Calcium in PDB 1l6r: Crystal Structure of Thermoplasma Acidophilum 0175 (APC0014)

The structure of Crystal Structure of Thermoplasma Acidophilum 0175 (APC0014), PDB code: 1l6r was solved by Y.Kim, A.Joachimiak, A.M.Edwards, X.Xu, M.Pennycooke, J.Gu, F.Cheung, D.Christendat, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.00 / 1.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	88.240, 99.244, 113.781, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.5

The binding sites of Calcium atom in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC0014) (pdb code 1l6r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC0014), PDB code: 1l6r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC0014)


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 Thermoplasma Acidophilum 0175 (APC0014) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:12.7 occ:1.00 OD1 A:ASN177 2.4 14.0 1.0 OD2 A:ASP8 2.4 13.6 1.0 OD2 A:ASP178 2.4 12.9 1.0 OD1 A:ASP174 2.4 12.0 1.0 O A:HOH940 2.5 16.7 1.0 O A:HOH941 2.7 16.4 1.0 OD1 A:ASP178 2.9 14.9 1.0 CG A:ASP178 3.0 12.9 1.0 OG A:SER175 3.1 16.6 1.0 CG A:ASN177 3.4 12.9 1.0 CG A:ASP8 3.4 13.1 1.0 CG A:ASP174 3.6 11.9 1.0 ND2 A:ASN177 3.7 12.5 1.0 O A:HOH936 3.9 18.0 1.0 OD1 A:ASP8 4.0 14.5 1.0 N A:SER175 4.1 12.8 1.0 OD2 A:ASP174 4.2 12.6 1.0 NZ A:LYS151 4.2 14.5 1.0 N A:ASP174 4.3 11.6 1.0 OD1 A:ASP10 4.3 17.2 0.3 CB A:SER175 4.3 14.4 1.0 CB A:ASP178 4.4 12.4 1.0 CA A:GLY11 4.4 11.3 1.0 CB A:ASP8 4.5 11.2 1.0 N A:ASP178 4.6 12.6 1.0 CA A:SER175 4.7 12.6 1.0 CB A:ASN177 4.7 13.2 1.0 CB A:ASP174 4.8 10.6 1.0 C A:ASN177 4.8 12.3 1.0 N A:GLY11 4.8 11.5 1.0 C A:ASP174 4.8 11.4 1.0 CA A:ASP174 4.8 11.0 1.0 O A:SER175 4.9 12.8 1.0 C A:SER175 5.0 12.4 1.0 CE A:LYS151 5.0 14.3 1.0 CA A:ASP178 5.0 11.6 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC0014)


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 Thermoplasma Acidophilum 0175 (APC0014) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:11.4 occ:1.00 OD2 A:ASP174 2.4 12.6 1.0 O A:HOH922 2.4 14.4 1.0 O A:HOH938 2.5 15.9 1.0 O A:HOH935 2.5 16.5 1.0 O A:HOH933 2.5 16.9 1.0 O A:GLY11 2.5 13.2 1.0 O A:HOH919 2.5 13.4 1.0 CG A:ASP174 3.4 11.9 1.0 C A:GLY11 3.5 11.6 1.0 CA A:GLY11 3.7 11.3 1.0 CB A:ASP174 4.0 10.6 1.0 O A:HOH913 4.2 13.2 1.0 O A:HOH915 4.2 11.9 1.0 O A:HOH936 4.3 18.0 1.0 OD1 A:ASP174 4.5 12.0 1.0 O A:HOH934 4.5 17.4 1.0 ND2 A:ASN193 4.5 13.4 1.0 O A:HOH1065 4.5 29.2 1.0 O A:ASP10 4.5 13.0 0.3 O A:ASP10 4.5 12.5 0.7 OD1 A:ASN193 4.5 12.6 1.0 N A:ASN12 4.7 11.0 1.0 O A:HOH924 4.7 14.7 1.0 O A:HOH964 4.9 21.3 1.0 N A:GLY11 4.9 11.5 1.0 CG A:ASN193 4.9 10.5 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC0014)


