Calcium in PDB 5da5: Crystal Structure of Rhodospirillum Rubrum RRU_A0973

The structure of Crystal Structure of Rhodospirillum Rubrum RRU_A0973, PDB code: 5da5 was solved by D.He, S.Vanden Hehier, A.Georgiev, K.Altenbach, E.Tarrant, C.L.Mackay, K.J.Waldron, D.J.Clarke, J.Marles-Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.63 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.184, 120.533, 140.250, 90.00, 95.36, 90.00
R / Rfree (%)	17.1 / 20.6

The structure of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 also contains other interesting chemical elements:

Iron

(Fe)

30 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 (pdb code 5da5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 28 binding sites of Calcium where determined in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973, PDB code: 5da5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 28 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973


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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:42.4 occ:1.00 OE1 J:GLU31 2.4 35.1 1.0 O A:HOH313 2.4 27.8 1.0 OE1 A:GLU31 2.5 41.0 1.0 O J:HOH314 2.5 28.0 1.0 O A:HOH316 2.6 51.1 1.0 OE2 A:GLU34 2.8 45.6 1.0 OE1 J:GLU34 2.9 56.1 1.0 O J:HOH331 3.5 34.9 1.0 CD A:GLU31 3.6 39.7 1.0 CD J:GLU31 3.6 45.2 1.0 O A:HOH303 3.6 43.1 1.0 O A:HOH306 3.8 41.3 1.0 H22 A:GOA202 3.8 42.5 1.0 HB3 J:GLU31 4.0 30.4 1.0 CD A:GLU34 4.0 56.7 1.0 OE2 A:GLU31 4.1 39.5 1.0 O J:HOH301 4.1 43.4 1.0 HB3 A:GLU31 4.1 31.3 1.0 CD J:GLU34 4.1 45.1 1.0 OE2 J:GLU31 4.3 43.0 1.0 HZ3 A:TRP38 4.4 72.4 1.0 HB3 A:GLU34 4.4 31.3 1.0 HA A:GLU31 4.4 29.0 1.0 HA J:GLU31 4.6 30.8 1.0 HG2 A:GLU34 4.6 44.9 1.0 CG J:GLU31 4.6 37.7 1.0 HB3 J:GLU34 4.7 26.6 1.0 C2 A:GOA202 4.7 35.4 1.0 CB J:GLU31 4.7 25.3 1.0 H21 A:GOA202 4.7 42.5 1.0 O A:GLU31 4.8 20.1 1.0 CG A:GLU31 4.8 35.2 1.0 CB A:GLU31 4.8 26.1 1.0 CG A:GLU34 4.8 37.4 1.0 HG3 J:GLU31 4.8 45.2 1.0 O J:GLU31 4.9 22.0 1.0 OE2 J:GLU34 4.9 66.9 1.0 HG2 J:GLU34 4.9 39.2 1.0 OE1 A:GLU34 5.0 55.7 1.0 HE3 A:TRP38 5.0 64.8 1.0

Calcium binding site 2 out of 28 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973


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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:38.7 occ:1.00 OE1 C:GLU31 2.3 42.2 1.0 O B:HOH316 2.4 31.8 1.0 OE1 B:GLU31 2.4 39.6 1.0 O C:HOH313 2.5 33.6 1.0 O B:HOH307 2.5 43.7 1.0 OE1 C:GLU34 2.7 45.0 1.0 OE2 B:GLU34 2.7 46.2 1.0 CD C:GLU31 3.5 40.9 1.0 O C:HOH310 3.5 33.2 1.0 CD B:GLU31 3.5 46.8 1.0 O C:HOH304 3.9 47.4 1.0 CD C:GLU34 3.9 47.5 1.0 O B:HOH318 3.9 40.8 1.0 CD B:GLU34 3.9 49.0 1.0 O B:HOH303 4.0 51.6 1.0 OE2 B:GLU31 4.1 50.4 1.0 HB3 C:GLU31 4.1 23.0 1.0 H22 B:GOA204 4.1 45.3 1.0 HB3 B:GLU31 4.1 27.6 1.0 OE2 C:GLU31 4.1 46.1 1.0 HB3 C:GLU34 4.5 24.2 1.0 HG2 B:GLU34 4.5 39.6 1.0 HA C:GLU31 4.6 25.5 1.0 HA B:GLU31 4.6 30.8 1.0 HB3 B:GLU34 4.6 32.9 1.0 HG2 C:GLU34 4.6 37.9 1.0 H21 B:GOA204 4.6 45.3 1.0 CG C:GLU31 4.6 27.6 1.0 OE2 C:GLU34 4.7 57.6 1.0 CG B:GLU31 4.7 30.1 1.0 CB C:GLU31 4.7 19.2 1.0 CB B:GLU31 4.8 23.0 1.0 CG C:GLU34 4.8 31.6 1.0 OE1 B:GLU34 4.8 53.9 1.0 CG B:GLU34 4.8 33.0 1.0 C2 B:GOA204 4.8 37.8 1.0 O C:GLU31 4.9 15.9 1.0 HG3 C:GLU31 4.9 33.1 1.0 O B:GLU31 4.9 21.5 1.0

