Calcium in PDB 2egd: Crystal Structure of Human S100A13 in the CA2+-Bound State

The structure of Crystal Structure of Human S100A13 in the CA2+-Bound State, PDB code: 2egd was solved by F.L.Imai, K.Nagata, N.Yonezawa, M.Nakano, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.14 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.774, 59.287, 77.624, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.4

The binding sites of Calcium atom in the Crystal Structure of Human S100A13 in the CA2+-Bound State (pdb code 2egd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human S100A13 in the CA2+-Bound State, PDB code: 2egd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human S100A13 in the CA2+-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human S100A13 in the CA2+-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:23.1 occ:1.00 O A:SER32 2.3 24.4 1.0 O A:ALA24 2.3 24.0 1.0 OE1 A:GLU37 2.4 25.3 1.0 O A:GLU27 2.4 22.4 1.0 O A:HOH313 2.4 27.9 1.0 O A:ARG29 2.5 25.8 1.0 OE2 A:GLU37 2.7 25.8 1.0 CD A:GLU37 2.9 24.2 1.0 C A:ALA24 3.3 24.1 1.0 C A:SER32 3.6 24.4 1.0 C A:ARG29 3.6 26.2 1.0 C A:GLU27 3.6 23.8 1.0 CA A:ALA24 3.8 25.1 1.0 N A:ARG29 4.1 26.1 1.0 C A:GLY28 4.2 26.1 1.0 N A:GLU27 4.2 23.2 1.0 N A:SER34 4.3 23.7 1.0 CG A:GLU37 4.4 24.4 1.0 CB A:ALA24 4.4 24.2 1.0 CA A:ARG29 4.4 26.4 1.0 N A:LEU33 4.4 24.1 1.0 CA A:LEU33 4.5 24.1 1.0 N A:SER32 4.5 25.4 1.0 N A:ARG25 4.5 24.2 1.0 O A:GLY28 4.5 25.5 1.0 CA A:LYS30 4.5 26.2 1.0 N A:LYS30 4.5 26.1 1.0 CA A:GLU27 4.5 24.1 1.0 OE2 A:GLU70 4.5 34.9 1.0 CA A:SER32 4.6 24.4 1.0 N A:GLY28 4.6 23.9 1.0 CA A:GLY28 4.6 25.3 1.0 OG A:SER32 4.7 25.9 1.0 CG A:GLU27 4.7 26.6 1.0 N A:GLN26 4.7 24.3 1.0 C A:LEU33 4.8 24.7 1.0 CA A:ARG25 4.8 24.8 1.0 C A:LYS30 4.8 26.2 1.0 C A:ARG25 5.0 24.1 1.0 O A:PHE23 5.0 25.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human S100A13 in the CA2+-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human S100A13 in the CA2+-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:22.7 occ:1.00 O A:HOH319 2.3 27.0 1.0 O A:GLU70 2.3 25.1 1.0 OD1 A:ASP64 2.3 26.3 1.0 OD1 A:ASP68 2.4 24.9 1.0 OD1 A:ASN66 2.4 24.6 1.0 OE1 A:GLU75 2.4 23.4 1.0 OE2 A:GLU75 2.6 25.0 1.0 CD A:GLU75 2.9 22.4 1.0 CG A:ASP68 3.3 25.6 1.0 CG A:ASP64 3.5 24.9 1.0 CG A:ASN66 3.5 26.6 1.0 C A:GLU70 3.5 25.1 1.0 OD2 A:ASP68 3.6 26.1 1.0 ND2 A:ASN66 3.9 30.9 1.0 CA A:ASP64 4.2 23.9 1.0 N A:GLU70 4.2 23.0 1.0 CB A:ASP64 4.2 23.7 1.0 OD2 A:ASP64 4.3 27.7 1.0 N A:ASP68 4.4 23.4 1.0 CG A:GLU75 4.4 22.6 1.0 CA A:LEU71 4.4 25.9 1.0 CA A:GLU70 4.4 24.0 1.0 N A:LEU71 4.4 24.2 1.0 C A:ASP64 4.4 23.8 1.0 N A:ASN66 4.5 24.6 1.0 CB A:ASP68 4.5 24.9 1.0 N A:LYS72 4.6 23.8 1.0 N A:VAL65 4.6 24.1 1.0 N A:GLN67 4.7 25.6 1.0 CD2 A:LEU71 4.7 25.3 1.0 CB A:ASN66 4.8 23.6 1.0 CA A:ASP68 4.8 24.6 1.0 N A:SER69 4.8 24.1 1.0 CB A:GLU70 4.9 25.3 1.0 C A:ASP68 4.9 24.2 1.0 C A:ASN66 4.9 24.8 1.0 C A:LEU71 5.0 25.5 1.0 CA A:ASN66 5.0 24.