Gfp Nuclear Transport Receptor Mimic 3B8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Gfp Nuclear Transport Receptor Mimic 3B8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:26.8
occ:1.00
 NA D:NA302 2.7 23.0 1.0
NE2 D:HIS169 3.1 20.7 1.0
NE2 D:HIS181 3.5 16.3 1.0
CE1 D:HIS181 3.5 15.2 1.0
CE1 D:HIS169 3.6 20.0 1.0
OG1 D:THR167 3.6 18.2 1.0
OG1 D:THR62 3.7 15.9 1.0
O D:THR59 3.8 15.8 1.0
CZ D:PHE100 3.9 16.6 1.0
CB D:ALA179 3.9 19.2 1.0
CE2 D:PHE100 3.9 15.3 1.0
O D:HOH450 4.0 15.7 1.0
CD2 D:HIS169 4.3 18.6 1.0
C D:THR59 4.3 14.8 1.0
CG2 D:ILE98 4.3 16.3 1.0
CA D:THR59 4.4 14.1 1.0
O D:PRO58 4.4 16.5 1.0
CG2 D:THR62 4.5 16.2 1.0
CB D:THR167 4.6 16.1 1.0
CB D:THR62 4.7 15.7 1.0
ND1 D:HIS181 4.7 16.2 1.0
CD1 D:ILE98 4.8 19.0 1.0
CD2 D:HIS181 4.8 15.3 1.0
CG2 D:THR167 4.8 18.0 1.0
ND1 D:HIS169 4.8 17.0 1.0
CE1 D:PHE100 5.0 16.0 1.0

Sodium binding site 6 out of 8 in 5mse

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Sodium binding site 6 out of 8 in the Gfp Nuclear Transport Receptor Mimic 3B8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Gfp Nuclear Transport Receptor Mimic 3B8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:23.0
occ:1.00
 NA D:NA301 2.7 26.8 1.0
O D:PRO58 2.8 16.5 1.0
N D:THR62 3.0 15.0 1.0
OG1 D:THR62 3.2 15.9 1.0
N D:VAL61 3.3 14.1 1.0
O D:HOH450 3.4 15.7 1.0
CG2 D:THR62 3.5 16.2 1.0
O D:THR59 3.5 15.8 1.0
C D:THR59 3.5 14.8 1.0
CB D:THR62 3.7 15.7 1.0
CZ D:PHE145 3.8 16.6 1.0
CA D:VAL61 3.8 15.1 1.0
CB D:VAL61 3.8 15.1 1.0
CE1 D:HIS169 3.8 20.0 1.0
C D:VAL61 3.9 16.0 1.0
C D:PRO58 3.9 14.2 1.0
CA D:THR62 3.9 15.5 1.0
CE1 D:PHE145 3.9 16.4 1.0
CA D:THR59 4.0 14.1 1.0
N D:LEU60 4.0 14.1 1.0
C D:LEU60 4.0 15.2 1.0
NE2 D:HIS169 4.3 20.7 1.0
N D:THR59 4.4 13.9 1.0
CA D:LEU60 4.4 15.2 1.0
O D:LEU60 4.7 14.9 1.0
CG2 D:VAL61 4.8 15.0 1.0
CG1 D:VAL61 4.8 15.6 1.0
NE2 D:HIS181 4.8 16.3 1.0
N D:THR63 5.0 16.0 1.0
CE2 D:PHE145 5.0 17.5 1.0
ND1 D:HIS169 5.0 17.0 1.0

Sodium binding site 7 out of 8 in 5mse

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Sodium binding site 7 out of 8 in the Gfp Nuclear Transport Receptor Mimic 3B8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Gfp Nuclear Transport Receptor Mimic 3B8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:21.3
occ:1.00
 O B:PRO58 2.7 16.6 1.0
NA B:NA302 2.8 29.1 1.0
N B:THR62 3.0 13.8 1.0
OG1 B:THR62 3.3 15.2 1.0
N B:VAL61 3.3 13.0 1.0
O B:THR59 3.5 14.4 1.0
O B:HOH432 3.5 15.1 1.0
C B:THR59 3.5 13.9 1.0
CG2 B:THR62 3.6 15.9 1.0
CZ B:PHE145 3.7 30.0 1.0
CB B:VAL61 3.8 13.9 1.0
CB B:THR62 3.8 14.6 1.0
CA B:VAL61 3.8 13.4 1.0
CE1 B:HIS169 3.8 19.6 1.0
C B:PRO58 3.8 14.9 1.0
CE1 B:PHE145 3.9 30.0 1.0
C B:VAL61 3.9 14.5 1.0
CA B:THR59 4.0 13.9 1.0
N B:LEU60 4.0 13.6 1.0
CA B:THR62 4.0 14.6 1.0
C B:LEU60 4.0 13.7 1.0
NE2 B:HIS169 4.2 18.7 1.0
N B:THR59 4.4 14.6 1.0
CA B:LEU60 4.4 13.2 1.0
CG2 B:VAL61 4.7 14.2 1.0
CG1 B:VAL61 4.7 14.6 1.0
O B:LEU60 4.8 13.4 1.0
NE2 B:HIS181 4.8 13.9 1.0
ND1 B:HIS169 5.0 17.1 1.0
CE2 B:PHE145 5.0 30.0 1.0

Sodium binding site 8 out of 8 in 5mse

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Sodium binding site 8 out of 8 in the Gfp Nuclear Transport Receptor Mimic 3B8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Gfp Nuclear Transport Receptor Mimic 3B8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:29.1
occ:1.00
 NA B:NA301 2.8 21.3 1.0
NE2 B:HIS169 3.1 18.7 1.0
NE2 B:HIS181 3.5 13.9 1.0
CE1 B:HIS181 3.5 16.2 1.0
CE1 B:HIS169 3.6 19.6 1.0
OG1 B:THR167 3.6 16.6 1.0
O B:THR59 3.7 14.4 1.0
OG1 B:THR62 3.7 15.2 1.0
CZ B:PHE100 3.8 15.7 1.0
CB B:ALA179 3.9 17.4 1.0
CE1 B:PHE100 3.9 15.3 1.0
O B:HOH432 4.0 15.1 1.0
CD2 B:HIS169 4.2 17.4 1.0
C B:THR59 4.3 13.9 1.0
CA B:THR59 4.3 13.9 1.0
CG2 B:ILE98 4.4 17.5 1.0
O B:PRO58 4.4 16.6 1.0
CG2 B:THR62 4.6 15.9 1.0
CB B:THR167 4.7 16.7 1.0
CB B:THR62 4.7 14.6 1.0
ND1 B:HIS181 4.8 15.5 1.0
CD1 B:ILE98 4.8 15.8 1.0
CG2 B:THR167 4.8 17.7 1.0
CD2 B:HIS181 4.8 14.5 1.0
ND1 B:HIS169 4.9 17.1 1.0
CE2 B:PHE100 4.9 15.9 1.0

Reference:

S.Frey, R.Rees, J.Schunemann, S.C.Ng, K.Funfgeld, T.Huyton, D.Gorlich. Surface Properties Determining Passage Rates of Proteins Through Nuclear Pores. Cell V. 174 202 2018.
ISSN: ISSN 1097-4172
PubMed: 29958108
DOI: 10.1016/J.CELL.2018.05.045
Page generated: Tue Dec 15 11:19:12 2020

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