Calcium in PDB 2h61: X-Ray Structure of Human CA2+-Loaded S100B

The structure of X-Ray Structure of Human CA2+-Loaded S100B, PDB code: 2h61 was solved by T.Ostendorp, C.W.Heizmann, P.M.H.Kroneck, G.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.32 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.400, 81.600, 71.500, 90.00, 107.00, 90.00
R / Rfree (%)	17.4 / 24.1

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the X-Ray Structure of Human CA2+-Loaded S100B (pdb code 2h61). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the X-Ray Structure of Human CA2+-Loaded S100B, PDB code: 2h61:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the X-Ray Structure of Human CA2+-Loaded S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Human CA2+-Loaded S100B within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:18.9 occ:1.00 O A:SER18 2.4 14.4 1.0 O A:ASP23 2.4 18.6 1.0 O A:HOH804 2.4 17.0 1.0 O A:GLU21 2.4 19.9 1.0 O A:LYS26 2.4 16.4 1.0 OE1 A:GLU31 2.5 13.0 1.0 OE2 A:GLU31 2.6 14.9 1.0 CD A:GLU31 2.8 15.1 1.0 C A:SER18 3.4 15.5 1.0 C A:ASP23 3.5 19.5 1.0 C A:GLU21 3.7 21.2 1.0 C A:LYS26 3.7 16.4 1.0 CA A:SER18 3.9 16.0 1.0 N A:GLU21 4.2 19.9 1.0 N A:ASP23 4.2 19.4 1.0 C A:GLY22 4.3 19.2 1.0 CG A:GLU31 4.3 12.1 1.0 N A:LYS28 4.4 15.6 1.0 CA A:ASP23 4.4 19.9 1.0 N A:LYS24 4.4 19.4 1.0 N A:LYS26 4.4 17.2 1.0 CA A:LYS24 4.4 20.1 1.0 CA A:GLU21 4.5 21.4 1.0 OE1 A:GLU67 4.5 16.4 1.0 CA A:LEU27 4.5 14.9 1.0 CB A:SER18 4.5 14.3 1.0 N A:LEU27 4.5 15.3 1.0 N A:GLY19 4.5 16.9 1.0 O A:GLY22 4.6 17.6 1.0 CG A:LYS28 4.6 17.6 1.0 O A:TYR17 4.6 18.8 1.0 N A:GLY22 4.6 20.8 1.0 CA A:LYS26 4.6 17.2 1.0 N A:ARG20 4.7 20.3 1.0 CA A:GLY22 4.7 18.6 1.0 CB A:GLU21 4.7 22.5 1.0 C A:LYS24 4.8 18.9 1.0 CA A:GLY19 4.8 17.5 1.0 CB A:ASP23 4.9 19.8 1.0 C A:LEU27 4.9 15.3 1.0 O A:HOH814 4.9 19.9 1.0 C A:GLY19 4.9 19.1 1.0

Calcium binding site 2 out of 18 in the X-Ray Structure of Human CA2+-Loaded S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Human CA2+-Loaded S100B within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:23.1 occ:1.00 OD1 A:ASP63 2.3 27.4 1.0 O A:HOH805 2.3 16.7 1.0 OD1 A:ASP61 2.4 16.5 1.0 O A:GLU67 2.4 16.3 1.0 OD1 A:ASP65 2.5 21.8 1.0 OE1 A:GLU72 2.5 18.3 1.0 OE2 A:GLU72 2.5 15.4 1.0 CD A:GLU72 2.9 16.9 1.0 CG A:ASP63 3.3 29.5 1.0 CG A:ASP65 3.4 22.8 1.0 CG A:ASP61 3.5 22.5 1.0 C A:GLU67 3.5 17.2 1.0 OD2 A:ASP65 3.7 22.2 1.0 OD2 A:ASP63 3.8 31.4 1.0 CA A:ASP61 4.0 22.1 1.0 CB A:ASP61 4.2 21.8 1.0 N A:ASP65 4.3 23.0 1.0 N A:GLU67 4.3 17.9 1.0 N A:CYS68 4.4 16.8 1.0 N A:ASP63 4.4 27.7 1.0 OD2 A:ASP61 4.4 22.2 1.0 CG A:GLU72 4.4 16.9 1.0 CA A:GLU67 4.4 17.5 1.0 N A:ASP69 4.4 16.5 1.0 C A:ASP61 4.4 23.8 1.0 CA A:CYS68 4.5 16.0 1.0 N A:ASN62 4.5 24.9 1.0 CB A:ASP63 4.6 27.0 1.0 CB A:ASP65 4.6 22.0 1.0 O A:HOH837 4.6 32.0 1.0 N A:GLY64 4.6 26.2 1.0 CA A:ASP63 4.8 27.3 1.0 CA A:ASP65 4.8 21.2 1.0 C A:ASP63 4.9 27.0 1.0 CG A:ASP69 4.9 17.2 1.0 C A:CYS68 4.9 16.8 1.0 OD2 A:ASP69 5.0 20.1 1.0

