Atomistry » Sodium » PDB 2czs-2e4r » 2d16
Atomistry »
  Sodium »
    PDB 2czs-2e4r »
      2d16 »

Sodium in PDB 2d16: Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3

Protein crystallography data

The structure of Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3, PDB code: 2d16 was solved by N.K.Lokanath, N.Kunishima, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.70 / 1.65
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 66.120, 66.120, 125.072, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 20.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3 (pdb code 2d16). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3, PDB code: 2d16:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2d16

Go back to Sodium Binding Sites List in 2d16
Sodium binding site 1 out of 4 in the Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3


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 PH1918 Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1001

b:22.1
occ:0.50
O A:HOH1009 2.4 18.0 1.0
O A:ILE130 2.4 19.0 1.0
C A:ILE130 3.1 17.6 1.0
CA A:ILE130 3.6 18.9 1.0
O A:HOH1046 3.9 28.6 1.0
N A:GLY131 4.2 18.4 1.0
CB A:ILE130 4.2 19.2 1.0
O A:VAL129 4.5 21.7 1.0
CA A:GLY131 4.6 18.8 1.0
N A:ILE130 4.8 18.6 1.0

Sodium binding site 2 out of 4 in 2d16

Go back to Sodium Binding Sites List in 2d16
Sodium binding site 2 out of 4 in the Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3


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 PH1918 Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1002

b:23.2
occ:0.50
O B:ILE130 2.4 18.7 1.0
O B:HOH1003 2.4 17.8 1.0
C B:ILE130 3.2 17.6 1.0
CA B:ILE130 3.6 18.5 1.0
O B:HOH1052 3.8 28.1 1.0
N B:GLY131 4.2 18.8 1.0
CB B:ILE130 4.3 18.1 1.0
O B:VAL129 4.5 21.2 1.0
CA B:GLY131 4.6 18.5 1.0
N B:ILE130 4.8 19.4 1.0

Sodium binding site 3 out of 4 in 2d16

Go back to Sodium Binding Sites List in 2d16
Sodium binding site 3 out of 4 in the Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3


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 PH1918 Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1003

b:22.3
occ:0.50
O C:HOH1005 2.4 18.8 1.0
O C:ILE130 2.5 18.9 1.0
C C:ILE130 3.2 18.4 1.0
CA C:ILE130 3.6 19.5 1.0
O C:HOH1056 3.9 24.9 1.0
N C:GLY131 4.2 18.6 1.0
CB C:ILE130 4.3 19.8 1.0
O C:VAL129 4.6 21.9 1.0
CA C:GLY131 4.6 18.2 1.0
N C:ILE130 4.9 18.8 1.0

Sodium binding site 4 out of 4 in 2d16

Go back to Sodium Binding Sites List in 2d16
Sodium binding site 4 out of 4 in the Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1004

b:25.0
occ:0.50
O D:ILE130 2.4 19.1 1.0
O D:HOH1124 2.4 17.8 1.0
C D:ILE130 3.1 17.7 1.0
CA D:ILE130 3.6 18.4 1.0
O D:HOH1040 3.8 29.8 1.0
N D:GLY131 4.2 19.1 1.0
CB D:ILE130 4.2 17.7 1.0
O D:VAL129 4.5 20.1 1.0
CA D:GLY131 4.6 18.3 1.0
N D:ILE130 4.8 17.2 1.0

Reference:

N.K.Lokanath, N.Kunishima. Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3 To Be Published.
Page generated: Mon Oct 7 02:11:03 2024

Last articles

W in 8QLN
W in 8RJA
V in 8WTN
Te in 8QLN
Re in 9GHX
Rb in 8Z5C
Ni in 9C0T
Ni in 9C0S
Ni in 9GP1
Ni in 9FYO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy