Atomistry » Sodium » PDB 8ad0-8b9z » 8b45
Atomistry »
  Sodium »
    PDB 8ad0-8b9z »
      8b45 »

Sodium in PDB 8b45: Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4

Protein crystallography data

The structure of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4, PDB code: 8b45 was solved by P.Kumar, F.J.O.Martin, W.M.Dawson, F.Zieleniewski, D.N.Woolfson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.47 / 1.60
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 85.515, 85.515, 85.515, 90, 90, 90
R / Rfree (%) 18.6 / 21.4

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 (pdb code 8b45). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4, PDB code: 8b45:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 8b45

Go back to Sodium Binding Sites List in 8b45
Sodium binding site 1 out of 12 in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:34.4
occ:1.00
O B:LYS21 2.8 23.0 1.0
O D:HOH204 2.8 24.5 1.0
NZ D:LYS7 3.3 49.3 1.0
C B:LYS21 3.7 21.1 1.0
CE D:LYS7 3.7 46.1 1.0
N B:AIB25 3.8 22.1 1.0
OE1 A:GLU23 3.8 57.7 1.0
CA B:LYS21 3.8 20.2 1.0
CB B:LYS21 3.9 21.1 1.0
CB B:ILE24 4.0 24.6 1.0
CB1 B:AIB25 4.0 24.5 1.0
CG2 B:ILE24 4.0 26.0 1.0
CB2 B:AIB25 4.1 26.3 1.0
CA B:AIB25 4.2 24.4 1.0
NZ B:LYS21 4.3 31.0 1.0
CE B:LYS21 4.5 27.3 1.0
C B:ILE24 4.5 23.8 1.0
CB D:LYS7 4.5 32.9 1.0
CG B:LYS21 4.6 22.5 1.0
O D:LYS7 4.7 22.3 1.0
CA B:ILE24 4.8 23.3 1.0
N B:TRP22 4.9 20.8 1.0
CD D:LYS7 4.9 43.3 1.0
CD A:GLU23 4.9 54.3 1.0
CG D:LYS7 4.9 36.4 1.0
CD1 B:ILE24 5.0 25.8 1.0

Sodium binding site 2 out of 12 in 8b45

Go back to Sodium Binding Sites List in 8b45
Sodium binding site 2 out of 12 in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na102

b:49.4
occ:1.00
OE1 B:GLU16 2.4 33.8 0.5
O B:GLU16 3.1 23.1 1.0
NZ C:LYS21 3.2 40.6 1.0
CA B:GLU16 3.5 21.1 1.0
CD B:GLU16 3.6 31.5 0.5
CB B:GLU16 3.6 24.9 1.0
CD C:LYS21 3.6 30.2 1.0
C B:GLU16 3.7 21.9 1.0
CB2 B:AIB19 3.8 23.4 1.0
CE C:LYS21 3.8 35.3 1.0
CG1 B:ILE20 3.9 22.6 1.0
CG B:GLU16 4.1 30.2 1.0
CG C:LYS21 4.2 26.6 1.0
CD1 B:ILE20 4.3 25.3 1.0
OE2 B:GLU16 4.6 30.0 0.0
N B:ILE20 4.7 19.4 1.0
N B:GLU16 4.9 20.8 1.0
N B:ILE17 5.0 18.9 1.0

Sodium binding site 3 out of 12 in 8b45

Go back to Sodium Binding Sites List in 8b45
Sodium binding site 3 out of 12 in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na101

b:50.0
occ:1.00
OE1 C:GLU16 2.7 53.7 1.0
O C:GLU16 2.8 25.0 1.0
CE A:LYS21 3.1 35.0 1.0
CB2 C:AIB19 3.3 26.4 1.0
CA C:GLU16 3.4 23.8 1.0
NZ A:LYS21 3.5 36.6 1.0
C C:GLU16 3.5 23.5 1.0
CD C:GLU16 3.6 44.3 1.0
CB C:GLU16 3.7 29.2 1.0
CG1 C:ILE20 4.0 24.8 1.0
CG C:GLU16 4.3 36.0 1.0
CD1 C:ILE20 4.4 26.1 1.0
CD A:LYS21 4.4 31.6 1.0
OE2 C:GLU16 4.4 60.5 1.0
N C:ILE20 4.5 22.1 1.0
CA C:AIB19 4.6 25.1 1.0
C C:AIB19 4.7 23.6 1.0
N C:GLU16 4.8 22.3 1.0
N C:ILE17 4.8 22.6 1.0
CG A:LYS21 4.8 29.3 1.0
O C:LYS15 4.9 23.4 1.0
N C:AIB19 5.0 24.0 1.0