Calcium binding site 3 out of 18 in the X-Ray Structure of Human CA2+-Loaded S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Human CA2+-Loaded S100B within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:32.6 occ:1.00 O B:ASP23 2.3 26.2 1.0 OE1 B:GLU31 2.3 24.9 1.0 O B:SER18 2.3 22.7 1.0 O B:GLU21 2.4 29.4 1.0 O B:HOH807 2.4 30.8 1.0 O B:LYS26 2.4 24.3 1.0 OE2 B:GLU31 2.5 23.0 1.0 CD B:GLU31 2.8 22.7 1.0 C B:ASP23 3.4 27.7 1.0 C B:SER18 3.4 24.7 1.0 C B:GLU21 3.6 29.6 1.0 C B:LYS26 3.6 25.2 1.0 CA B:SER18 4.0 23.9 1.0 N B:GLU21 4.1 29.5 1.0 N B:ASP23 4.2 28.5 1.0 CG B:GLU31 4.3 21.3 1.0 N B:LYS24 4.3 27.9 1.0 CA B:ASP23 4.3 28.0 1.0 C B:GLY22 4.3 28.9 1.0 N B:LYS28 4.4 23.3 1.0 CA B:LYS24 4.4 29.0 1.0 CA B:GLU21 4.4 30.1 1.0 CA B:LEU27 4.5 21.9 1.0 N B:LYS26 4.5 28.1 1.0 N B:LEU27 4.5 23.1 1.0 N B:GLY22 4.5 28.6 1.0 O B:TYR17 4.5 24.5 1.0 N B:GLY19 4.6 25.2 1.0 CA B:LYS26 4.6 26.6 1.0 OE1 B:GLU67 4.6 27.9 1.0 CA B:GLY22 4.6 28.5 1.0 CB B:GLU21 4.7 30.4 1.0 O B:GLY22 4.7 28.7 1.0 O B:HOH808 4.7 30.2 1.0 CG B:LYS28 4.8 26.5 1.0 CB B:SER18 4.8 22.9 1.0 CB B:ASP23 4.8 28.2 1.0 C B:LYS24 4.8 29.1 1.0 C B:LEU27 4.8 23.0 1.0 N B:ARG20 4.9 29.0 1.0 CD B:LYS28 4.9 32.7 1.0 CA B:GLY19 5.0 26.9 1.0

Calcium binding site 4 out of 18 in the X-Ray Structure of Human CA2+-Loaded S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Human CA2+-Loaded S100B within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca804 b:32.7 occ:1.00 OD1 B:ASP61 2.1 31.4 1.0 O B:HOH839 2.2 35.1 1.0 O B:GLU67 2.3 25.2 1.0 OD1 B:ASP65 2.4 29.5 1.0 OE1 B:GLU72 2.5 23.9 1.0 OD1 B:ASP63 2.5 34.0 1.0 OE2 B:GLU72 2.7 29.4 1.0 CD B:GLU72 3.0 25.3 1.0 CG B:ASP65 3.3 29.5 1.0 CG B:ASP61 3.3 29.6 1.0 C B:GLU67 3.4 24.9 1.0 CG B:ASP63 3.5 35.2 1.0 OD2 B:ASP65 3.6 26.6 1.0 OD2 B:ASP63 3.9 33.5 1.0 N B:GLU67 4.1 26.4 1.0 CA B:ASP61 4.1 29.9 1.0 OD2 B:ASP61 4.2 25.1 1.0 CB B:ASP61 4.2 29.2 1.0 N B:CYS68 4.3 24.2 1.0 CA B:CYS68 4.3 24.4 1.0 CA B:GLU67 4.3 25.3 1.0 N B:ASP63 4.3 35.9 1.0 N B:ASP69 4.4 24.7 1.0 N B:ASN62 4.4 33.7 1.0 N B:ASP65 4.4 32.0 1.0 CG B:GLU72 4.5 26.0 1.0 CB B:ASP65 4.5 30.0 1.0 C B:ASP61 4.6 31.6 1.0 N B:GLY66 4.6 29.4 1.0 CB B:ASP63 4.7 36.0 1.0 C B:CYS68 4.8 24.5 1.0 N B:GLY64 4.8 35.9 1.0 CA B:ASP65 4.8 30.4 1.0 CA B:ASP63 4.8 36.4 1.0 C B:ASP63 4.9 36.2 1.0 C B:ASP65 4.9 29.9 1.0 CB B:GLU67 4.9 25.9 1.0