Calcium binding site 3 out of 28 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973


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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:76.2 occ:1.00 O C:HOH330 2.4 48.7 1.0 O C:ASP44 2.6 28.9 1.0 C C:ASP44 3.7 29.3 1.0 HA C:ASP44 4.0 34.2 1.0 HA C:ALA45 4.4 34.6 1.0 CA C:ASP44 4.4 28.5 1.0 HB3 C:ASP44 4.7 40.5 1.0 O D:VAL14 4.7 38.9 1.0 HE3 D:LYS16 4.7 81.0 1.0 O C:SER46 4.7 29.3 1.0 N C:ALA45 4.8 28.3 1.0 CA C:ALA45 4.9 28.8 1.0

Calcium binding site 4 out of 28 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973


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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca203 b:85.1 occ:1.00 OE2 D:GLU61 2.7 63.0 1.0 NE2 D:HIS57 3.5 24.7 1.0 CD D:GLU61 3.6 41.2 1.0 OE1 E:GLU64 3.7 37.5 1.0 HE1 D:HIS57 3.8 38.6 1.0 OE1 D:GLU61 3.9 40.0 1.0 CE1 D:HIS57 4.0 32.1 1.0 CD E:GLU64 4.2 40.6 1.0 OE2 E:GLU64 4.3 53.9 1.0 CD2 D:HIS57 4.6 23.5 1.0 HD2 D:HIS57 4.9 28.2 1.0 CG D:GLU61 4.9 42.3 1.0 HG3 D:GLU61 5.0 50.8 1.0

Calcium binding site 5 out of 28 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973


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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca204 b:40.4 occ:1.00 OE1 D:GLU31 2.4 34.6 1.0 OE1 E:GLU31 2.4 43.6 1.0 O D:HOH317 2.5 33.9 1.0 O D:HOH320 2.6 49.5 1.0 O E:HOH313 2.7 34.1 1.0 OE1 D:GLU34 2.7 44.8 1.0 OE2 E:GLU34 2.9 51.5 1.0 CD D:GLU31 3.5 36.0 1.0 CD E:GLU31 3.6 40.6 1.0 O E:HOH333 3.7 33.8 1.0 O D:HOH312 3.8 33.5 1.0 O E:HOH307 3.9 46.2 1.0 CD D:GLU34 3.9 49.4 1.0 OE2 D:GLU31 4.0 44.3 1.0 OE2 E:GLU31 4.1 48.1 1.0 CD E:GLU34 4.1 47.4 1.0 H22 D:GOA202 4.2 41.5 1.0 HB3 D:GLU31 4.2 26.4 1.0 HB3 E:GLU31 4.2 26.1 1.0 O D:HOH316 4.4 47.3 1.0 HB3 D:GLU34 4.4 28.0 1.0 HA D:GLU31 4.6 20.9 1.0 HG2 D:GLU34 4.6 40.8 1.0 HA E:GLU31 4.6 26.0 1.0 HB3 E:GLU34 4.6 30.1 1.0 CG D:GLU31 4.7 28.6 1.0 OE2 D:GLU34 4.7 47.1 1.0 CG E:GLU31 4.8 33.1 1.0 CG D:GLU34 4.8 34.0 1.0 O D:GLU31 4.8 17.0 1.0 CB D:GLU31 4.8 22.0 1.0 HG2 E:GLU34 4.9 45.8 1.0 CB E:GLU31 4.9 21.7 1.0 OE1 E:GLU34 4.9 55.9 1.0 O E:GLU31 4.9 23.1 1.0 O12 D:GOA202 4.9 32.1 1.0

