Cobalt in PDB 9ayp: Mycolicibacterium Smegmatis Clps with Bound CO2+

The structure of Mycolicibacterium Smegmatis Clps with Bound CO2+, PDB code: 9ayp was solved by C.J.Presloid, J.Jiang, P.C.Beardslee, H.R.Anderson, T.M.Swayne, K.R.Schmitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.44 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.578, 52.145, 54.575, 90, 90, 90
R / Rfree (%)	16.3 / 18.7

The structure of Mycolicibacterium Smegmatis Clps with Bound CO2+ also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Cobalt atom in the Mycolicibacterium Smegmatis Clps with Bound CO2+ (pdb code 9ayp). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Mycolicibacterium Smegmatis Clps with Bound CO2+, PDB code: 9ayp:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Mycolicibacterium Smegmatis Clps with Bound CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Mycolicibacterium Smegmatis Clps with Bound CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:87.1 occ:1.00 NE2 B:HIS65 2.7 48.7 1.0 HD2 B:HIS65 2.7 41.0 1.0 CD2 B:HIS65 2.9 34.1 1.0 OD1 B:ASN66 3.8 28.5 1.0 CE1 B:HIS65 3.9 46.6 1.0 CG B:HIS65 4.2 27.5 1.0 HE1 B:HIS65 4.4 56.0 1.0 ND1 B:HIS65 4.6 40.4 1.0

Cobalt binding site 2 out of 8 in the Mycolicibacterium Smegmatis Clps with Bound CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Mycolicibacterium Smegmatis Clps with Bound CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:13.3 occ:1.00 OE1 B:GLU78 2.1 8.5 1.0 O B:HOH313 2.1 10.3 1.0 O B:HOH353 2.1 8.1 1.0 OE1 B:GLU81 2.2 12.5 1.0 O B:HOH307 2.2 11.4 1.0 CD B:GLU78 3.1 11.5 1.0 CD B:GLU81 3.1 14.0 1.0 OE2 B:GLU78 3.4 12.3 1.0 OE2 B:GLU81 3.4 13.0 1.0 O B:HOH348 3.8 20.8 1.0 HA B:GLU78 3.9 15.0 1.0 O B:HOH373 4.2 28.9 1.0 O B:HOH358 4.2 21.9 1.0 O B:HOH376 4.4 40.0 1.0 CG B:GLU78 4.4 12.6 1.0 HB2 B:GLU81 4.5 15.9 1.0 CG B:GLU81 4.5 10.6 1.0 HB3 B:GLU78 4.6 12.8 1.0 HB3 B:GLU81 4.6 15.9 1.0 HG2 B:GLU78 4.8 15.2 1.0 CA B:GLU78 4.8 12.4 1.0 CB B:GLU81 4.8 13.2 1.0 CB B:GLU78 4.9 10.6 1.0 HG3 B:GLU81 5.0 12.7 1.0

Cobalt binding site 3 out of 8 in the Mycolicibacterium Smegmatis Clps with Bound CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Mycolicibacterium Smegmatis Clps with Bound CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:68.2 occ:1.00 NE2 B:HIS88 2.6 31.1 1.0 CD2 B:HIS88 2.8 32.2 1.0 CE1 B:HIS88 3.0 31.0 1.0 HD2 B:HIS88 3.1 38.7 1.0 CG B:HIS88 3.3 26.1 1.0 ND1 B:HIS88 3.4 31.6 1.0 HE1 B:HIS88 3.5 37.2 1.0 O B:HOH362 3.7 20.2 1.0 CO B:CO206 4.0 49.8 0.5 HD1 B:HIS88 4.0 38.0 1.0 CO B:CO205 4.2 44.7 0.5 HB2 B:HIS88 4.3 18.3 1.0 CB B:HIS88 4.4 15.2 1.0 HB3 B:HIS88 4.5 18.3 1.0 O B:HOH350 4.5 27.0 1.0

Cobalt binding site 4 out of 8 in the Mycolicibacterium Smegmatis Clps with Bound CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Mycolicibacterium Smegmatis Clps with Bound CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co204 b:69.0 occ:1.00 HE1 B:HIS65 1.7 56.0 1.0 HD1 B:HIS65 1.9 48.5 1.0 CE1 B:HIS65 2.1 46.6 1.0 ND1 B:HIS65 2.2 40.4 1.0 NE2 B:HIS65 3.4 48.7 1.0 O B:HOH324 3.6 27.2 1.0 CG B:HIS65 3.6 27.5 1.0 OD1 B:ASP33 3.7 19.8 1.0 OD2 B:ASP33 3.8 15.6 1.0 HA B:HIS65 4.1 20.6 1.0 CD2 B:HIS65 4.2 34.1 1.0 CG B:ASP33 4.2 16.0 1.0 CB B:HIS65 4.6 19.9 1.0 HB2 B:HIS65 4.7 24.0 1.0 CA B:HIS65 4.8 17.2 1.0 O B:HIS65 4.9 18.6 1.0 O B:ASP34 4.9 21.8 1.0 CA B:PRO35 5.0 32.3 1.0

