Calcium in PDB 5l89: Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A

The structure of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, PDB code: 5l89 was solved by D.He, S.Hughes, S.Vanden-Hehir, 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)	48.84 / 2.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	97.783, 120.281, 140.534, 90.00, 95.41, 90.00
R / Rfree (%)	18.6 / 22.1

The binding sites of Calcium atom in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A (pdb code 5l89). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, PDB code: 5l89:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A


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 Mutant E32A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:71.3 occ:1.00 O C:HOH307 2.4 43.8 1.0 O C:ASP44 2.5 55.1 1.0 C C:ASP44 3.7 37.7 1.0 HG22 D:VAL14 3.8 57.3 1.0 HA C:ASP44 3.9 43.7 1.0 HG23 D:VAL14 4.2 57.3 1.0 HE2 D:LYS16 4.2 86.0 1.0 CA C:ASP44 4.3 36.4 1.0 HA C:ALA45 4.4 42.3 1.0 CG2 D:VAL14 4.4 47.8 1.0 O D:VAL14 4.5 51.2 1.0 HB3 C:ASP44 4.5 48.2 1.0 HE3 D:LYS16 4.6 86.0 1.0 HG21 D:VAL14 4.7 57.3 1.0 N C:ALA45 4.7 35.2 1.0 CE D:LYS16 4.9 71.7 1.0 O C:SER46 4.9 41.7 1.0 CB C:ASP44 4.9 40.1 1.0 CA C:ALA45 5.0 35.3 1.0

Calcium binding site 2 out of 9 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A


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 Mutant E32A within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:74.6 occ:1.00 O G:HOH314 2.2 39.5 1.0 OE1 I:GLU31 2.6 70.0 1.0 OE1 G:GLU34 3.0 48.1 1.0 HG2 G:GLU31 3.4 67.7 1.0 OE2 I:GLU34 3.8 64.0 1.0 CD I:GLU31 3.8 71.3 1.0 CD G:GLU34 4.1 56.4 1.0 HA G:GLU31 4.2 35.1 1.0 HB3 G:GLU34 4.2 41.6 1.0 HB3 I:GLU31 4.3 34.5 1.0 CG G:GLU31 4.3 56.4 1.0 OE2 G:GLU31 4.4 61.7 1.0 OE2 I:GLU31 4.5 71.7 1.0 HZ3 G:TRP38 4.7 78.3 1.0 HA I:GLU31 4.7 43.8 1.0 O G:GLU31 4.7 21.8 1.0 HB3 I:GLU34 4.8 50.5 1.0 OE2 G:GLU34 4.8 68.5 1.0 CD I:GLU34 4.8 59.7 1.0 HZ3 I:TRP38 4.8 73.9 1.0 CD G:GLU31 4.9 70.7 1.0 HG3 G:GLU31 4.9 67.7 1.0 CG I:GLU31 4.9 46.3 1.0 CB I:GLU31 4.9 28.8 1.0 CA G:GLU31 5.0 29.3 1.0 CB G:GLU34 5.0 34.7 1.0

Calcium binding site 3 out of 9 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A


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 Mutant E32A within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca201 b:78.5 occ:1.00 OE2 M:GLU31 2.4 68.4 1.0 OE1 L:GLU31 2.6 63.2 1.0 OE2 L:GLU34 3.1 62.3 1.0 OE1 M:GLU34 3.2 57.9 1.0 CD M:GLU31 3.2 75.6 1.0 OE1 M:GLU31 3.5 64.8 1.0 CD L:GLU31 3.8 56.7 1.0 CD L:GLU34 4.0 53.1 1.0 CD M:GLU34 4.2 58.5 1.0 HZ3 M:TRP38 4.2 71.2 1.0 HH2 M:TRP38 4.2 73.4 1.0 OE2 L:GLU31 4.3 63.6 1.0 OE1 L:GLU34 4.4 61.1 1.0 CZ3 M:TRP38 4.5 59.4 1.0 HB3 L:GLU31 4.5 43.3 1.0 HG2 M:GLU31 4.5 61.2 1.0 CH2 M:TRP38 4.5 61.2 1.0 CG M:GLU31 4.5 51.0 1.0 OE2 M:GLU34 4.6 73.2 1.0 HA L:GLU31 4.8 37.7 1.0 HB3 M:GLU34 4.8 41.1 1.0 HB3 L:GLU34 4.8 47.8 1.0 CG L:GLU31 4.9 40.4 1.0 HA M:GLU31 4.9 34.3 1.0 HH2 L:TRP38 4.9 78.7 1.0

Calcium binding site 4 out of 9 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A


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 Mutant E32A within 5.0Å range: probe atom residue distance (Å) B Occ N:Ca201 b:72.0 occ:1.00 O N:ASP44 2.5 47.2 1.0 O N:HOH302 2.6 51.5 1.0 O N:HOH312 2.6 38.8 1.0 HA N:ASP44 3.3 35.0 1.0 C N:ASP44 3.5 35.5 1.0 CA N:ASP44 3.9 29.2 1.0 O N:VAL43 4.1 41.6 1.0 O N:SER46 4.3 47.0 1.0 HE3 M:LYS16 4.5 85.8 1.0 N N:ALA45 4.7 37.6 1.0 HB3 N:ASP44 4.7 43.4 1.0 HA N:ALA45 4.8 39.7 1.0 CB N:ASP44 4.9 36.2 1.0 C N:VAL43 4.9 32.7 1.0 N N:ASP44 4.9 32.6 1.0

Calcium binding site 5 out of 9 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A


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 Mutant E32A within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca201 b:91.3 occ:1.00 OE2 R:GLU31 2.5 80.0 1.0 OE1 P:GLU31 3.1 84.7 1.0 OE1 P:GLU34 3.1 65.1 1.0 OE1 R:GLU34 3.2 65.2 1.0 OE2 P:GLU31 3.3 61.4 1.0 CD P:GLU31 3.6 72.7 1.0 CD R:GLU31 3.6 80.0 1.0 O P:HOH305 3.7 48.4 1.0 CD P:GLU34 4.0 60.0 1.0 CD R:GLU34 4.0 55.3 1.0 OE1 R:GLU31 4.1 70.3 1.0 OE2 P:GLU34 4.2 66.5 1.0 OE2 R:GLU34 4.2 62.0 1.0 HH2 R:TRP38 4.3 80.3 1.0 HZ3 R:TRP38 4.5 79.5 1.0 HH2 P:TRP38 4.5 81.6 1.0 HZ3 P:TRP38 4.6 85.5 1.0 CH2 R:TRP38 4.7 66.9 1.0 CZ3 R:TRP38 4.8 66.2 1.0 HG3 R:GLU31 4.8 95.4 1.0 CG R:GLU31 4.9 79.5 1.0 CH2 P:TRP38 4.9 68.0 1.0 CZ3 P:TRP38 4.9 71.3 1.0

Calcium binding site 6 out of 9 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A


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 Mutant E32A within 5.0Å range: probe atom residue distance (Å) B Occ Q:Ca201 b:74.0 occ:1.00 O S:HOH211 2.4 47.8 1.0 OE2 S:GLU31 2.9 64.8 1.0 OE2 Q:GLU31 3.1 60.1 1.0 OE2 S:GLU34 3.4 65.8 1.0 OE1 Q:GLU34 3.4 65.2 1.0 HG3 Q:GLU31 3.4 68.5 1.0 CD S:GLU31 3.9 55.5 1.0 CD Q:GLU31 4.0 55.7 1.0 CG Q:GLU31 4.1 57.1 1.0 CD Q:GLU34 4.3 57.7 1.0 CD S:GLU34 4.4 55.2 1.0 HZ3 S:TRP38 4.4 75.2 1.0 HB3 S:GLU31 4.4 41.3 1.0 HZ3 Q:TRP38 4.5 82.7 1.0 OE1 S:GLU31 4.5 59.2 1.0 HG2 Q:GLU31 4.5 68.5 1.0 HB3 S:GLU34 4.7 47.1 1.0 HA Q:GLU31 4.7 39.9 1.0 HA S:GLU31 4.7 34.4 1.0 HB3 Q:GLU34 4.7 39.2 1.0 HH2 S:TRP38 4.7 76.7 1.0 CZ3 S:TRP38 4.8 62.7 1.0 HG3 S:GLU31 4.8 53.5 1.0 CG S:GLU31 4.8 44.6 1.0 OE2 Q:GLU34 4.8 61.7 1.0 CZ3 Q:TRP38 4.9 68.9 1.0 HH2 Q:TRP38 4.9 81.7 1.0 OE1 S:GLU34 4.9 62.1 1.0 CH2 S:TRP38 4.9 63.9 1.0

Calcium binding site 7 out of 9 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A


