Calcium in PDB 6sv1: Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant

The structure of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant, PDB code: 6sv1 was solved by J.Marles-Wright, D.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.73 / 2.19
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	97.794, 120.136, 139.335, 90.00, 95.20, 90.00
R / Rfree (%)	17.1 / 20.7

The structure of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant also contains other interesting chemical elements:

Iron

(Fe)

30 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant (pdb code 6sv1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant, PDB code: 6sv1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant


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 E34A Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:84.3 occ:1.00 O B:HOH322 2.3 44.1 1.0 OE2 B:GLU61 2.5 55.8 1.0 OE1 C:GLU64 3.2 55.8 1.0 CD B:GLU61 3.4 49.4 1.0 OE1 B:GLU61 3.4 42.3 1.0 O C:HOH307 3.6 47.0 1.0 OE2 C:GLU61 3.8 49.9 1.0 CD C:GLU64 3.9 54.6 1.0 OE2 C:GLU64 4.1 61.9 1.0 CD C:GLU61 4.3 45.6 1.0 HE1 B:HIS57 4.4 56.6 1.0 HG2 C:GLU61 4.4 45.6 1.0 NE2 B:HIS57 4.5 50.5 1.0 OE1 C:GLU61 4.7 42.4 1.0 CE1 B:HIS57 4.8 47.2 1.0 CG B:GLU61 4.8 42.0 1.0 CG C:GLU61 4.9 38.0 1.0 HE2 C:HIS65 5.0 36.9 1.0 HG2 B:GLU61 5.0 50.4 1.0

Calcium binding site 2 out of 18 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant


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 E34A Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:56.3 occ:1.00 O C:HOH304 2.3 40.8 1.0 O C:HOH324 2.4 45.4 1.0 OE2 C:GLU91 2.5 36.1 1.0 OE1 C:GLU91 2.6 33.6 1.0 CD C:GLU91 2.8 39.6 1.0 O C:PHE89 3.9 31.2 1.0 HA C:THR90 4.1 45.4 1.0 CG C:GLU91 4.3 31.9 1.0 O C:HOH303 4.4 42.3 1.0 HG2 C:GLU91 4.6 38.2 1.0 HG3 C:GLU91 4.7 38.2 1.0 C C:PHE89 4.9 31.8 1.0 CA C:THR90 5.0 37.8 1.0 HB2 C:GLU91 5.0 35.8 1.0

Calcium binding site 3 out of 18 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant


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 E34A Variant within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:53.3 occ:1.00 O D:HOH303 2.5 37.2 1.0 O D:HOH319 2.8 30.4 1.0 OD1 D:ASP40 2.8 32.3 1.0 OE2 Q:GLU91 2.9 46.7 1.0 O Q:HOH310 2.9 44.9 1.0 HH12 D:ARG59 3.5 41.3 1.0 CG D:ASP40 3.6 32.3 1.0 HH11 D:ARG59 3.7 41.3 1.0 HH11 C:ARG22 3.7 59.1 1.0 NH1 D:ARG59 3.8 34.4 1.0 OD2 D:ASP40 3.8 35.8 1.0 OD1 D:ASP44 4.0 42.1 1.0 CD Q:GLU91 4.1 53.4 1.0 HG1 C:THR19 4.2 39.9 1.0 OG1 C:THR19 4.3 33.2 1.0 HG12 D:VAL43 4.3 35.7 1.0 HE C:ARG22 4.4 52.5 1.0 NH1 C:ARG22 4.5 49.2 1.0 HZ2 C:LYS16 4.5 98.4 1.0 O D:HOH315 4.6 31.9 1.0 HD2 C:LYS16 4.6 63.4 1.0 HG2 Q:GLU91 4.6 67.9 1.0 O Q:HOH311 4.6 42.1 1.0 HG11 D:VAL43 4.7 35.7 1.0 CZ D:ARG59 4.7 33.3 1.0 HB D:VAL43 4.8 38.1 1.0 HA D:ASP40 4.8 32.2 1.0 O D:ASP40 4.8 27.6 1.0 CG D:ASP44 4.9 34.7 1.0 HH12 C:ARG22 4.9 59.1 1.0 OE1 Q:GLU91 4.9 47.7 1.0 CG1 D:VAL43 4.9 29.7 1.0 HG23 C:THR19 5.0 37.1 1.0 CG Q:GLU91 5.0 56.6 1.0

Calcium binding site 4 out of 18 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant


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 E34A Variant within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca202 b:66.1 occ:1.00 OD2 H:ASP48 2.5 36.7 1.0 OE1 H:GLU50 2.5 76.3 1.0 O F:HOH329 2.8 38.0 1.0 OD1 H:ASP48 3.1 37.6 1.0 CG H:ASP48 3.2 34.3 1.0 CD H:GLU50 3.4 72.8 1.0 HB2 H:GLU50 3.4 47.0 1.0 HE1 F:TRP72 3.4 37.3 1.0 OD1 F:ASN76 3.7 35.0 1.0 HD21 F:ASN76 3.7 38.7 1.0 HG2 H:GLU50 4.1 75.5 1.0 CG H:GLU50 4.1 62.9 1.0 NE1 F:TRP72 4.2 31.1 1.0 OE2 H:GLU50 4.2 70.1 1.0 H H:GLU50 4.2 35.7 1.0 CB H:GLU50 4.2 39.1 1.0 ND2 F:ASN76 4.4 32.3 1.0 HD2 H:PRO49 4.4 40.5 1.0 CG F:ASN76 4.5 29.5 1.0 HZ2 F:TRP72 4.6 33.9 1.0 CB H:ASP48 4.6 27.1 1.0 HB3 H:GLU50 4.8 47.0 1.0 HB2 H:ASP48 4.9 32.5 1.0 H H:LEU51 4.9 32.6 1.0 N H:GLU50 5.0 29.8 1.0 CE2 F:TRP72 5.0 29.9 1.0 HA H:ASP48 5.0 41.6 1.0 CD1 F:TRP72 5.0 28.3 1.0

