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Calcium in PDB 5d7f: X-Ray Structure of Ca(2+)-S100B with Human Rage-Derived W72 Peptide

Protein crystallography data

The structure of X-Ray Structure of Ca(2+)-S100B with Human Rage-Derived W72 Peptide, PDB code: 5d7f was solved by J.L.Jensen, C.L.Colbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.20 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.089, 59.824, 47.563, 90.00, 111.65, 90.00
R / Rfree (%) 15.7 / 18.3

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of Ca(2+)-S100B with Human Rage-Derived W72 Peptide (pdb code 5d7f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Structure of Ca(2+)-S100B with Human Rage-Derived W72 Peptide, PDB code: 5d7f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5d7f

Go back to Calcium Binding Sites List in 5d7f
Calcium binding site 1 out of 4 in the X-Ray Structure of Ca(2+)-S100B with Human Rage-Derived W72 Peptide


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 Ca(2+)-S100B with Human Rage-Derived W72 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:16.9
occ:1.00
 O A:GLU22 2.3 21.6 1.0
O A:SER19 2.3 16.6 1.0
O A:LYS27 2.3 17.3 1.0
O A:HOH912 2.4 20.2 1.0
O A:ASP24 2.4 20.3 1.0
OE1 A:GLU32 2.4 16.2 1.0
OE2 A:GLU32 2.6 16.7 1.0
CD A:GLU32 2.9 15.4 1.0
C A:SER19 3.4 15.6 1.0
C A:GLU22 3.5 23.9 1.0
C A:ASP24 3.5 20.9 1.0
C A:LYS27 3.6 16.1 1.0
CA A:SER19 3.9 15.1 1.0
N A:GLU22 4.1 21.2 1.0
N A:ASP24 4.2 23.5 1.0
C A:GLY23 4.3 25.4 1.0
CA A:GLU22 4.4 24.4 1.0
N A:LYS29 4.4 14.0 1.0
OE1 A:GLU68 4.4 24.0 1.0
CG A:GLU32 4.4 14.4 1.0
CA A:ASP24 4.4 23.1 1.0
N A:LYS25 4.4 21.1 1.0
CA A:LYS25 4.5 21.5 1.0
N A:LYS27 4.5 17.0 1.0
N A:LEU28 4.5 13.9 1.0
CA A:LEU28 4.5 14.2 1.0
CB A:SER19 4.5 16.1 1.0
N A:GLY23 4.5 24.6 1.0
N A:GLY20 4.5 17.1 1.0
CA A:LYS27 4.6 17.3 1.0
O A:GLY23 4.6 25.7 1.0
O A:TYR18 4.7 14.8 1.0
CA A:GLY23 4.7 25.6 1.0
O A:HOH910 4.8 29.9 1.0
N A:ARG21 4.8 19.7 1.0
C A:LYS25 4.8 21.7 1.0
CB A:ASP24 4.8 24.5 1.0
C A:LEU28 4.9 13.8 1.0
CG A:LYS29 4.9 20.8 1.0
CB A:GLU22 4.9 29.2 1.0
CA A:GLY20 5.0 19.8 1.0
CD A:LYS29 5.0 27.1 1.0

Calcium binding site 2 out of 4 in 5d7f

Go back to Calcium Binding Sites List in 5d7f
Calcium binding site 2 out of 4 in the X-Ray Structure of Ca(2+)-S100B with Human Rage-Derived W72 Peptide


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 Ca(2+)-S100B with Human Rage-Derived W72 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:16.2
occ:1.00
 OD1 A:ASP62 2.3 19.2 1.0
O A:GLU68 2.3 16.7 1.0
OD1 A:ASP66 2.3 21.2 1.0
OD1 A:ASP64 2.4 23.9 1.0
O A:HOH948 2.4 22.4 1.0
OE1 A:GLU73 2.4 17.2 1.0
OE2 A:GLU73 2.6 17.7 1.0
CD A:GLU73 2.9 16.2 1.0
CG A:ASP66 3.3 24.2 1.0
CG A:ASP64 3.4 25.4 1.0
CG A:ASP62 3.4 18.5 1.0
C A:GLU68 3.5 15.6 1.0
OD2 A:ASP66 3.7 26.6 1.0
OD2 A:ASP64 3.9 28.8 1.0
CA A:ASP62 4.1 18.2 1.0
CB A:ASP62 4.2 17.8 1.0
N A:GLU68 4.2 16.7 1.0
OD2 A:ASP62 4.3 20.0 1.0
N A:ASP66 4.3 22.5 1.0
N A:ASP64 4.3 25.1 1.0
N A:CYS69 4.4 14.5 1.0
CA A:GLU68 4.4 16.3 1.0
CG A:GLU73 4.4 15.2 1.0
N A:ASP70 4.4 14.4 1.0
CA A:CYS69 4.5 14.7 1.0
CB A:ASP66 4.5 25.2 1.0
C A:ASP62 4.5 20.2 1.0
CB A:ASP64 4.6 25.7 1.0
N A:GLY65 4.6 24.0 1.0
N A:ASN63 4.6 21.8 1.0
CA A:ASP64 4.7 25.0 1.0
CA A:ASP66 4.8 23.2 1.0
C A:ASP64 4.8 26.3 1.0
N A:GLY67 4.8 18.6 1.0
CG A:ASP70 4.9 19.1 1.0
C A:CYS69 4.9 14.2 1.0
CB A:GLU68 5.0 18.9 1.0
OD2 A:ASP70 5.0 23.8 1.0

