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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Thu Dec 28 11:32:21 2023

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