Calcium binding site 5 out of 18 in the X-Ray Structure of Human CA2+-Loaded S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of Human CA2+-Loaded S100B within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca805 b:20.4 occ:1.00 O C:ASP23 2.3 19.1 1.0 O C:HOH812 2.4 20.0 1.0 O C:LYS26 2.4 21.1 1.0 O C:SER18 2.4 20.2 1.0 OE1 C:GLU31 2.4 16.3 1.0 O C:GLU21 2.5 21.4 1.0 OE2 C:GLU31 2.6 19.3 1.0 CD C:GLU31 2.9 18.6 1.0 C C:SER18 3.4 21.2 1.0 C C:ASP23 3.5 20.6 1.0 C C:LYS26 3.6 19.4 1.0 C C:GLU21 3.7 22.0 1.0 CA C:SER18 3.9 19.4 1.0 N C:GLU21 4.1 22.7 1.0 N C:ASP23 4.2 21.3 1.0 CA C:ASP23 4.3 19.2 1.0 N C:LYS28 4.3 20.2 1.0 CA C:LEU27 4.4 19.7 1.0 OE1 C:GLU67 4.4 19.9 1.0 CG C:GLU31 4.4 17.8 1.0 C C:GLY22 4.4 21.3 1.0 N C:LYS24 4.4 21.9 1.0 N C:LEU27 4.4 19.5 1.0 N C:LYS26 4.4 20.6 1.0 CA C:LYS24 4.4 22.7 1.0 CA C:GLU21 4.5 22.8 1.0 CB C:SER18 4.6 19.7 1.0 N C:GLY19 4.6 20.9 1.0 O C:TYR17 4.6 21.0 1.0 CA C:LYS26 4.6 19.6 1.0 CB C:ASP23 4.6 17.9 1.0 O C:HOH811 4.7 25.6 1.0 N C:GLY22 4.7 20.7 1.0 C C:LEU27 4.7 20.6 1.0 O C:GLY22 4.7 22.9 1.0 C C:LYS24 4.8 22.8 1.0 CB C:GLU21 4.8 23.8 1.0 N C:ARG20 4.8 22.0 1.0 CA C:GLY22 4.8 20.5 1.0 CG C:LYS28 4.9 21.0 1.0 CD C:LYS28 4.9 21.3 1.0 N C:HIS25 4.9 22.1 1.0 CA C:GLY19 5.0 21.9 1.0

Calcium binding site 6 out of 18 in the X-Ray Structure of Human CA2+-Loaded S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of Human CA2+-Loaded S100B within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca806 b:29.6 occ:1.00 O C:HOH809 2.2 23.0 1.0 OD1 C:ASP61 2.3 23.3 1.0 OD1 C:ASP63 2.3 24.4 1.0 O C:GLU67 2.3 20.4 1.0 OE1 C:GLU72 2.4 18.3 1.0 OE2 C:GLU72 2.5 21.2 1.0 OD1 C:ASP65 2.8 22.7 1.0 CD C:GLU72 2.8 22.4 1.0 CG C:ASP63 3.3 30.2 1.0 CG C:ASP65 3.4 27.2 1.0 CG C:ASP61 3.4 25.4 1.0 C C:GLU67 3.5 20.7 1.0 OD2 C:ASP63 3.7 30.4 1.0 OD2 C:ASP65 3.8 24.1 1.0 CA C:ASP61 4.2 27.9 1.0 OD2 C:ASP61 4.3 25.6 1.0 CB C:ASP61 4.3 27.2 1.0 N C:ASP65 4.3 26.8 1.0 N C:GLU67 4.3 21.6 1.0 CG C:GLU72 4.3 18.9 1.0 N C:CYS68 4.4 21.0 1.0 N C:ASP63 4.4 29.9 1.0 N C:ASP69 4.4 18.9 1.0 CA C:CYS68 4.4 19.5 1.0 CA C:GLU67 4.4 21.5 1.0 CB C:ASP65 4.5 24.8 1.0 CB C:ASP63 4.5 29.9 1.0 C C:ASP61 4.6 28.6 1.0 N C:GLY64 4.6 28.5 1.0 CA C:ASP63 4.7 29.7 1.0 N C:ASN62 4.7 29.6 1.0 CA C:ASP65 4.8 25.8 1.0 C C:ASP63 4.8 29.3 1.0 C C:CYS68 4.9 19.1 1.0 CG C:ASP69 4.9 23.9 1.0 N C:GLY66 4.9 24.2 1.0 O C:HOH843 4.9 33.9 1.0