Calcium binding site 3 out of 4 in 5d7f

Go back to Calcium Binding Sites List in 5d7f
Calcium binding site 3 out of 4 in the X-Ray Structure of Ca(2+)-S100B with Human Rage-Derived W72 Peptide


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 Ca(2+)-S100B with Human Rage-Derived W72 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:16.6
occ:1.00
 O B:GLU22 2.3 22.7 1.0
O B:LYS27 2.3 17.0 1.0
O B:SER19 2.3 16.3 1.0
O B:HOH913 2.4 19.9 1.0
O B:ASP24 2.4 20.5 1.0
OE1 B:GLU32 2.4 16.0 1.0
OE2 B:GLU32 2.6 16.6 1.0
CD B:GLU32 2.9 15.3 1.0
C B:SER19 3.4 15.4 1.0
C B:GLU22 3.5 24.5 1.0
C B:ASP24 3.6 20.5 1.0
C B:LYS27 3.6 15.4 1.0
CA B:SER19 3.9 15.2 1.0
N B:GLU22 4.1 21.3 1.0
N B:ASP24 4.2 23.2 1.0
C B:GLY23 4.3 25.7 1.0
CA B:GLU22 4.4 24.2 1.0
N B:LYS29 4.4 13.7 1.0
CG B:GLU32 4.4 14.8 1.0
OE1 B:GLU68 4.4 20.5 0.7
CA B:ASP24 4.4 22.9 1.0
N B:LYS25 4.4 21.5 1.0
CA B:LYS25 4.5 21.6 1.0
N B:LYS27 4.5 16.9 1.0
N B:LEU28 4.5 13.9 1.0
CA B:LEU28 4.5 13.9 1.0
N B:GLY23 4.5 25.5 1.0
CB B:SER19 4.5 16.0 1.0
N B:GLY20 4.5 16.4 1.0
CA B:LYS27 4.6 17.0 1.0
O B:GLY23 4.7 26.4 1.0
O B:TYR18 4.7 15.2 1.0
O B:HOH920 4.7 29.4 1.0
CA B:GLY23 4.7 25.9 1.0
N B:ARG21 4.8 19.9 1.0
C B:LYS25 4.8 21.6 1.0
CB B:ASP24 4.9 24.5 1.0
C B:LEU28 4.9 13.4 1.0
CB B:GLU22 4.9 27.8 1.0
CG B:LYS29 4.9 20.6 1.0
CA B:GLY20 5.0 19.2 1.0

Calcium binding site 4 out of 4 in 5d7f

Go back to Calcium Binding Sites List in 5d7f
Calcium binding site 4 out of 4 in the X-Ray Structure of Ca(2+)-S100B with Human Rage-Derived W72 Peptide


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 Ca(2+)-S100B with Human Rage-Derived W72 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:16.2
occ:1.00
 O B:GLU68 2.3 17.2 1.0
OD1 B:ASP62 2.3 18.7 1.0
OD1 B:ASP64 2.3 23.3 1.0
OD1 B:ASP66 2.4 20.8 1.0
OE1 B:GLU73 2.4 17.0 1.0
O B:HOH948 2.5 20.8 1.0
OE2 B:GLU73 2.6 17.4 1.0
CD B:GLU73 2.9 15.6 1.0
CG B:ASP66 3.3 23.3 1.0
CG B:ASP64 3.4 25.5 1.0
CG B:ASP62 3.4 17.8 1.0
C B:GLU68 3.5 15.0 1.0
OD2 B:ASP66 3.8 25.4 1.0
OD2 B:ASP64 3.8 28.5 1.0
CA B:ASP62 4.1 18.3 1.0
CB B:ASP62 4.2 17.3 1.0
N B:GLU68 4.2 16.2 1.0
OD2 B:ASP62 4.3 20.1 1.0
N B:ASP66 4.3 22.1 1.0
N B:ASP64 4.3 24.5 1.0
N B:CYS69 4.4 14.1 1.0
CA B:GLU68 4.4 15.3 1.0
N B:ASP70 4.4 14.0 1.0
CG B:GLU73 4.4 15.5 1.0
CA B:CYS69 4.5 13.9 1.0
C B:ASP62 4.5 20.7 1.0
CB B:ASP66 4.5 23.5 1.0
CB B:ASP64 4.6 25.9 1.0
N B:ASN63 4.6 21.4 1.0
N B:GLY65 4.6 23.6 1.0
CA B:ASP64 4.7 25.1 1.0
CA B:ASP66 4.8 22.2 1.0
N B:GLY67 4.8 18.9 1.0
C B:ASP64 4.8 25.9 1.0
CG B:ASP70 4.9 19.0 1.0
OD2 B:ASP70 4.9 23.6 1.0
C B:CYS69 4.9 14.2 1.0
CB B:GLU68 5.0 17.5 1.0

Reference:

J.L.Jensen, C.L.Colbert. X-Ray Structure of Ca(2+)-S100B with Human Rage-Derived W72 Peptide To Be Published.
Page generated: Sun Jul 14 17:49:10 2024

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