Calcium binding site 6 out of 28 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973


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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca206 b:75.5 occ:1.00 OE2 E:GLU61 2.6 45.9 1.0 OE1 E:GLU61 3.0 44.3 1.0 OE1 D:GLU64 3.0 37.6 1.0 CD E:GLU61 3.2 42.3 1.0 OE2 D:GLU61 3.5 63.0 1.0 HG2 D:GLU61 3.8 50.8 1.0 CD D:GLU61 3.9 41.2 1.0 CD D:GLU64 4.0 45.3 1.0 HE1 E:HIS57 4.0 37.2 1.0 CG D:GLU61 4.4 42.3 1.0 OE1 D:GLU61 4.5 40.0 1.0 HE2 D:HIS65 4.5 31.9 1.0 OE2 D:GLU64 4.6 48.4 1.0 CE1 E:HIS57 4.6 31.0 1.0 HB3 D:GLU61 4.7 34.1 1.0 NE2 E:HIS57 4.7 31.5 1.0 CG E:GLU61 4.7 41.4 1.0 HB3 D:GLU64 4.8 21.6 1.0 HG2 D:GLU64 4.8 31.8 1.0 HG2 E:GLU61 4.9 49.6 1.0 CG D:GLU64 4.9 26.5 1.0

Calcium binding site 7 out of 28 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973


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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca203 b:68.5 occ:1.00 O F:ASP44 2.3 30.9 1.0 O E:HOH302 2.4 47.0 1.0 O F:HOH316 2.5 36.3 1.0 O F:HOH332 2.8 44.8 1.0 O F:HOH304 3.3 41.6 1.0 C F:ASP44 3.5 27.9 1.0 HA F:ASP44 3.8 29.7 1.0 HA F:ALA45 4.1 29.6 1.0 CA F:ASP44 4.2 24.7 1.0 HZ2 E:LYS16 4.3 74.2 1.0 HZ1 E:LYS16 4.3 74.2 1.0 N F:ALA45 4.5 27.3 1.0 O F:SER46 4.5 20.2 1.0 HB3 F:ASP44 4.6 27.6 1.0 O E:VAL14 4.6 37.0 1.0 CA F:ALA45 4.7 24.6 1.0 NZ E:LYS16 4.7 61.9 1.0 O F:VAL43 4.7 24.6 1.0 HB E:VAL14 4.8 47.7 1.0 C F:ALA45 4.9 28.0 1.0 HZ3 E:LYS16 5.0 74.2 1.0 CB F:ASP44 5.0 23.0 1.0

Calcium binding site 8 out of 28 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973


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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca205 b:37.4 occ:1.00 O F:HOH309 2.4 31.2 1.0 OE1 H:GLU31 2.4 44.2 1.0 OE1 F:GLU31 2.5 37.7 1.0 O H:HOH304 2.5 30.2 1.0 O H:HOH323 2.7 40.6 1.0 OE1 H:GLU34 2.8 49.6 1.0 OE1 F:GLU34 2.9 46.8 1.0 CD H:GLU31 3.5 41.2 1.0 CD F:GLU31 3.6 41.4 1.0 OE2 H:GLU31 3.9 44.8 1.0 H21 F:GOA202 4.0 43.1 1.0 O F:HOH320 4.0 41.9 1.0 CD H:GLU34 4.0 44.8 1.0 HB3 H:GLU31 4.0 26.9 1.0 O H:HOH305 4.1 43.5 1.0 HB3 F:GLU31 4.1 25.4 1.0 CD F:GLU34 4.1 52.4 1.0 O F:HOH303 4.2 40.3 1.0 OE2 F:GLU31 4.2 48.2 1.0 HA H:GLU31 4.4 25.4 1.0 H22 F:GOA202 4.5 43.1 1.0 HB3 H:GLU34 4.5 25.9 1.0 HA F:GLU31 4.6 26.9 1.0 CG H:GLU31 4.6 28.1 1.0 HG2 H:GLU34 4.6 38.9 1.0 CB H:GLU31 4.7 22.4 1.0 HB3 F:GLU34 4.7 28.0 1.0 C2 F:GOA202 4.7 36.0 1.0 CG F:GLU31 4.8 34.8 1.0 O H:GLU31 4.8 20.2 1.0 CB F:GLU31 4.8 21.2 1.0 HG2 F:GLU34 4.8 41.6 1.0 O F:GLU31 4.8 20.1 1.0 CG H:GLU34 4.9 32.4 1.0 OE2 H:GLU34 4.9 53.3 1.0 OE2 F:GLU34 5.0 48.9 1.0 CA H:GLU31 5.0 21.1 1.0

