Calcium in PDB 1umn: Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis

The structure of Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis, PDB code: 1umn was solved by A.Kauko, S.Haataja, A.Pulliainen, J.Finne, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.08 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.735, 138.168, 142.707, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.4

The structure of Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis (pdb code 1umn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis, PDB code: 1umn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis


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 Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2173 b:35.2 occ:1.00 O C:HOH2053 2.3 38.9 1.0 OD1 A:ASP63 2.5 25.0 1.0 O A:HOH2043 2.5 23.9 1.0 O C:HOH2052 2.5 28.8 1.0 O A:HOH2044 2.6 45.1 1.0 CG A:ASP63 3.4 24.3 1.0 OD2 A:ASP63 3.6 24.9 1.0 O A:HOH2056 4.2 38.1 1.0 OD2 C:ASP74 4.5 20.6 1.0 O A:HOH2022 4.6 36.9 1.0 OD1 C:ASP74 4.7 20.4 1.0 CB A:ASP63 4.8 21.6 1.0 O A:ASP63 4.8 18.6 1.0

Calcium binding site 2 out of 16 in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis


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 Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2173 b:31.5 occ:1.00 O D:HOH2074 2.3 35.9 1.0 O D:HOH2064 2.4 40.8 1.0 O B:HOH2045 2.4 22.8 1.0 OD1 B:ASP63 2.5 21.9 1.0 O B:HOH2043 2.5 42.9 1.0 O D:HOH2073 2.7 24.4 1.0 CG B:ASP63 3.5 20.9 1.0 OD2 B:ASP63 3.8 23.4 1.0 O B:HOH2057 3.9 33.7 1.0 OD2 D:ASP74 4.5 17.6 1.0 OD1 D:ASP74 4.6 16.9 1.0 O D:HOH2075 4.7 24.4 1.0 O B:HOH2021 4.7 28.8 1.0 CB B:ASP63 4.8 19.6 1.0 O B:ASP63 4.9 17.6 1.0

Calcium binding site 3 out of 16 in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis


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 Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2173 b:34.3 occ:1.00 O A:HOH2024 2.2 41.0 1.0 O A:HOH2061 2.3 39.1 1.0 O C:HOH2038 2.4 45.1 1.0 OD1 C:ASP63 2.4 24.9 1.0 O A:HOH2063 2.4 24.2 1.0 O C:HOH2037 2.6 21.9 1.0 CG C:ASP63 3.4 23.9 1.0 OD2 C:ASP63 3.8 25.2 1.0 O C:HOH2046 4.1 23.9 1.0 OD2 A:ASP74 4.4 22.5 1.0 O C:HOH2018 4.5 31.9 1.0 OD1 A:ASP74 4.6 22.5 1.0 O A:HOH2060 4.7 26.6 1.0 CB C:ASP63 4.8 22.4 1.0 CG A:ASP74 4.9 22.2 1.0 O C:ASP63 4.9 20.8 1.0

Calcium binding site 4 out of 16 in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis


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 Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1175 b:27.3 occ:1.00 O D:HOH2114 2.4 24.1 1.0 O D:HOH2116 2.5 27.2 1.0 O D:HOH2032 2.5 40.4 1.0 O G:HOH2129 2.5 25.2 1.0 O D:HOH2112 2.5 39.5 1.0 O D:HOH2014 4.5 25.9 1.0 O D:ASN108 4.5 21.8 1.0 O D:HOH2031 4.7 31.8 1.0 O D:TYR107 4.7 19.9 1.0 CA D:ASN108 4.7 21.3 1.0 C D:ASN108 4.8 20.9 1.0 O G:GLY167 4.8 20.5 1.0 O D:ARG51 4.9 17.4 1.0 O D:VAL109 4.9 18.8 1.0

Calcium binding site 5 out of 16 in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis


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 Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2173 b:33.6 occ:1.00 O B:HOH2064 2.5 30.0 1.0 OD1 D:ASP63 2.5 23.3 1.0 O B:HOH2065 2.5 24.2 1.0 O D:HOH2049 2.5 31.9 1.0 O D:HOH2051 2.6 18.7 1.0 O B:HOH2024 2.6 39.5 1.0 CG D:ASP63 3.4 21.8 1.0 OD2 D:ASP63 3.5 24.0 1.0 O D:HOH2065 4.1 25.7 1.0 OD2 B:ASP74 4.5 19.1 1.0 OD1 B:ASP74 4.6 19.1 1.0 CB D:ASP63 4.8 20.2 1.0 O D:HOH2022 4.8 36.2 1.0 O D:ASP63 4.9 16.5 1.0 O B:HOH2056 4.9 24.5 1.0