Calcium binding site 7 out of 18 in the X-Ray Structure of Human CA2+-Loaded S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of X-Ray Structure of Human CA2+-Loaded S100B within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca807 b:22.9 occ:1.00 O D:ASP23 2.3 22.6 1.0 O D:SER18 2.3 18.6 1.0 OE1 D:GLU31 2.3 19.4 1.0 O D:HOH820 2.4 19.7 1.0 O D:LYS26 2.4 19.9 1.0 O D:GLU21 2.5 23.6 1.0 OE2 D:GLU31 2.7 18.9 1.0 CD D:GLU31 2.9 19.7 1.0 C D:SER18 3.4 19.3 1.0 C D:ASP23 3.4 23.3 1.0 C D:LYS26 3.6 20.1 1.0 C D:GLU21 3.6 24.5 1.0 CA D:SER18 3.9 20.6 1.0 N D:GLU21 4.1 23.5 1.0 N D:ASP23 4.2 23.2 1.0 N D:LYS24 4.3 24.4 1.0 CA D:LYS24 4.3 25.5 1.0 CA D:ASP23 4.3 23.1 1.0 C D:GLY22 4.4 23.1 1.0 N D:LYS28 4.4 18.1 1.0 CG D:GLU31 4.4 21.0 1.0 CA D:GLU21 4.4 24.8 1.0 CB D:SER18 4.5 18.0 1.0 N D:LEU27 4.5 18.9 1.0 CA D:LEU27 4.5 19.0 1.0 N D:GLY19 4.5 20.2 1.0 N D:LYS26 4.5 21.3 1.0 OE1 D:GLU67 4.6 29.2 1.0 N D:GLY22 4.6 24.2 1.0 CA D:LYS26 4.6 20.0 1.0 O D:GLY22 4.7 22.3 1.0 C D:LYS24 4.8 25.1 1.0 CA D:GLY22 4.8 23.5 1.0 O D:TYR17 4.8 19.4 1.0 CB D:ASP23 4.8 23.3 1.0 N D:ARG20 4.8 22.0 1.0 CA D:GLY19 4.8 20.9 1.0 C D:LEU27 4.9 19.0 1.0 CG D:LYS28 4.9 20.2 1.0 CB D:GLU21 4.9 24.9 1.0 CD D:LYS28 4.9 27.1 1.0 C D:GLY19 5.0 21.4 1.0

Calcium binding site 8 out of 18 in the X-Ray Structure of Human CA2+-Loaded S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of X-Ray Structure of Human CA2+-Loaded S100B within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca808 b:18.7 occ:1.00 OD1 D:ASP65 2.2 17.1 1.0 OD1 D:ASP61 2.3 17.5 1.0 O D:GLU67 2.4 13.9 1.0 OD2 D:ASP63 2.4 15.7 1.0 O D:HOH821 2.4 17.0 1.0 OE1 D:GLU72 2.5 21.8 1.0 OE2 D:GLU72 2.7 17.0 1.0 CD D:GLU72 2.9 19.4 1.0 CG D:ASP65 3.2 17.9 1.0 CG D:ASP63 3.3 22.9 1.0 CG D:ASP61 3.5 19.0 1.0 C D:GLU67 3.5 17.5 1.0 OD1 D:ASP63 3.5 25.1 1.0 OD2 D:ASP65 3.7 18.9 1.0 N D:GLU67 4.1 17.5 1.0 N D:ASP65 4.2 19.1 1.0 CA D:ASP61 4.2 18.6 1.0 CB D:ASP61 4.3 19.1 1.0 OD2 D:ASP61 4.3 15.1 1.0 N D:ASP69 4.3 17.9 1.0 CB D:ASP65 4.4 18.6 1.0 N D:ASP63 4.4 21.3 1.0 CA D:GLU67 4.4 18.3 1.0 CG D:GLU72 4.4 17.6 1.0 N D:CYS68 4.4 16.7 1.0 CA D:CYS68 4.4 17.2 1.0 N D:GLY64 4.5 19.5 1.0 CB D:ASP63 4.5 19.7 1.0 C D:ASP61 4.5 19.6 1.0 CA D:ASP65 4.7 18.8 1.0 N D:ASN62 4.7 20.7 1.0 N D:GLY66 4.8 17.1 1.0 CA D:ASP63 4.8 21.3 1.0 C D:ASP63 4.8 20.7 1.0 CG D:ASP69 4.8 20.1 1.0 C D:CYS68 4.8 18.4 1.0 C D:ASP65 4.9 18.2 1.0 OD2 D:ASP69 4.9 21.0 1.0 OD1 D:ASP69 4.9 17.6 1.0