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human S100A13 in the CA2+-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human S100A13 in the CA2+-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:23.1 occ:1.00 O B:HOH311 2.4 25.6 1.0 O B:SER32 2.4 24.5 1.0 O B:GLU27 2.4 25.9 1.0 O B:ALA24 2.4 26.1 1.0 OE1 B:GLU37 2.4 24.3 1.0 O B:ARG29 2.4 23.6 1.0 OE2 B:GLU37 2.7 24.5 1.0 CD B:GLU37 2.9 21.4 1.0 C B:ALA24 3.5 24.4 1.0 C B:SER32 3.6 25.6 1.0 C B:ARG29 3.6 23.5 1.0 C B:GLU27 3.6 25.8 1.0 CA B:ALA24 4.0 24.8 1.0 N B:GLU27 4.1 24.8 1.0 N B:ARG29 4.2 23.8 1.0 C B:GLY28 4.2 25.5 1.0 N B:SER34 4.3 25.9 1.0 CG B:GLU37 4.4 22.9 1.0 CA B:LEU33 4.4 24.9 1.0 N B:SER32 4.4 24.4 1.0 N B:LEU33 4.4 25.3 1.0 CA B:LYS30 4.5 23.0 1.0 N B:LYS30 4.5 22.7 1.0 CA B:ARG29 4.5 24.3 1.0 CA B:GLU27 4.5 25.2 1.0 CB B:ALA24 4.5 25.6 1.0 O B:GLY28 4.6 25.1 1.0 OE1 B:GLU70 4.6 30.5 1.0 CA B:SER32 4.6 25.2 1.0 N B:GLY28 4.6 25.4 1.0 CA B:GLY28 4.6 26.1 1.0 N B:ARG25 4.6 24.8 1.0 CG B:GLU27 4.6 26.0 1.0 N B:GLN26 4.7 24.7 1.0 C B:LYS30 4.7 23.5 1.0 C B:LEU33 4.8 24.8 1.0 OG B:SER32 4.9 29.4 1.0 C B:ARG25 4.9 24.5 1.0 CA B:ARG25 4.9 23.9 1.0 O B:PHE23 5.0 24.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human S100A13 in the CA2+-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human S100A13 in the CA2+-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:24.8 occ:1.00 OD1 B:ASP64 2.2 23.9 1.0 O B:HOH320 2.3 31.1 1.0 OE1 B:GLU75 2.4 23.5 1.0 O B:GLU70 2.4 24.7 1.0 OD1 B:ASN66 2.4 22.4 1.0 OD1 B:ASP68 2.4 20.9 1.0 OE2 B:GLU75 2.6 23.1 1.0 CD B:GLU75 2.8 21.1 1.0 CG B:ASP64 3.3 25.4 1.0 CG B:ASP68 3.3 25.2 1.0 C B:GLU70 3.6 23.8 1.0 CG B:ASN66 3.6 26.9 1.0 OD2 B:ASP68 3.7 28.7 1.0 CA B:ASP64 4.0 25.0 1.0 CB B:ASP64 4.1 24.5 1.0 OD2 B:ASP64 4.1 26.2 1.0 N B:ASP68 4.2 24.0 1.0 ND2 B:ASN66 4.2 28.3 1.0 N B:GLU70 4.3 23.1 1.0 N B:ASN66 4.3 25.0 1.0 C B:ASP64 4.4 25.4 1.0 CG B:GLU75 4.4 22.9 1.0 CA B:LEU71 4.4 25.1 1.0 CA B:GLU70 4.4 23.9 1.0 O B:HOH321 4.4 32.2 1.0 N B:LEU71 4.5 23.2 1.0 N B:VAL65 4.5 25.7 1.0 CB B:ASP68 4.5 24.9 1.0 N B:LYS72 4.6 24.9 1.0 O B:HOH307 4.6 28.4 1.0 N B:GLN67 4.6 24.0 1.0 CB B:ASN66 4.7 25.2 1.0 CD2 B:LEU71 4.8 26.2 1.0 CA B:ASP68 4.8 24.8 1.0 CB B:GLU70 4.8 24.8 1.0 C B:ASN66 4.8 24.1 1.0 CA B:ASN66 4.8 24.8 1.0 N B:SER69 4.9 24.3 1.0 O B:ASP64 5.0 25.1 1.0

F.L.Imai, K.Nagata, N.Yonezawa, M.Nakano, M.Tanokura. Crystal Structure of Human S100A13 in the CA2+-Bound State Acta Crystallogr.,Sect.F V. 64 70 2008.
ISSN: ESSN 1744-3091
PubMed: 18259052
DOI: 10.1107/S1744309107068236