Atomistry » Sodium » PDB 5mft-5mse » 5mse
Atomistry »
  Sodium »
    PDB 5mft-5mse »
      5mse »

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

Go back to Sodium Binding Sites List in 5mse
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

Go back to Sodium Binding Sites List in 5mse
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

Go back to Sodium Binding Sites List in 5mse
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

Go back to Sodium Binding Sites List in 5mse
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

Go back to Sodium Binding Sites List in 5mse
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

Go back to Sodium Binding Sites List in 5mse
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

Go back to Sodium Binding Sites List in 5mse
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

Go back to Sodium Binding Sites List in 5mse
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: Mon Oct 7 22:45:09 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy