Cobalt in PDB 6mr1: Rbcs-Like Subdomain of Ccmm

The structure of Rbcs-Like Subdomain of Ccmm, PDB code: 6mr1 was solved by P.Ryan, M.S.Kimber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.29 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.900, 73.560, 76.570, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.5

The structure of Rbcs-Like Subdomain of Ccmm also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cobalt atom in the Rbcs-Like Subdomain of Ccmm (pdb code 6mr1). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Rbcs-Like Subdomain of Ccmm, PDB code: 6mr1:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Rbcs-Like Subdomain of Ccmm


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Rbcs-Like Subdomain of Ccmm within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:20.6 occ:0.97 O A:HOH554 1.9 23.8 1.0 O A:HOH535 2.1 25.8 1.0 OE2 A:GLU307 2.1 17.8 1.0 NE2 A:HIS235 2.2 16.7 1.0 CD A:GLU307 3.0 16.8 1.0 CD2 A:HIS235 3.1 16.0 1.0 CE1 A:HIS235 3.2 17.9 1.0 HD2 A:HIS235 3.2 19.2 1.0 OE1 A:GLU307 3.3 16.7 1.0 HE1 A:HIS235 3.4 21.5 1.0 O4 A:SO4402 4.0 38.7 0.9 O A:HOH562 4.1 44.8 1.0 ND1 A:HIS235 4.3 17.4 1.0 CG A:HIS235 4.3 15.8 1.0 O A:HOH518 4.3 26.2 1.0 CG A:GLU307 4.5 15.0 1.0 HB A:THR230 4.5 16.9 1.0 HZ A:PHE305 4.6 18.1 1.0 HG3 A:GLU307 4.6 18.1 1.0 O A:HOH574 4.7 47.6 1.0 HE1 A:PHE305 4.8 17.8 1.0 HB2 A:GLU307 4.8 16.8 1.0 HG1 A:THR230 4.9 17.2 1.0 HG22 A:THR234 5.0 31.8 0.4 O3 A:SO4402 5.0 35.2 0.9

Cobalt binding site 2 out of 3 in the Rbcs-Like Subdomain of Ccmm


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Rbcs-Like Subdomain of Ccmm within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:19.2 occ:0.98 O B:HOH504 1.8 20.3 1.0 O B:HOH557 2.0 24.2 1.0 OE2 B:GLU307 2.0 16.9 1.0 NE2 B:HIS235 2.2 17.4 1.0 O B:HOH552 2.2 23.6 1.0 CD B:GLU307 3.0 15.9 1.0 CD2 B:HIS235 3.1 15.3 1.0 CE1 B:HIS235 3.2 18.0 1.0 HD2 B:HIS235 3.2 18.4 1.0 OE1 B:GLU307 3.3 16.4 1.0 HE1 B:HIS235 3.4 21.6 1.0 O1 B:SO4405 4.2 49.7 0.9 CG B:HIS235 4.3 15.8 1.0 ND1 B:HIS235 4.3 18.2 1.0 O B:HOH515 4.3 37.2 1.0 CG B:GLU307 4.4 15.3 1.0 O B:HOH581 4.5 37.3 1.0 HG3 B:GLU307 4.5 18.4 1.0 HB B:THR230 4.6 18.3 1.0 HZ B:PHE305 4.6 19.5 1.0 HE1 B:PHE305 4.7 19.6 1.0 HB2 B:GLU307 4.8 16.8 1.0 HA B:TYR232 4.8 18.9 1.0 HG1 B:THR230 5.0 17.9 1.0

Cobalt binding site 3 out of 3 in the Rbcs-Like Subdomain of Ccmm


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Rbcs-Like Subdomain of Ccmm within 5.0Å range: probe atom residue distance (Å) B Occ B:Co402 b:15.0 occ:1.00 N B:SCN404 1.9 29.4 1.0 N B:SCN403 1.9 14.8 1.0 OE1 B:GLU285 1.9 15.1 1.0 CD B:GLU285 2.7 16.1 1.0 OE2 B:GLU285 2.7 16.6 1.0 C B:SCN403 2.9 15.3 1.0 C B:SCN404 3.1 30.6 1.0 HE21 B:GLN281 3.4 20.8 1.0 HG3 B:GLN281 3.7 19.6 1.0 CG B:GLU285 4.1 15.5 1.0 HG2 B:GLN281 4.1 19.6 1.0 NE2 B:GLN281 4.2 17.3 1.0 CG B:GLN281 4.3 16.4 1.0 HG2 B:GLU285 4.3 18.6 1.0 HG3 B:GLU285 4.4 18.6 1.0 S B:SCN403 4.6 15.5 1.0 HE22 B:GLN281 4.7 20.8 1.0 CD B:GLN281 4.7 18.3 1.0 S B:SCN404 4.8 31.4 1.0 O B:HOH537 4.9 20.6 1.0

P.Ryan, T.J.B.Forrester, C.Wroblewski, T.M.G.Kenney, E.N.Kitova, J.S.Klassen, M.S.Kimber. The Small Rbcs-Like Domains of the Beta-Carboxysome Structural Protein Ccmm Bind Rubisco at A Site Distinct From That Binding the Rbcs Subunit. J. Biol. Chem. V. 294 2593 2019.
ISSN: ESSN 1083-351X
PubMed: 30591587
DOI: 10.1074/JBC.RA118.006330