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 Mutant E32A within 5.0Å range: probe atom residue distance (Å) B Occ U:Ca201 b:40.8 occ:0.47 HZ1 V:LYS63 1.9 50.4 1.0 OD2 V:ASP40 2.6 44.6 1.0 OD2 U:ASP77 2.6 43.0 1.0 HD2 V:ARG59 2.8 42.1 1.0 NZ V:LYS63 2.8 42.0 1.0 HZ2 V:LYS63 3.2 50.4 1.0 HZ3 V:LYS63 3.3 50.4 1.0 O U:HOH307 3.3 24.3 1.0 HE U:ARG22 3.3 44.0 1.0 HE3 V:LYS63 3.4 49.0 1.0 CG V:ASP40 3.4 42.1 1.0 HE2 V:LYS63 3.5 49.0 1.0 CE V:LYS63 3.5 40.9 1.0 CD V:ARG59 3.6 35.1 1.0 NE U:ARG22 3.7 36.7 1.0 CG U:ASP77 3.7 39.5 1.0 OD1 V:ASP40 3.8 32.9 1.0 HH21 U:ARG22 3.8 42.0 1.0 NE V:ARG59 3.8 43.4 1.0 HD2 U:ARG22 4.0 39.7 1.0 CZ U:ARG22 4.1 31.8 1.0 NH2 U:ARG22 4.1 35.0 1.0 HE V:ARG59 4.1 52.1 1.0 HH11 V:ARG59 4.1 35.0 1.0 CZ V:ARG59 4.1 38.6 1.0 HD3 V:ARG59 4.1 42.1 1.0 OD1 U:ASP77 4.2 44.6 1.0 NH1 V:ARG59 4.3 29.1 1.0 CD U:ARG22 4.3 33.0 1.0 HG2 V:ARG59 4.5 38.6 1.0 HG13 V:VAL36 4.5 40.2 1.0 HB2 V:ASP40 4.6 40.0 1.0 HD3 U:ARG22 4.6 39.7 1.0 CG V:ARG59 4.6 32.1 1.0 HH22 U:ARG22 4.7 42.0 1.0 CB V:ASP40 4.7 33.4 1.0 HH12 V:ARG59 4.8 35.0 1.0 HB2 U:ASP77 4.8 41.0 1.0 HG3 V:ARG59 4.9 38.6 1.0 NH2 V:ARG59 4.9 43.4 1.0 HG12 V:VAL36 4.9 40.2 1.0 OD1 V:ASP60 4.9 45.5 1.0 CB U:ASP77 5.0 34.2 1.0 CD V:LYS63 5.0 38.7 1.0 NH1 U:ARG22 5.0 37.6 1.0

Calcium binding site 8 out of 9 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A


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 Mutant E32A within 5.0Å range: probe atom residue distance (Å) B Occ V:Ca201 b:72.2 occ:1.00 OE1 V:GLU31 3.3 72.7 1.0 HB3 V:GLU31 3.4 51.9 1.0 OE1 W:GLU31 3.7 72.6 1.0 HB3 W:GLU31 3.8 50.7 1.0 HB2 W:ALA35 4.0 33.5 1.0 OE1 W:GLU34 4.2 66.6 1.0 O W:GLU31 4.3 37.7 1.0 CB V:GLU31 4.3 43.2 1.0 HB3 W:GLU34 4.3 49.1 1.0 HA W:GLU31 4.3 50.1 1.0 HA V:GLU31 4.4 41.9 1.0 CD V:GLU31 4.4 64.4 1.0 HB2 V:ALA35 4.4 29.9 1.0 OE2 V:GLU34 4.5 48.7 1.0 O V:GLU31 4.5 33.5 1.0 CB W:GLU31 4.7 42.2 1.0 HB3 V:GLU34 4.8 37.7 1.0 CD W:GLU31 4.8 72.1 1.0 CA V:GLU31 4.8 34.9 1.0 HZ3 W:TRP38 4.8 83.5 1.0 CA W:GLU31 4.8 41.7 1.0 CG V:GLU31 4.8 52.4 1.0 C W:GLU31 4.8 34.8 1.0 CB W:ALA35 4.9 27.9 1.0 HB2 V:GLU31 4.9 51.9 1.0 H W:ALA35 4.9 36.5 1.0 C V:GLU31 5.0 32.4 1.0 HG3 V:GLU31 5.0 62.8 1.0

Calcium binding site 9 out of 9 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A


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 Mutant E32A within 5.0Å range: probe atom residue distance (Å) B Occ d:Ca201 b:83.8 occ:1.00 OE1 d:GLU31 3.0 70.2 1.0 OE1 d:GLU34 3.2 63.1 1.0 OE2 U:GLU34 3.3 63.6 1.0 HG2 U:GLU31 3.9 45.5 1.0 HZ3 d:TRP38 3.9 76.8 1.0 CD d:GLU34 4.2 61.3 1.0 CD d:GLU31 4.2 67.6 1.0 HB3 d:GLU31 4.2 47.5 1.0 CD U:GLU34 4.3 64.5 1.0 CZ3 d:TRP38 4.4 64.0 1.0 HH2 d:TRP38 4.4 75.9 1.0 HB3 d:GLU34 4.5 43.1 1.0 HB3 U:GLU31 4.5 39.0 1.0 HA d:GLU31 4.6 42.5 1.0 CH2 d:TRP38 4.7 63.2 1.0 OE2 d:GLU34 4.7 70.2 1.0 HZ3 U:TRP38 4.8 89.6 1.0 OE1 U:GLU34 4.8 70.4 1.0 HB3 U:GLU34 4.8 41.5 1.0 CG U:GLU31 4.8 38.0 1.0 HA U:GLU31 4.9 40.5 1.0 CB d:GLU31 5.0 39.6 1.0 HH2 U:TRP38 5.0 92.2 1.0

D.He, S.Hughes, S.Vanden-Hehir, A.Georgiev, K.Altenbach, E.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