Calcium binding site 6 out of 16 in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2173 b:42.5 occ:1.00 O E:HOH2020 2.3 47.6 1.0 OD1 E:ASP63 2.4 25.5 1.0 O G:HOH2058 2.4 33.2 1.0 O E:HOH2046 2.5 28.2 1.0 O G:HOH2056 2.7 32.8 1.0 CG E:ASP63 3.3 24.7 1.0 OD2 E:ASP63 3.5 26.5 1.0 O E:HOH2057 3.8 31.0 1.0 O E:HOH2022 4.3 32.7 1.0 OD2 G:ASP74 4.5 21.0 1.0 OD1 G:ASP74 4.6 21.0 1.0 CB E:ASP63 4.7 23.1 1.0 O G:HOH2055 4.7 30.1 1.0 O E:ASP63 4.8 20.4 1.0

Calcium binding site 7 out of 16 in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca2173 b:35.1 occ:1.00 O F:HOH2048 2.4 22.4 1.0 O H:HOH2044 2.5 34.2 1.0 OD1 F:ASP63 2.5 23.6 1.0 O H:HOH2045 2.5 33.1 1.0 O F:HOH2027 2.8 53.1 1.0 CG F:ASP63 3.5 22.3 1.0 OD2 F:ASP63 3.7 24.7 1.0 O F:HOH2054 3.9 29.6 1.0 OD2 H:ASP74 4.5 21.8 1.0 OD1 H:ASP74 4.6 21.8 1.0 O F:HOH2026 4.8 35.4 1.0 CB F:ASP63 4.8 20.7 1.0 O F:ASP63 4.9 18.0 1.0 O H:HOH2046 4.9 23.9 1.0 CG H:ASP74 5.0 21.9 1.0

Calcium binding site 8 out of 16 in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1174 b:28.9 occ:1.00 O G:HOH2097 2.4 28.9 1.0 O G:HOH2086 2.5 25.8 1.0 O G:ASN108 2.7 27.4 1.0 C G:ASN108 3.9 27.0 1.0 OE1 G:GLU113 4.4 23.8 1.0 CB G:ASN108 4.5 27.4 1.0 CA G:VAL109 4.7 26.4 1.0 OE2 G:GLU113 4.7 24.5 1.0 N G:VAL109 4.8 26.8 1.0 CA G:ASN108 4.9 26.9 1.0

Calcium binding site 9 out of 16 in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca2173 b:34.8 occ:1.00 O E:HOH2059 2.4 33.3 1.0 OD1 G:ASP63 2.4 26.6 1.0 O G:HOH2042 2.5 30.2 1.0 O E:HOH2025 2.5 41.9 1.0 O G:HOH2044 2.6 25.4 1.0 O E:HOH2060 2.6 33.5 1.0 CG G:ASP63 3.4 25.0 1.0 OD2 G:ASP63 3.6 26.4 1.0 O G:HOH2053 3.8 37.1 1.0 O E:HOH2062 4.2 38.5 1.0 OD2 E:ASP74 4.4 23.5 1.0 O G:HOH2022 4.6 35.5 1.0 OD1 E:ASP74 4.6 23.0 1.0 O E:HOH2061 4.7 30.0 1.0 CB G:ASP63 4.7 23.4 1.0 O G:ASP63 4.8 20.6 1.0 CG E:ASP74 5.0 23.2 1.0

Calcium binding site 10 out of 16 in the Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca2173 b:36.2 occ:1.00 O F:HOH2059 2.4 25.5 1.0 O H:HOH2029 2.5 39.5 1.0 O H:HOH2028 2.5 22.7 1.0 OD1 H:ASP63 2.6 22.4 1.0 O F:HOH2055 2.6 36.5 1.0 CG H:ASP63 3.5 21.8 1.0 OD2 H:ASP63 3.7 24.2 1.0 O H:HOH2039 4.2 36.2 1.0 OD2 F:ASP74 4.5 19.8 1.0 O H:HOH2013 4.5 31.9 1.0 OD1 F:ASP74 4.6 17.2 1.0 O F:HOH2056 4.8 20.6 1.0 CB H:ASP63 4.9 20.4 1.0 O H:ASP63 4.9 17.4 1.0

A.Kauko, S.Haataja, A.T.Pulliainen, J.Finne, A.C.Papageorgiou. Crystal Structure of Streptococcus Suis Dps-Like Peroxide Resistance Protein Dpr: Implications For Iron Incorporation. J. Mol. Biol. V. 338 547 2004.
ISSN: ISSN 0022-2836
PubMed: 15081812
DOI: 10.1016/J.JMB.2004.03.009