Calcium binding site 9 out of 28 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973


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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca203 b:39.3 occ:1.00 O I:HOH323 2.4 32.2 1.0 O G:HOH321 2.4 30.5 1.0 OE1 I:GLU31 2.4 39.9 1.0 O I:HOH318 2.5 40.1 1.0 OE1 G:GLU31 2.5 41.1 1.0 OE1 G:GLU34 2.7 51.6 1.0 OE2 I:GLU34 3.0 43.6 1.0 CD I:GLU31 3.5 36.7 1.0 CD G:GLU31 3.6 44.9 1.0 O I:HOH314 3.6 35.7 1.0 H21 G:GOA202 3.7 43.8 1.0 O G:HOH325 3.9 39.9 1.0 CD G:GLU34 3.9 46.5 1.0 OE2 I:GLU31 4.0 34.6 1.0 O G:HOH317 4.0 51.3 1.0 HB3 I:GLU31 4.1 24.4 1.0 OE2 G:GLU31 4.1 48.7 1.0 HB3 G:GLU31 4.1 26.7 1.0 O I:HOH308 4.2 41.8 1.0 CD I:GLU34 4.2 46.0 1.0 H22 G:GOA202 4.5 43.8 1.0 HB3 G:GLU34 4.5 29.1 1.0 HA G:GLU31 4.5 28.3 1.0 HA I:GLU31 4.5 24.4 1.0 C2 G:GOA202 4.5 36.5 1.0 HB3 I:GLU34 4.6 33.0 1.0 CG I:GLU31 4.7 31.8 1.0 OE2 G:GLU34 4.7 55.0 1.0 HG2 I:GLU34 4.7 45.9 1.0 CG G:GLU31 4.7 36.3 1.0 CB I:GLU31 4.8 20.3 1.0 CB G:GLU31 4.8 22.3 1.0 HG2 G:GLU34 4.8 41.3 1.0 O G:GLU31 4.8 18.0 1.0 O I:GLU31 4.8 18.2 1.0 CG G:GLU34 4.9 34.4 1.0 CG I:GLU34 5.0 38.2 1.0

Calcium binding site 10 out of 28 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973


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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca201 b:57.5 occ:1.00 OD1 I:ASN76 2.6 27.3 1.0 O G:HOH309 2.6 42.3 1.0 O G:HOH301 2.7 41.5 1.0 HD21 I:ASN76 3.4 24.6 1.0 O I:HOH336 3.5 36.4 1.0 CG I:ASN76 3.5 31.9 1.0 ND2 I:ASN76 3.9 20.5 1.0 OD2 G:ASP48 4.0 41.6 1.0 HA I:ASN76 4.7 26.2 1.0 HD22 I:ASN76 4.7 24.6 1.0 OE2 G:GLU50 4.8 75.8 1.0 CB I:ASN76 4.9 20.6 1.0 O I:ARG75 5.0 20.8 1.0 HE1 I:TRP72 5.0 28.9 1.0 CG G:ASP48 5.0 34.3 1.0

D.He, S.Hughes, S.Vanden-Hehir, A.Georgiev, K.Altenbach, E.J.Tarrant, C.L.Mackay, K.J.Waldron, D.J.Clarke, J.Marles-Wright. Structural Characterization of Encapsulated Ferritin Provides Insight Into Iron Storage in Bacterial Nanocompartments. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27529188
DOI: 10.7554/ELIFE.18972