Sodium binding site 4 out of 12 in 8b45

Go back to Sodium Binding Sites List in 8b45
Sodium binding site 4 out of 12 in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:43.7
occ:0.60
O B:HOH210 2.6 29.5 0.5
OE2 D:GLU23 2.8 45.1 1.0
CG D:GLU23 2.9 33.7 1.0
O D:AIB19 3.0 21.0 1.0
CD D:GLU23 3.3 35.6 1.0
CB1 D:AIB19 3.5 23.9 1.0
C D:AIB19 3.7 20.5 1.0
C4 B:PGE103 3.8 43.5 0.8
CA D:AIB19 3.9 21.6 1.0
CD1 D:TRP22 4.0 32.3 1.0
O3 B:PGE103 4.0 47.8 0.8
CB2 D:AIB19 4.1 23.0 1.0
CB D:GLU23 4.1 26.3 1.0
C5 B:PGE103 4.4 50.9 0.8
N D:GLU23 4.4 20.5 1.0
C3 B:PGE103 4.5 42.5 0.8
OE1 D:GLU23 4.5 40.2 1.0
CB D:TRP22 4.5 24.0 1.0
CG D:TRP22 4.6 28.9 1.0
CA D:GLU23 4.7 23.4 1.0
N D:ILE20 4.8 19.4 1.0
NE1 D:TRP22 4.9 39.0 0.8

Sodium binding site 5 out of 12 in 8b45

Go back to Sodium Binding Sites List in 8b45
Sodium binding site 5 out of 12 in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na102

b:51.8
occ:1.00
OE1 D:GLU16 2.5 47.0 0.8
O D:GLU16 3.1 22.0 1.0
CA D:GLU16 3.4 22.9 1.0
CD D:GLU16 3.6 41.2 0.8
CB D:GLU16 3.6 27.4 1.0
CB2 D:AIB19 3.7 23.0 1.0
C D:GLU16 3.7 21.5 1.0
CG1 D:ILE20 3.9 20.2 1.0
CG D:GLU16 4.1 34.1 1.0
CD1 D:ILE20 4.2 22.2 1.0
N D:ILE20 4.6 19.4 1.0
OE2 D:GLU16 4.6 46.7 0.8
N D:GLU16 4.7 21.0 1.0
CA D:AIB19 4.9 21.6 1.0
N D:ILE17 4.9 18.3 1.0
O D:LYS15 5.0 23.1 1.0

Sodium binding site 6 out of 12 in 8b45

Go back to Sodium Binding Sites List in 8b45
Sodium binding site 6 out of 12 in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na103

b:41.4
occ:1.00
NZ D:LYS14 2.9 33.4 1.0
CD D:LYS14 3.6 26.1 1.0
CE D:LYS14 3.7 29.2 1.0
OE2 A:GLU16 4.2 48.5 1.0
CG D:LYS14 4.4 20.7 1.0
CG2 D:ILE10 4.8 23.8 1.0
O D:HOH202 5.0 31.7 1.0

Sodium binding site 7 out of 12 in 8b45

Go back to Sodium Binding Sites List in 8b45
Sodium binding site 7 out of 12 in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na101

b:44.9
occ:1.00
OE1 A:GLU16 2.2 47.9 1.0
O B:HOH202 2.6 21.4 1.0
CD A:GLU16 3.1 40.8 1.0
OE2 A:GLU16 3.2 48.5 1.0
CG B:LYS14 3.7 21.6 1.0
CD B:LYS14 3.7 24.6 1.0
NZ D:LYS14 3.8 33.4 1.0
O D:HOH205 3.8 23.9 1.0
O D:HOH202 3.9 31.7 1.0
CB B:LYS14 4.0 18.9 1.0
CE B:LYS14 4.0 29.7 1.0
CE D:LYS14 4.1 29.2 1.0
CA B:LYS14 4.3 18.2 1.0
CG A:GLU16 4.5 39.4 1.0
CG2 B:ILE17 4.6 19.7 1.0
CD1 B:ILE17 4.7 23.8 1.0
NZ B:LYS14 4.7 36.1 1.0
O B:LYS14 4.7 18.3 1.0
CB B:ILE17 4.8 19.9 1.0

