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Sodium in PDB 2rgi: Crystal Structure of CA2+-Free S100A2 at 1.6 A Resolution

Protein crystallography data

The structure of Crystal Structure of CA2+-Free S100A2 at 1.6 A Resolution, PDB code: 2rgi was solved by M.Koch, J.Diez, G.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.28 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.516, 57.820, 59.794, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of CA2+-Free S100A2 at 1.6 A Resolution (pdb code 2rgi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of CA2+-Free S100A2 at 1.6 A Resolution, PDB code: 2rgi:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2rgi

Go back to Sodium Binding Sites List in 2rgi
Sodium binding site 1 out of 3 in the Crystal Structure of CA2+-Free S100A2 at 1.6 A Resolution


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 CA2+-Free S100A2 at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na98

b:9.4
occ:1.00
 O A:GLU23 2.2 13.7 1.0
O A:LYS28 2.3 10.4 1.0
O A:HOH105 2.3 14.9 1.0
O A:HOH106 2.3 17.0 1.0
O A:ASP25 2.4 9.5 1.0
O A:SER20 2.5 9.1 1.0
C A:LYS28 3.4 11.0 1.0
C A:SER20 3.4 7.7 1.0
C A:GLU23 3.5 13.5 1.0
C A:ASP25 3.5 11.3 1.0
CA A:SER20 3.7 7.2 1.0
O A:HOH110 3.9 10.3 1.0
N A:ASP25 4.0 13.3 1.0
N A:GLU23 4.1 12.5 1.0
C A:GLY24 4.1 13.4 1.0
CA A:LEU29 4.2 11.9 1.0
CB A:SER20 4.2 8.1 1.0
N A:LEU29 4.2 12.4 1.0
CA A:LYS28 4.3 11.1 1.0
N A:LYS28 4.3 10.4 1.0
CA A:GLU23 4.3 13.6 1.0
CA A:ASP25 4.3 12.2 1.0
N A:LYS26 4.3 11.1 1.0
O A:HOH112 4.4 18.3 1.0
N A:GLY24 4.4 13.7 1.0
CB A:LYS28 4.4 11.6 1.0
CA A:LYS26 4.4 11.0 1.0
CA A:GLY24 4.5 13.7 1.0
O A:GLY24 4.6 13.1 1.0
CB A:GLU23 4.7 14.1 1.0
OE1 A:GLU33 4.7 15.9 1.0
N A:SER21 4.7 8.1 1.0
OE1 A:GLN69 4.7 17.0 1.0
O A:TYR19 4.8 7.9 1.0
CB A:LEU29 4.8 12.6 1.0
C A:LYS26 4.8 10.4 1.0
N A:GLN22 4.9 11.5 1.0
CB A:ASP25 4.9 12.2 1.0
N A:SER20 5.0 7.4 1.0

Sodium binding site 2 out of 3 in 2rgi

Go back to Sodium Binding Sites List in 2rgi
Sodium binding site 2 out of 3 in the Crystal Structure of CA2+-Free S100A2 at 1.6 A Resolution


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 CA2+-Free S100A2 at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na99

b:29.0
occ:1.00
 O A:HOH189 2.2 17.2 1.0
O A:LEU42 2.3 12.8 1.0
O A:HIS39 2.3 15.1 1.0
C A:HIS39 3.2 15.0 1.0
O A:LEU38 3.3 13.3 1.0
C A:LEU42 3.3 14.2 1.0
O A:PRO43 3.4 15.1 1.0
CA A:HIS39 3.6 13.7 1.0
C A:PRO43 3.6 16.2 1.0
O A:HOH125 3.7 32.2 1.0
O A:HOH190 4.0 35.7 1.0
CA A:PRO43 4.1 15.7 1.0
N A:PRO43 4.1 15.5 1.0
O A:HOH179 4.2 35.2 1.0
N A:LEU42 4.2 13.7 1.0
N A:SER44 4.2 16.9 1.0
CA A:LEU42 4.2 13.8 1.0
C A:LEU38 4.2 12.0 1.0
O A:HOH115 4.3 22.4 1.0
N A:LYS40 4.4 13.1 1.0
N A:HIS39 4.4 13.6 1.0
CA A:SER44 4.5 17.6 1.0
CB A:LEU42 4.6 13.8 1.0
CB A:HIS39 4.8 14.7 1.0
C A:LYS40 5.0 14.3 1.0
CA A:LYS40 5.0 14.3 1.0

Sodium binding site 3 out of 3 in 2rgi

Go back to Sodium Binding Sites List in 2rgi
Sodium binding site 3 out of 3 in the Crystal Structure of CA2+-Free S100A2 at 1.6 A Resolution


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 CA2+-Free S100A2 at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na98

b:9.4
occ:1.00
 O B:HOH109 2.3 9.9 1.0
O B:LYS28 2.3 8.9 1.0
O B:GLU23 2.3 13.9 1.0
O B:SER20 2.5 8.7 1.0
O B:ASP25 2.5 10.2 1.0
O B:HOH107 2.5 12.3 1.0
C B:LYS28 3.4 8.9 1.0
C B:SER20 3.4 8.2 1.0
C B:GLU23 3.5 14.9 1.0
C B:ASP25 3.6 11.0 1.0
CA B:SER20 3.7 8.3 1.0
O B:HOH104 3.9 15.1 1.0
N B:ASP25 4.0 12.2 1.0
C B:GLY24 4.1 13.1 1.0
O B:HOH114 4.2 19.3 1.0
CB B:SER20 4.2 8.6 1.0
N B:GLU23 4.2 15.1 1.0
CA B:LEU29 4.2 9.8 1.0
N B:LEU29 4.3 9.2 1.0
N B:LYS28 4.3 8.4 1.0
CA B:LYS28 4.3 9.8 1.0
CA B:GLU23 4.4 16.0 1.0
CA B:ASP25 4.4 12.0 1.0
N B:GLY24 4.4 13.8 1.0
N B:LYS26 4.4 9.7 1.0
CA B:GLY24 4.5 13.0 1.0
CA B:LYS26 4.5 9.0 1.0
O B:GLY24 4.6 12.7 1.0
CB B:LYS28 4.6 10.5 1.0
OE1 B:GLN69 4.7 14.9 1.0
N B:SER21 4.7 8.7 1.0
O B:TYR19 4.9 8.7 1.0
CB B:LEU29 4.9 11.2 1.0
CB B:GLU23 4.9 17.4 1.0
CG B:GLU23 4.9 21.4 1.0
C B:LYS26 4.9 8.4 1.0
N B:GLN22 5.0 11.1 1.0

Reference:

M.Koch, J.Diez, G.Fritz. Crystal Structure of CA2+ -Free S100A2 at 1.6-A Resolution. J.Mol.Biol. V. 378 931 2008.
ISSN: ISSN 0022-2836
PubMed: 18394645
DOI: 10.1016/J.JMB.2008.03.019
Page generated: Mon Oct 7 04:21:31 2024

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