Calcium binding site 9 out of 18 in the X-Ray Structure of Human CA2+-Loaded S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of X-Ray Structure of Human CA2+-Loaded S100B within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca817 b:36.0 occ:1.00 O D:HOH822 2.1 33.6 1.0 O D:HOH823 2.2 28.4 1.0 O E:SER41 2.4 22.7 1.0 OD1 D:ASP12 2.4 20.9 1.0 O E:HOH904 2.5 35.5 1.0 O E:LEU44 2.6 35.9 1.0 OD2 D:ASP12 2.7 22.5 1.0 CG D:ASP12 2.9 19.4 1.0 C E:SER41 3.4 24.5 1.0 C E:LEU44 3.8 34.7 1.0 O D:HOH824 3.9 24.9 1.0 CA E:SER41 4.1 24.1 1.0 O C:HOH846 4.3 36.0 1.0 CA E:GLU45 4.3 35.4 1.0 N E:GLU46 4.4 34.6 1.0 CB D:ASP12 4.4 18.9 1.0 N E:GLU45 4.4 35.1 1.0 N E:HIS42 4.4 26.6 1.0 O E:HOH905 4.5 24.5 1.0 C E:GLU45 4.6 34.8 1.0 CB E:SER41 4.6 26.2 1.0 O E:HOH915 4.7 34.0 1.0 CA E:HIS42 4.7 26.8 1.0 N E:LEU44 4.8 33.3 1.0 CA E:LEU44 4.9 34.3 1.0 C E:HIS42 4.9 28.6 1.0

Calcium binding site 10 out of 18 in the X-Ray Structure of Human CA2+-Loaded S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of X-Ray Structure of Human CA2+-Loaded S100B within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca809 b:26.9 occ:1.00 O E:HOH902 2.1 32.2 1.0 OE1 E:GLU31 2.3 20.9 1.0 O E:ASP23 2.3 28.4 1.0 O E:LYS26 2.3 22.9 1.0 O E:SER18 2.4 24.8 1.0 O E:GLU21 2.5 24.2 1.0 OE2 E:GLU31 2.5 26.3 1.0 CD E:GLU31 2.7 20.3 1.0 C E:SER18 3.4 25.1 1.0 C E:ASP23 3.5 28.3 1.0 C E:LYS26 3.6 24.1 1.0 C E:GLU21 3.7 25.8 1.0 CA E:SER18 3.8 25.1 1.0 N E:GLU21 4.2 25.0 1.0 CG E:GLU31 4.3 20.4 1.0 N E:LYS28 4.3 23.6 1.0 CA E:LEU27 4.3 24.1 1.0 N E:ASP23 4.4 27.6 1.0 N E:LYS26 4.4 26.4 1.0 N E:LEU27 4.4 23.8 1.0 C E:GLY22 4.4 27.8 1.0 N E:LYS24 4.4 27.9 1.0 CA E:LYS24 4.4 28.4 1.0 CA E:GLU21 4.4 25.4 1.0 CA E:ASP23 4.5 28.3 1.0 CB E:SER18 4.5 24.4 1.0 N E:GLY19 4.5 24.3 1.0 O E:HOH921 4.5 42.3 1.0 CA E:LYS26 4.6 24.8 1.0 O E:TYR17 4.6 24.3 1.0 O E:GLY22 4.6 28.4 1.0 OE1 E:GLU67 4.7 36.1 1.0 N E:GLY22 4.7 26.2 1.0 CB E:GLU21 4.7 24.9 1.0 C E:LYS24 4.7 27.7 1.0 CB E:ASP23 4.8 27.8 1.0 C E:LEU27 4.8 24.7 1.0 N E:ARG20 4.8 26.6 1.0 CA E:GLY22 4.8 27.2 1.0 CG E:LYS28 4.9 24.5 1.0 C E:GLY19 5.0 26.3 1.0

T.Ostendorp, E.Leclerc, A.Galichet, M.Koch, N.Demling, B.Weigle, C.W.Heizmann, P.M.Kroneck, G.Fritz. Structural and Functional Insights Into Rage Activation By Multimeric S100B. Embo J. V. 26 3868 2007.
ISSN: ISSN 0261-4189
PubMed: 17660747
DOI: 10.1038/SJ.EMBOJ.7601805