Sodium binding site 8 out of 12 in 8b45

Go back to Sodium Binding Sites List in 8b45
Sodium binding site 8 out of 12 in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na102

b:49.9
occ:1.00
O A:GLU16 2.9 26.2 1.0
NZ B:LYS21 3.2 31.0 1.0
CA A:GLU16 3.4 29.7 1.0
C A:GLU16 3.6 25.5 1.0
CB A:GLU16 3.6 33.4 1.0
CB2 A:AIB19 3.7 28.6 1.0
CG1 A:ILE20 3.7 26.3 1.0
CD B:LYS21 3.8 24.6 1.0
CE B:LYS21 3.8 27.3 1.0
CG A:GLU16 4.2 39.4 1.0
OE2 A:GLU16 4.2 48.5 1.0
CD1 A:ILE20 4.2 26.4 1.0
N A:ILE20 4.4 24.1 1.0
CG B:LYS21 4.5 22.5 1.0
CD A:GLU16 4.6 40.8 1.0
N A:ILE17 4.8 22.9 1.0
N A:GLU16 4.8 28.6 1.0
CB A:ILE20 4.9 23.6 1.0
CA A:AIB19 4.9 28.4 1.0
C A:AIB19 5.0 27.6 1.0

Sodium binding site 9 out of 12 in 8b45

Go back to Sodium Binding Sites List in 8b45
Sodium binding site 9 out of 12 in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na103

b:51.4
occ:1.00
NA A:NA104 2.2 56.1 1.0
O A:GLU2 2.8 33.5 1.0
CE B:LYS7 3.1 45.4 1.0
CG A:GLU2 3.3 52.4 1.0
CA A:GLU2 3.5 36.5 1.0
C A:GLU2 3.5 34.6 1.0
CB2 A:AIB5 3.6 30.1 1.0
CG1 A:ILE6 3.8 31.3 1.0
CD1 A:ILE6 3.8 35.7 1.0
CB A:GLU2 3.8 44.1 1.0
O D:HOH212 4.3 47.2 1.0
CD B:LYS7 4.5 40.2 1.0
CD A:GLU2 4.5 60.5 1.0
N A:ILE6 4.5 26.4 1.0
OE2 A:GLU2 4.7 72.3 1.0
N A:GLU2 4.8 34.9 1.0
CA A:AIB5 4.8 27.2 1.0
O A:GLY1 4.8 32.2 1.0
N A:ILE3 4.8 32.6 1.0
CG2 B:ILE3 4.9 44.1 1.0
CG B:LYS7 5.0 34.4 1.0
CB A:ILE6 5.0 28.4 1.0
C A:AIB5 5.0 26.5 1.0

Sodium binding site 10 out of 12 in 8b45

Go back to Sodium Binding Sites List in 8b45
Sodium binding site 10 out of 12 in the Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na104

b:56.1
occ:1.00
NA A:NA103 2.2 51.4 1.0
O D:HOH212 3.3 47.2 1.0
CB2 A:AIB5 3.5 30.1 1.0
CE B:LYS7 3.5 45.4 1.0
CD1 A:ILE6 3.6 35.7 1.0
CG1 A:ILE6 4.3 31.3 1.0
O A:GLU2 4.4 33.5 1.0
CD B:LYS7 4.4 40.2 1.0
OE1 A:GLU9 4.5 43.5 1.0
N A:ILE6 4.5 26.4 1.0
C A:AIB5 4.6 26.5 1.0
CA A:AIB5 4.7 27.2 1.0
CG B:LYS7 4.8 34.4 1.0

Reference:

P.Kumar, F.J.O.Martin, W.M.Dawson, F.Zieleniewski, D.N.Woolfson. Structure of Cc-Tri with Aib@B,C: Cc-Tri-(Ubuc)4 To Be Published.
Page generated: Wed Oct 9 10:35:17 2024

Last articles

Zn in 9FS1
Zn in 9FS3
Zn in 9FS2
Zn in 9H3H
Zn in 9F29
Zn in 9F2A
Zn in 9EY2
Zn in 9F26
Zn in 9E8J
Zn in 9E8N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy