Calcium in PDB 1mr8: Migration Inhibitory Factor-Related Protein 8 From Human

The structure of Migration Inhibitory Factor-Related Protein 8 From Human, PDB code: 1mr8 was solved by K.Ishikawa, A.Nakagawa, I.Tanaka, J.Nishihira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.500, 52.500, 128.600, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 23.4

The binding sites of Calcium atom in the Migration Inhibitory Factor-Related Protein 8 From Human (pdb code 1mr8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Migration Inhibitory Factor-Related Protein 8 From Human, PDB code: 1mr8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Migration Inhibitory Factor-Related Protein 8 From Human


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Migration Inhibitory Factor-Related Protein 8 From Human within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:11.3 occ:1.00 OD1 A:ASP59 2.4 10.0 1.0 O A:ALA65 2.4 10.1 1.0 OD1 A:ASN61 2.5 14.9 1.0 OD1 A:ASP63 2.5 10.6 1.0 O A:HOH140 2.6 14.9 1.0 OE2 A:GLU70 2.6 9.6 1.0 OE1 A:GLU70 2.6 13.4 1.0 CD A:GLU70 3.0 13.6 1.0 CG A:ASP63 3.3 10.1 1.0 CG A:ASP59 3.5 15.6 1.0 OD2 A:ASP63 3.5 10.7 1.0 C A:ALA65 3.6 10.5 1.0 CG A:ASN61 3.6 14.1 1.0 CA A:ASP59 4.1 13.0 1.0 ND2 A:ASN61 4.2 11.1 1.0 N A:ALA65 4.3 11.8 1.0 N A:ASP63 4.3 14.4 1.0 OD2 A:ASP59 4.3 17.1 1.0 CB A:ASP59 4.3 13.0 1.0 N A:VAL66 4.4 10.6 1.0 CG A:GLU70 4.5 11.9 1.0 CA A:VAL66 4.5 10.1 1.0 CA A:ALA65 4.5 10.3 1.0 C A:ASP59 4.5 12.1 1.0 N A:ASN61 4.5 14.4 1.0 N A:ILE60 4.6 13.0 1.0 CB A:ASP63 4.6 10.4 1.0 N A:THR62 4.6 12.1 1.0 N A:ASN67 4.8 10.1 1.0 CB A:ASN61 4.8 11.4 1.0 CA A:ASP63 4.9 13.1 1.0

Calcium binding site 2 out of 4 in the Migration Inhibitory Factor-Related Protein 8 From Human


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Migration Inhibitory Factor-Related Protein 8 From Human within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:33.1 occ:1.00 O A:ALA28 2.4 15.3 1.0 O A:LYS23 2.5 13.7 1.0 O A:SER20 2.5 15.6 1.0 O A:HOH141 2.5 14.4 1.0 O A:ASN25 2.5 11.4 1.0 C A:SER20 3.4 14.9 1.0 C A:ASN25 3.6 10.4 1.0 CE2 A:TYR30 3.6 8.9 1.0 C A:ALA28 3.6 15.5 1.0 C A:LYS23 3.7 15.8 1.0 CA A:SER20 3.7 12.3 1.0 N A:LYS23 3.9 15.8 1.0 CA A:PHE26 4.0 11.6 1.0 CD2 A:TYR30 4.1 11.2 1.0 N A:ALA28 4.1 12.4 1.0 N A:PHE26 4.2 9.2 1.0 O A:TYR19 4.3 12.6 1.0 CA A:ALA28 4.3 15.2 1.0 N A:ASN25 4.3 12.9 1.0 CA A:LYS23 4.4 14.5 1.0 C A:PHE26 4.4 13.0 1.0 OD2 A:ASP33 4.5 15.3 1.0 CZ A:TYR30 4.5 10.4 1.0 N A:LEU21 4.5 14.2 1.0 C A:GLY24 4.5 15.5 1.0 N A:ILE22 4.5 13.7 1.0 CB A:SER20 4.5 9.1 1.0 N A:VAL29 4.6 15.3 1.0 CA A:ASN25 4.6 12.5 1.0 CD1 A:PHE26 4.7 10.0 1.0 N A:GLY24 4.7 13.9 1.0 OH A:TYR30 4.7 10.7 1.0 CB A:ALA28 4.7 12.8 1.0 CA A:VAL29 4.7 13.6 1.0 N A:HIS27 4.8 13.8 1.0 CA A:GLY24 4.9 15.1 1.0 O A:GLY24 4.9 15.5 1.0 N A:SER20 4.9 12.2 1.0 CG A:LYS23 4.9 13.1 1.0 CA A:LEU21 4.9 15.3 1.0 C A:LEU21 5.0 15.6 1.0 O A:PHE26 5.0 12.5 1.0 C A:ILE22 5.0 16.8 1.0

Calcium binding site 3 out of 4 in the Migration Inhibitory Factor-Related Protein 8 From Human