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 Thermoplasma Acidophilum 0175 (APC0014) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:16.9 occ:1.00 O A:HOH921 3.1 15.9 1.0 O A:HOH910 3.1 11.5 1.0 O A:HOH953 3.2 16.0 1.0 N A:TYR140 3.3 10.2 1.0 O A:SER138 3.5 11.0 1.0 N A:ASN44 3.7 10.2 1.0 C A:GLY43 3.9 10.6 1.0 CA A:GLY139 3.9 11.2 1.0 CA A:ASN44 3.9 9.8 1.0 ND2 A:ASN44 4.0 13.3 1.0 CB A:ASN44 4.0 12.0 1.0 CB A:TYR140 4.0 12.0 1.0 NE2 A:HIS143 4.1 12.4 1.0 CD1 A:TYR140 4.1 11.8 1.0 C A:GLY139 4.1 11.3 1.0 CG A:ASN44 4.1 12.0 1.0 CA A:TYR140 4.2 10.1 1.0 CE1 A:HIS143 4.2 7.1 1.0 O A:GLY43 4.2 11.4 1.0 C A:SER138 4.3 10.5 1.0 CA A:GLY43 4.4 10.6 1.0 N A:SER141 4.5 9.8 1.0 CG A:TYR140 4.6 11.8 1.0 OD1 A:ASP10 4.6 14.3 0.7 N A:GLY139 4.6 10.7 1.0 OD2 A:ASP10 4.6 14.5 0.5 CG A:ASP10 4.7 14.1 0.6 O A:HOH914 4.8 12.1 1.0 N A:GLY43 4.8 10.2 1.0 C A:TYR140 4.8 9.7 1.0 NH2 A:ARG108 4.8 10.9 1.0 OD1 A:ASN44 4.9 12.4 1.0 OG A:SER141 4.9 10.9 1.0 OG A:SER42 5.0 17.2 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC0014)


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 Thermoplasma Acidophilum 0175 (APC0014) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:13.4 occ:1.00 OD1 B:ASP174 2.4 14.7 1.0 OD2 B:ASP8 2.4 14.1 1.0 O B:ASP10 2.5 14.3 1.0 O B:HOH921 2.5 15.8 1.0 OD2 B:ASP178 2.5 15.4 1.0 O B:HOH924 2.6 16.4 1.0 OG B:SER175 2.6 17.8 1.0 CG B:ASP8 3.4 15.3 1.0 CG B:ASP178 3.5 15.8 1.0 CG B:ASP174 3.5 15.5 1.0 OD1 B:ASP178 3.6 17.1 1.0 C B:ASP10 3.7 12.9 1.0 CB B:SER175 3.7 17.6 1.0 ND2 B:ASN12 3.8 14.7 1.0 OD1 B:ASP8 3.9 14.1 1.0 N B:SER175 3.9 15.6 1.0 OD2 B:ASP174 4.0 16.9 1.0 O B:HOH997 4.2 24.6 1.0 N B:ASP174 4.4 13.6 1.0 CA B:SER175 4.4 16.9 1.0 CB B:ASP10 4.5 12.8 1.0 CB B:ASP8 4.5 13.9 1.0 CA B:ASP10 4.5 12.2 1.0 O B:HOH1135 4.5 25.8 1.0 OD2 B:ASP10 4.6 15.7 1.0 OD1 B:ASN177 4.6 21.7 1.0 N B:GLY11 4.6 14.7 1.0 CA B:GLY11 4.7 15.9 1.0 CB B:ASP174 4.7 13.9 1.0 C B:ASP174 4.7 15.2 1.0 N B:ASP10 4.8 12.0 1.0 CA B:ASP174 4.8 13.6 1.0 CB B:ASP178 4.8 14.9 1.0 ND2 B:ASN177 4.8 20.8 1.0 O B:HOH913 4.9 14.4 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC0014)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Thermoplasma Acidophilum 0175 (APC0014) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca905 b:17.4 occ:1.00 OD1 B:ASN44 3.3 17.1 1.0 N B:VAL45 3.3 10.3 1.0 CA B:ASN44 3.5 11.3 1.0 CB B:ASN44 3.6 12.2 1.0 CG2 B:VAL45 3.7 11.6 1.0 CG2 B:THR104 3.8 11.4 1.0 CG2 B:VAL48 3.8 11.9 1.0 CG B:ASN44 3.8 13.6 1.0 C B:ASN44 3.9 10.3 1.0 CG1 B:VAL45 4.1 12.1 1.0 CB B:THR104 4.1 11.1 1.0 CB B:VAL48 4.2 10.1 1.0 CB B:VAL45 4.3 10.6 1.0 O B:HOH950 4.3 14.9 1.0 CA B:VAL45 4.4 9.6 1.0 CG1 B:VAL48 4.4 11.6 1.0 OG1 B:THR104 4.5 12.4 1.0 NH2 B:ARG108 4.7 9.8 0.3 N B:ASN44 4.8 11.5 1.0 O B:HOH959 4.9 15.9 1.0

Y.Kim, A.F.Yakunin, E.Kuznetsova, X.Xu, M.Pennycooke, J.Gu, F.Cheung, M.Proudfoot, C.H.Arrowsmith, A.Joachimiak, A.M.Edwards, D.Christendat. Structure- and Function-Based Characterization of A New Phosphoglycolate Phosphatase From Thermoplasma Acidophilum. J.Biol.Chem. V. 279 517 2004.
ISSN: ISSN 0021-9258
PubMed: 14555659
DOI: 10.1074/JBC.M306054200