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Sodium in PDB 3exx: Structure of the T6 Human Insulin Derivative with Nickel at 1.35 A Resolution

Protein crystallography data

The structure of Structure of the T6 Human Insulin Derivative with Nickel at 1.35 A Resolution, PDB code: 3exx was solved by B.Prugovecki, D.Matkovic-Calogovic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.41 / 1.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 81.411, 81.411, 33.752, 90.00, 90.00, 120.00
R / Rfree (%) 12.4 / 17.1

Other elements in 3exx:

The structure of Structure of the T6 Human Insulin Derivative with Nickel at 1.35 A Resolution also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the T6 Human Insulin Derivative with Nickel at 1.35 A Resolution (pdb code 3exx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the T6 Human Insulin Derivative with Nickel at 1.35 A Resolution, PDB code: 3exx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3exx

Go back to Sodium Binding Sites List in 3exx
Sodium binding site 1 out of 2 in the Structure of the T6 Human Insulin Derivative with Nickel at 1.35 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the T6 Human Insulin Derivative with Nickel at 1.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na32

b:16.7
occ:1.00
O B:HOH42 2.8 23.1 1.0
O B:VAL2 2.8 9.2 1.0
N A:LEU13 2.8 7.3 1.0
CB B:PHE1 3.4 13.6 1.0
C B:VAL2 3.5 9.1 1.0
CA A:SER12 3.5 7.2 1.0
CB A:SER12 3.6 7.1 1.0
CG A:LEU13 3.6 9.7 1.0
C A:SER12 3.7 7.3 1.0
CB A:LEU13 3.7 7.5 1.0
CA A:LEU13 3.8 7.0 1.0
N B:VAL2 3.9 12.0 1.0
C B:PHE1 3.9 14.1 1.0
N B:ASN3 4.3 9.6 1.0
CA B:VAL2 4.3 10.8 1.0
CA B:PHE1 4.3 13.0 1.0
O B:PHE1 4.3 21.2 1.0
O B:HOH75 4.3 32.8 0.6
O B:HOH63 4.3 26.5 0.4
CD2 A:TYR14 4.4 13.6 1.0
OD1 B:ASN3 4.4 19.8 1.0
CA B:ASN3 4.4 9.7 1.0
CD1 A:LEU13 4.5 11.8 1.0
N A:TYR14 4.5 8.0 1.0
CG B:PHE1 4.6 11.2 1.0
NE2 B:GLN4 4.6 10.0 0.6
OG A:SER12 4.6 9.0 1.0
CE2 A:TYR14 4.6 14.1 1.0
CD2 A:LEU13 4.7 10.4 1.0
C A:LEU13 4.8 7.5 1.0
CD1 B:PHE1 4.9 16.4 1.0
O A:SER12 4.9 7.3 1.0
CG B:GLN4 4.9 7.6 0.6
N A:SER12 4.9 7.5 1.0

Sodium binding site 2 out of 2 in 3exx

Go back to Sodium Binding Sites List in 3exx
Sodium binding site 2 out of 2 in the Structure of the T6 Human Insulin Derivative with Nickel at 1.35 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the T6 Human Insulin Derivative with Nickel at 1.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na32

b:13.9
occ:1.00
O D:PHE25 2.8 7.0 1.0
O D:HOH73 2.9 17.1 1.0
N D:THR27 2.9 7.2 1.0
CA D:TYR26 3.3 6.6 1.0
CG2 C:ILE2 3.4 13.7 1.0
OG1 D:THR27 3.4 13.0 1.0
C D:TYR26 3.6 7.6 1.0
C D:PHE25 3.6 7.7 1.0
CD1 D:PHE25 3.7 8.9 1.0
CD1 C:TYR19 3.7 10.1 1.0
CB C:ILE2 3.8 11.5 1.0
CD1 C:ILE2 3.8 12.4 1.0
N D:TYR26 3.8 7.5 1.0
CA D:THR27 4.0 8.2 1.0
CE1 D:PHE25 4.0 10.3 1.0
CG C:TYR19 4.1 8.6 1.0
C D:THR27 4.3 8.4 1.0
CB D:THR27 4.3 10.3 1.0
CB C:TYR19 4.3 9.0 1.0
CD2 D:TYR26 4.4 9.7 1.0
O D:THR27 4.4 8.7 1.0
CE1 C:TYR19 4.4 11.0 1.0
CG1 C:ILE2 4.4 9.7 1.0
CB D:TYR26 4.5 7.2 1.0
CG D:PHE25 4.6 8.6 1.0
O C:HOH44 4.7 22.7 1.0
O D:TYR26 4.8 8.9 1.0
CG D:TYR26 4.9 8.1 1.0
CA D:PHE25 4.9 7.7 1.0
CG2 D:THR27 4.9 13.8 1.0
CD1 D:LEU15 5.0 12.4 1.0

Reference:

B.Prugovecki, E.Dodson, G.Dodson, D.Matkovic-Calogovic. Structure of the T6 Human Nickel Insulin Derivative at 1.35 A Resolution. Croatica Chemica Acta V. 82 433 2009.
ISSN: ISSN 0011-1643
Page generated: Tue Dec 15 06:10:12 2020

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