Calcium binding site 5 out of 18 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant


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 E34A Variant within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca203 b:69.8 occ:1.00 O H:ASP44 2.4 38.1 1.0 O H:HOH328 2.4 55.4 1.0 O H:HOH303 3.1 39.3 1.0 C H:ASP44 3.6 31.5 1.0 HA H:ASP44 3.8 37.5 1.0 CA H:ASP44 4.3 31.3 1.0 HA H:ALA45 4.3 38.6 1.0 O H:SER46 4.5 31.5 1.0 N H:ALA45 4.6 28.7 1.0 HB3 H:ASP44 4.7 36.6 1.0 O H:VAL43 4.8 30.3 1.0 O G:VAL14 4.8 41.9 1.0 CA H:ALA45 4.8 32.1 1.0 HB G:VAL14 5.0 53.1 1.0 C H:ALA45 5.0 30.4 1.0

Calcium binding site 6 out of 18 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant


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 E34A Variant within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca202 b:69.7 occ:1.00 OE1 I:GLU18 2.1 59.9 1.0 CD I:GLU18 2.9 62.8 1.0 OE2 I:GLU18 2.9 61.3 1.0 HH12 I:ARG22 4.1 43.8 1.0 CG I:GLU18 4.3 49.3 1.0 HG3 I:GLU18 4.6 59.1 1.0 NH1 I:ARG22 4.8 36.5 1.0 HG2 I:GLU18 4.9 59.1 1.0 HB2 I:GLU18 4.9 42.3 1.0

Calcium binding site 7 out of 18 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant


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 E34A Variant within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca202 b:72.8 occ:1.00 O J:HOH312 2.3 46.9 1.0 O J:ASP44 2.5 41.2 1.0 C J:ASP44 3.6 37.8 1.0 HA J:ASP44 3.8 46.0 1.0 CA J:ASP44 4.2 38.3 1.0 O J:SER46 4.3 34.0 1.0 HZ1 I:LYS16 4.3 91.6 1.0 HZ3 I:LYS16 4.3 91.6 1.0 HA J:ALA45 4.5 44.8 1.0 O J:VAL43 4.6 34.5 1.0 N J:ALA45 4.7 34.3 1.0 NZ I:LYS16 4.7 76.3 1.0 HB3 J:ASP44 4.8 51.5 1.0 CA J:ALA45 4.9 37.3 1.0 C J:ALA45 5.0 32.8 1.0

Calcium binding site 8 out of 18 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant


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 E34A Variant within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca203 b:77.9 occ:1.00 OE2 J:GLU61 2.6 56.2 1.0 CD J:GLU61 3.5 45.3 1.0 OE1 A:GLU64 3.7 52.4 1.0 OE1 J:GLU61 3.7 47.3 1.0 NE2 J:HIS57 3.8 37.9 1.0 HE1 J:HIS57 3.9 46.1 1.0 CD A:GLU64 4.2 49.9 1.0 OE2 A:GLU64 4.2 56.7 1.0 CE1 J:HIS57 4.3 38.5 1.0 OE2 A:GLU61 4.6 49.4 1.0 CG J:GLU61 4.9 39.5 1.0

Calcium binding site 9 out of 18 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant


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 E34A Variant within 5.0Å range: probe atom residue distance (Å) B Occ K:Ca202 b:73.0 occ:1.00 OD1 K:ASN76 2.6 46.0 1.0 O T:HOH311 2.8 44.8 1.0 O T:HOH312 3.5 48.0 1.0 CG K:ASN76 3.5 39.2 1.0 HD21 K:ASN76 3.7 47.0 1.0 ND2 K:ASN76 4.0 39.2 1.0 HA K:ASN76 4.4 46.1 1.0 OE1 T:GLU50 4.4 51.3 1.0 OD2 T:ASP48 4.5 39.6 1.0 CB K:ASN76 4.7 33.8 1.0 O K:ARG75 4.8 41.8 1.0 HD22 K:ASN76 4.8 47.0 1.0 HB3 K:ASN76 4.9 40.5 1.0

Calcium binding site 10 out of 18 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 E34A Variant


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 E34A Variant within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca202 b:74.0 occ:1.00 O L:HOH316 2.4 47.5 1.0 O L:ASP44 2.8 53.7 1.0 HZ1 K:LYS16 3.2 88.5 1.0 HZ2 K:LYS16 3.5 88.5 1.0 HA L:ASP44 3.6 54.6 1.0 NZ K:LYS16 3.8 73.8 1.0 C L:ASP44 3.9 41.6 1.0 CA L:ASP44 4.2 45.5 1.0 HZ3 K:LYS16 4.3 88.5 1.0 O L:VAL43 4.6 45.4 1.0 O L:SER46 4.7 40.5 1.0 HB3 L:ASP44 4.7 51.6 1.0 HE3 K:LYS16 4.7 93.0 1.0 CE K:LYS16 4.9 77.5 1.0

C.Piergentili, J.Ross, D.He, K.J.Gallagher, W.A.Stanley, L.Adam, C.L.Mackay, A.Basle, K.J.Waldron, D.J.Clarke, J.Marles-Wright. Dissecting the Structural and Functional Roles of A Putative Metal Entry Site in Encapsulated Ferritins. J.Biol.Chem. V. 295 15511 2020.
ISSN: ESSN 1083-351X
PubMed: 32878987
DOI: 10.1074/JBC.RA120.014502