Atomistry » Sodium » PDB 4nxz-4obo » 4nyp
Atomistry »
  Sodium »
    PDB 4nxz-4obo »
      4nyp »

Sodium in PDB 4nyp: The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+

Protein crystallography data

The structure of The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+, PDB code: 4nyp was solved by B.Bagautdinov, T.H.Tahirov, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.822, 123.774, 50.667, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.9

Sodium Binding Sites:

The binding sites of Sodium atom in the The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+ (pdb code 4nyp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+, PDB code: 4nyp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4nyp

Go back to Sodium Binding Sites List in 4nyp
Sodium binding site 1 out of 3 in the The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1001

b:22.1
occ:1.00
OE2 C:GLU47 2.1 22.8 1.0
OE2 F:GLU15 2.3 36.2 1.0
OE2 A:GLU15 2.4 40.8 1.0
OE1 F:GLU15 2.5 37.6 1.0
OE1 A:GLU15 2.5 40.4 1.0
CD F:GLU15 2.7 34.9 1.0
CD A:GLU15 2.8 37.7 1.0
CD C:GLU47 3.1 25.2 1.0
OE1 C:GLU47 3.4 25.1 1.0
NH1 E:ARG36 3.9 43.2 1.0
O F:HOH282 3.9 50.8 1.0
NH2 E:ARG36 4.2 43.2 1.0
CG A:GLU15 4.2 34.4 1.0
CG F:GLU15 4.2 31.5 1.0
CB F:TRP11 4.3 20.7 1.0
CE2 C:PHE38 4.3 21.1 1.0
NZ A:LYS19 4.4 33.5 1.0
CZ E:ARG36 4.4 43.4 1.0
CG C:GLU47 4.5 24.5 1.0
OE1 F:GLU12 4.5 36.8 1.0
CZ C:PHE38 4.5 22.6 1.0
O E:HOH374 4.6 39.4 1.0
O F:TRP11 4.7 17.7 1.0
C F:TRP11 4.7 19.0 1.0
CB C:GLU47 4.7 24.4 1.0
CE A:LYS19 4.9 30.3 1.0
CB A:GLU15 4.9 28.1 1.0
N F:GLU12 4.9 20.2 1.0
O F:HOH251 5.0 41.7 1.0

Sodium binding site 2 out of 3 in 4nyp

Go back to Sodium Binding Sites List in 4nyp
Sodium binding site 2 out of 3 in the The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:26.8
occ:1.00
O B:HOH314 2.2 23.2 1.0
O A:HOH1107 2.3 23.5 1.0
O C:HOH311 2.3 36.9 1.0
O B:HOH308 2.4 37.2 1.0
O A:HOH1127 2.4 23.1 1.0
O C:HOH329 2.5 24.2 1.0
O A:HOH1199 4.0 31.6 1.0
OD2 B:ASP86 4.1 19.7 1.0
OD2 C:ASP86 4.2 18.9 1.0
OD1 A:ASP86 4.2 26.9 1.0
OD2 A:ASP86 4.2 24.0 1.0
OD1 B:ASP86 4.2 18.8 1.0
OD1 C:ASP86 4.3 17.0 1.0
O C:HOH337 4.4 53.4 1.0
O A:ASP84 4.5 22.0 1.0
O C:ASP84 4.5 21.9 1.0
CG B:ASP86 4.6 19.7 1.0
CG A:ASP86 4.7 26.1 1.0
O B:ASP84 4.7 22.4 1.0
CG C:ASP86 4.7 17.7 1.0

Sodium binding site 3 out of 3 in 4nyp

Go back to Sodium Binding Sites List in 4nyp
Sodium binding site 3 out of 3 in the The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:26.8
occ:1.00
O E:HOH312 2.3 31.3 1.0
O D:HOH349 2.3 35.6 1.0
O F:HOH278 2.3 31.9 1.0
O D:HOH341 2.4 39.4 1.0
O F:HOH206 2.4 19.8 1.0
O E:HOH341 2.5 20.9 1.0
OD2 D:ASP86 4.1 18.6 1.0
OD2 F:ASP86 4.2 21.5 1.0
OD2 E:ASP86 4.3 22.0 1.0
O F:HOH276 4.3 33.7 1.0
OD1 E:ASP86 4.4 21.9 1.0
OD1 D:ASP86 4.4 22.5 1.0
O F:ASP84 4.5 21.5 1.0
OD1 F:ASP86 4.5 23.6 1.0
O D:ASP84 4.5 19.1 1.0
O E:ASP84 4.5 17.9 1.0
O F:HOH217 4.7 46.4 1.0
CG D:ASP86 4.7 20.0 1.0
CG F:ASP86 4.8 19.9 1.0
CG E:ASP86 4.8 20.7 1.0

Reference:

B.Bagautdinov, T.H.Tahirov. The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii Complexed with Na+ To Be Published.
Page generated: Mon Oct 7 17:20:00 2024

Last articles

Mg in 4FRG
Mg in 4FS2
Mg in 4FMA
Mg in 4FR8
Mg in 4FS1
Mg in 4FRZ
Mg in 4FQF
Mg in 4FR3
Mg in 4FPV
Mg in 4FNJ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy