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 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy