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Sodium in PDB 4eib: Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.

Protein crystallography data

The structure of Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding., PDB code: 4eib was solved by P.Stephen, K.C.Cheng, P.C.Lyu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.82 / 1.86
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 66.945, 66.945, 44.356, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 23.6

Other elements in 4eib:

The structure of Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Sodium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. (pdb code 4eib). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding., PDB code: 4eib:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 4eib

Go back to Sodium Binding Sites List in 4eib
Sodium binding site 1 out of 12 in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.


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 Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:25.6
occ:1.00
CB A:ALA12 3.6 11.7 1.0
CA A:ALA12 3.8 12.9 1.0
N A:ALA12 4.4 12.4 1.0
C A:SER11 4.9 13.4 1.0
O A:SER11 4.9 16.1 1.0

Sodium binding site 2 out of 12 in 4eib

Go back to Sodium Binding Sites List in 4eib
Sodium binding site 2 out of 12 in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.


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 Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:28.8
occ:1.00
OD1 A:ASN13 2.9 15.3 1.0
CG A:ASN13 3.9 12.8 1.0
O A:ALA12 3.9 10.9 1.0
CB A:ASN13 4.1 10.9 1.0
NE2 A:GLN15 4.5 12.7 1.0
C A:ALA12 4.8 13.4 1.0

Sodium binding site 3 out of 12 in 4eib

Go back to Sodium Binding Sites List in 4eib
Sodium binding site 3 out of 12 in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.


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 Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:32.1
occ:1.00
N A:ASN8 3.0 11.7 1.0
O A:TYR6 3.0 12.2 1.0
OD1 A:ASN8 3.1 12.1 1.0
O A:HOH310 3.2 23.0 1.0
CA A:ASP7 3.3 10.7 1.0
O A:HOH326 3.5 21.4 1.0
C A:ASP7 3.6 11.1 1.0
C A:TYR6 3.6 11.7 1.0
CG A:ASN8 3.7 13.0 1.0
N A:ASP7 3.9 10.5 1.0
OD1 A:ASP7 3.9 13.5 1.0
CA A:ASN8 4.1 10.5 1.0
N A:ASN9 4.3 11.2 1.0
ND2 A:ASN8 4.3 15.7 1.0
CB A:ASP7 4.4 11.3 1.0
C A:ASN8 4.4 10.5 1.0
CB A:ASN8 4.4 11.4 1.0
CB A:TYR6 4.6 10.7 1.0
N A:ASN10 4.6 12.2 1.0
CG A:ASP7 4.6 11.8 1.0
CA A:TYR6 4.7 11.2 1.0
O A:ASP7 4.8 10.1 1.0
CL A:CL211 4.8 34.5 1.0

Sodium binding site 4 out of 12 in 4eib

Go back to Sodium Binding Sites List in 4eib
Sodium binding site 4 out of 12 in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.


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 Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:24.5
occ:1.00
N A:GLY63 3.1 19.3 1.0
CA A:GLY63 3.5 17.8 1.0
N A:GLY98 3.8 18.6 1.0
CA A:GLY98 3.8 19.1 1.0
O A:HOH331 3.8 32.3 1.0
CB A:ASP62 3.9 18.2 1.0
CG A:ASP62 4.2 19.6 1.0
O A:GLY98 4.2 16.3 1.0
C A:ASP62 4.3 18.6 1.0
C A:LYS97 4.3 24.3 1.0
C A:GLY98 4.3 17.6 1.0
C A:GLY63 4.4 21.6 1.0
CB A:LYS97 4.4 28.5 1.0
N A:SER64 4.4 23.1 1.0
CA A:ASP62 4.6 15.0 1.0
OD2 A:ASP62 4.6 23.3 1.0
OD1 A:ASP62 4.7 22.2 1.0
O A:LYS97 4.8 27.8 1.0
CA A:LYS97 5.0 24.4 1.0

Sodium binding site 5 out of 12 in 4eib

Go back to Sodium Binding Sites List in 4eib
Sodium binding site 5 out of 12 in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:27.7
occ:1.00
OH A:TYR103 2.7 12.3 1.0
CZ A:TYR103 3.7 13.1 1.0
CE1 A:TYR103 3.8 13.0 1.0
CD A:LYS105 3.9 15.0 1.0
CG2 A:VAL59 4.1 15.8 1.0
NZ A:LYS105 4.2 22.2 1.0
CE A:LYS105 4.2 20.3 1.0
CB A:ASN70 4.4 13.5 1.0
CG1 A:VAL59 4.6 10.9 1.0
CG A:LYS105 4.8 12.8 1.0
OD1 A:ASN70 4.8 18.9 1.0
CB A:VAL59 4.8 11.6 1.0
CG A:ASN70 4.8 13.4 1.0
O A:ASN70 5.0 14.7 1.0

Sodium binding site 6 out of 12 in 4eib

Go back to Sodium Binding Sites List in 4eib
Sodium binding site 6 out of 12 in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na210

b:28.3
occ:1.00
N A:TYR34 3.1 16.4 1.0
O A:TYR34 3.4 16.4 1.0
CA A:SER33 3.4 18.2 1.0
CB A:SER33 3.6 19.9 1.0
C A:SER33 3.7 15.8 1.0
CD2 A:TYR34 3.9 22.5 1.0
CA A:TYR34 4.2 14.7 1.0
C A:TYR34 4.3 14.5 1.0
CE2 A:TYR34 4.3 24.7 1.0
CG A:TYR34 4.6 17.0 1.0
O A:ASP32 4.7 16.5 1.0
N A:SER33 4.8 17.7 1.0
OG A:SER33 4.9 18.9 1.0
O A:SER33 4.9 12.9 1.0
CB A:TYR34 4.9 15.1 1.0

Sodium binding site 7 out of 12 in 4eib

Go back to Sodium Binding Sites List in 4eib
Sodium binding site 7 out of 12 in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:30.4
occ:1.00
N B:SER83 2.9 17.3 1.0
OG B:SER83 3.5 19.2 1.0
CB B:SER83 3.6 18.5 1.0
CA B:ILE82 3.6 13.9 1.0
C B:ILE82 3.7 16.3 1.0
O B:PRO81 3.8 18.8 1.0
CA B:SER83 3.8 17.0 1.0
CG2 B:ILE82 4.4 16.9 1.0
CB B:ILE82 4.6 13.2 1.0
C B:PRO81 4.6 15.3 1.0
N B:ILE82 4.6 15.6 1.0
O B:SER83 4.7 13.3 1.0
C B:SER83 4.8 14.7 1.0
O B:ILE82 4.9 15.1 1.0

Sodium binding site 8 out of 12 in 4eib

Go back to Sodium Binding Sites List in 4eib
Sodium binding site 8 out of 12 in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na206

b:29.4
occ:1.00
N B:TYR34 3.1 17.3 1.0
O B:TYR34 3.4 17.2 1.0
CA B:SER33 3.4 17.1 1.0
CB B:SER33 3.6 20.1 1.0
C B:SER33 3.8 16.0 1.0
CD2 B:TYR34 4.0 22.2 1.0
C B:TYR34 4.2 16.4 1.0
CA B:TYR34 4.2 17.2 1.0
CE2 B:TYR34 4.3 26.7 1.0
CG B:TYR34 4.6 18.9 1.0
O B:ASP32 4.7 15.0 1.0
N B:SER33 4.8 15.8 1.0
CB B:TYR34 4.9 15.9 1.0
OG B:SER33 5.0 18.2 1.0
O B:SER33 5.0 13.2 1.0

Sodium binding site 9 out of 12 in 4eib

Go back to Sodium Binding Sites List in 4eib
Sodium binding site 9 out of 12 in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na207

b:27.7
occ:1.00
O B:HOH343 2.8 19.5 1.0
NE2 B:GLN30 2.9 21.8 1.0
CG B:GLN30 3.6 15.8 1.0
CB B:ALA27 3.7 14.7 1.0
CD B:GLN30 3.7 19.7 1.0
CB B:GLN30 4.2 12.4 1.0
O B:VAL29 4.5 9.5 1.0
OE1 B:GLN30 4.9 27.4 1.0
CA B:GLN30 4.9 11.6 1.0

Sodium binding site 10 out of 12 in 4eib

Go back to Sodium Binding Sites List in 4eib
Sodium binding site 10 out of 12 in the Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight Into the Altered Selectivity on Carbohydrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na208

b:26.3
occ:1.00
O B:ALA75 2.7 18.9 1.0
O B:HOH310 2.8 30.2 1.0
N B:SER93 3.0 13.1 1.0
CA B:PHE92 3.3 14.7 1.0
O B:SER93 3.4 13.8 1.0
CB B:PHE92 3.6 11.8 1.0
C B:PHE92 3.6 12.7 1.0
C B:ALA75 3.9 15.5 1.0
N A:NH4203 4.0 8.8 1.0
C B:SER93 4.0 16.9 1.0
CG2 B:ILE74 4.0 9.6 1.0
CA B:SER93 4.1 15.0 1.0
CA B:ALA76 4.4 14.8 1.0
O B:THR91 4.5 12.3 1.0
N B:PHE92 4.6 12.8 1.0
N B:ALA76 4.6 14.5 1.0
O A:SER93 4.7 13.0 1.0
O A:HOH308 4.7 16.2 1.0
N B:ALA75 4.8 12.8 1.0
O B:PHE92 4.8 12.6 1.0
CB B:SER93 4.9 16.3 1.0
CA B:ALA75 4.9 14.7 1.0
CG B:PHE92 5.0 13.6 1.0
C B:THR91 5.0 11.6 1.0

Reference:

P.Stephen, K.C.Cheng, P.C.Lyu. Crystal Structure of Circular Permuted ROCBM21 (CP90): Dimerisation and Proximity of Binding Sites Plos One V. 7 50488 2012.
ISSN: ESSN 1932-6203
PubMed: 23226294
DOI: 10.1371/JOURNAL.PONE.0050488
Page generated: Tue Dec 15 06:38:54 2020

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