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Migration Inhibitory Factor-Related Protein 8 From Human within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:13.4 occ:1.00 O B:ALA65 2.3 14.2 1.0 OD1 B:ASN61 2.4 14.3 1.0 OD1 B:ASP59 2.4 10.8 1.0 OD1 B:ASP63 2.6 8.8 1.0 OE2 B:GLU70 2.6 6.9 1.0 OE1 B:GLU70 2.6 13.1 1.0 O B:HOH165 2.6 28.5 1.0 CD B:GLU70 2.9 13.1 1.0 CG B:ASP63 3.3 13.5 1.0 CG B:ASN61 3.5 14.9 1.0 C B:ALA65 3.5 13.9 1.0 CG B:ASP59 3.5 13.2 1.0 OD2 B:ASP63 3.5 14.2 1.0 ND2 B:ASN61 4.0 18.2 1.0 CA B:ASP59 4.1 12.2 1.0 N B:ASP63 4.2 16.7 1.0 N B:ALA65 4.3 12.7 1.0 N B:ASN61 4.3 16.0 1.0 CB B:ASP59 4.3 11.4 1.0 OD2 B:ASP59 4.4 16.3 1.0 N B:VAL66 4.4 12.3 1.0 CA B:VAL66 4.4 10.3 1.0 C B:ASP59 4.4 13.6 1.0 CA B:ALA65 4.4 11.6 1.0 CG B:GLU70 4.5 7.9 1.0 CB B:ASP63 4.5 13.0 1.0 N B:ILE60 4.5 15.7 1.0 N B:ASN67 4.5 9.8 1.0 N B:THR62 4.6 13.9 1.0 CB B:ASN61 4.7 13.5 1.0 CA B:ASP63 4.8 13.3 1.0 CA B:ASN61 4.8 15.2 1.0 C B:ASN61 4.8 13.9 1.0 ND2 B:ASN67 4.9 11.4 1.0 CB B:ALA65 4.9 11.9 1.0 C B:VAL66 5.0 10.4 1.0 CG B:ASN67 5.0 13.5 1.0 O B:ASP59 5.0 13.2 1.0 N B:GLY64 5.0 11.6 1.0

Calcium binding site 4 out of 4 in the Migration Inhibitory Factor-Related Protein 8 From Human


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Migration Inhibitory Factor-Related Protein 8 From Human within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:35.6 occ:1.00 O B:ALA28 2.4 12.1 1.0 O B:HOH166 2.4 7.9 1.0 O B:SER20 2.4 11.1 1.0 O B:LYS23 2.4 13.6 1.0 O B:ASN25 2.6 15.1 1.0 C B:SER20 3.3 11.8 1.0 C B:ALA28 3.5 13.4 1.0 CA B:SER20 3.6 11.3 1.0 C B:LYS23 3.6 15.6 1.0 C B:ASN25 3.7 14.7 1.0 CE2 B:TYR30 3.7 7.7 1.0 N B:LYS23 4.1 14.0 1.0 O B:HOH134 4.2 30.1 1.0 CD2 B:TYR30 4.2 6.1 1.0 C B:GLY24 4.2 16.5 1.0 CB B:SER20 4.3 9.6 1.0 N B:ASN25 4.3 15.5 1.0 N B:ALA28 4.3 14.3 1.0 CA B:ALA28 4.3 12.4 1.0 N B:LEU21 4.4 12.0 1.0 O B:GLY24 4.4 18.9 1.0 OD2 B:ASP33 4.4 14.6 1.0 N B:PHE26 4.5 14.9 1.0 O B:TYR19 4.5 14.4 1.0 CA B:LYS23 4.5 14.2 1.0 CA B:PHE26 4.5 11.9 1.0 N B:VAL29 4.5 10.2 1.0 N B:GLY24 4.6 14.2 1.0 CB B:ALA28 4.6 11.4 1.0 CA B:GLY24 4.6 14.1 1.0 CA B:ASN25 4.6 14.5 1.0 CZ B:TYR30 4.6 10.8 1.0 CA B:VAL29 4.6 10.4 1.0 C B:PHE26 4.7 11.9 1.0 OH B:TYR30 4.8 14.1 1.0 N B:ILE22 4.8 12.1 1.0 N B:SER20 4.8 10.7 1.0 O B:PHE26 4.9 13.1 1.0 C B:LEU21 4.9 14.2 1.0 CA B:LEU21 5.0 14.5 1.0

K.Ishikawa, A.Nakagawa, I.Tanaka, M.Suzuki, J.Nishihira. The Structure of Human MRP8, A Member of the S100 Calcium-Binding Protein Family, By Mad Phasing at 1.9 A Resolution. Acta Crystallogr.,Sect.D V. 56 559 2000.
ISSN: ISSN 0907-4449
PubMed: 10771424
DOI: 10.1107/S0907444900002833