Cobalt binding site 5 out of 8 in the Mycolicibacterium Smegmatis Clps with Bound CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Mycolicibacterium Smegmatis Clps with Bound CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co205 b:44.7 occ:0.50 CO B:CO206 2.1 49.8 0.5 HE1 B:HIS88 2.3 37.2 1.0 NE2 B:HIS88 2.6 31.1 1.0 CE1 B:HIS88 2.7 31.0 1.0 CD2 B:HIS88 3.9 32.2 1.0 ND1 B:HIS88 4.0 31.6 1.0 CO B:CO203 4.2 68.2 1.0 HD2 B:HIS88 4.5 38.7 1.0 HD1 B:HIS88 4.5 38.0 1.0 CG B:HIS88 4.6 26.1 1.0 O B:HOH350 4.9 27.0 1.0

Cobalt binding site 6 out of 8 in the Mycolicibacterium Smegmatis Clps with Bound CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Mycolicibacterium Smegmatis Clps with Bound CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co206 b:49.8 occ:0.50 CO B:CO205 2.1 44.7 0.5 NE2 B:HIS88 2.4 31.1 1.0 CD2 B:HIS88 3.4 32.2 1.0 CE1 B:HIS88 3.4 31.0 1.0 HD2 B:HIS88 3.5 38.7 1.0 HE1 B:HIS88 3.6 37.2 1.0 CO B:CO203 4.0 68.2 1.0 ND1 B:HIS88 4.5 31.6 1.0 CG B:HIS88 4.5 26.1 1.0

Cobalt binding site 7 out of 8 in the Mycolicibacterium Smegmatis Clps with Bound CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Mycolicibacterium Smegmatis Clps with Bound CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Co201 b:34.0 occ:1.00 NE2 A:HIS65 1.9 14.6 1.0 O A:HOH374 2.2 30.2 1.0 O A:HOH358 2.3 18.7 1.0 O A:HOH357 2.3 24.5 1.0 O A:HOH313 2.4 28.0 1.0 CD2 A:HIS65 2.7 20.0 1.0 O A:HOH343 2.8 27.5 1.0 HD2 A:HIS65 2.8 24.0 1.0 CE1 A:HIS65 3.0 31.9 1.0 HE1 A:HIS65 3.3 38.3 1.0 CG A:HIS65 3.9 21.5 1.0 ND1 A:HIS65 4.0 26.6 1.0 OD2 A:ASP33 4.2 14.8 1.0 OD1 A:ASP33 4.3 16.1 1.0 O A:HOH350 4.3 25.7 1.0 HA A:PRO35 4.4 24.3 1.0 O A:HOH349 4.5 24.5 1.0 CG A:ASP33 4.7 14.5 1.0 O A:ASP34 4.7 17.7 1.0 HD1 A:HIS65 4.9 32.0 1.0 O A:HOH363 4.9 31.1 1.0

Cobalt binding site 8 out of 8 in the Mycolicibacterium Smegmatis Clps with Bound CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Mycolicibacterium Smegmatis Clps with Bound CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Co202 b:22.9 occ:1.00 O B:HOH305 2.0 24.7 1.0 O A:HOH323 2.0 19.1 1.0 OD1 B:ASP99 2.0 20.8 1.0 O B:HOH317 2.0 19.1 1.0 OD1 A:ASP99 2.1 20.3 1.0 O A:HOH302 2.3 24.7 1.0 CG B:ASP99 3.0 18.9 1.0 CG A:ASP99 3.1 17.9 1.0 H B:ARG100 3.1 35.4 1.0 OD2 B:ASP99 3.3 19.2 1.0 OD2 A:ASP99 3.5 19.8 1.0 O A:HOH370 3.7 22.1 1.0 O B:HOH364 3.7 28.9 1.0 HB2 B:ARG100 3.8 40.8 1.0 N B:ARG100 4.0 29.5 1.0 H A:ARG100 4.1 31.8 1.0 HA B:ASP99 4.1 21.2 1.0 HA A:ASP99 4.2 20.6 1.0 O A:ARG100 4.2 22.6 1.0 OXT B:ARG100 4.4 26.6 1.0 CB B:ASP99 4.4 19.0 1.0 CB A:ASP99 4.4 21.4 1.0 HG2 B:ARG100 4.5 47.5 1.0 CB B:ARG100 4.6 34.0 1.0 HG11 A:VAL28 4.6 15.0 1.0 O B:HOH330 4.6 28.6 1.0 CA B:ASP99 4.6 17.6 1.0 N A:ARG100 4.7 26.4 1.0 HG11 B:VAL28 4.7 14.9 1.0 CA B:ARG100 4.7 30.1 1.0 CA A:ASP99 4.8 17.1 1.0 HB2 A:ASP99 4.8 25.7 1.0 C B:ASP99 4.8 23.3 1.0 HB3 B:ASP99 4.9 22.9 1.0 HB2 B:ASP99 4.9 22.9 1.0 CG B:ARG100 5.0 39.5 1.0 C B:ARG100 5.0 33.2 1.0

C.J.Presloid, J.Jiang, P.Kandel, H.R.Anderson, P.C.Beardslee, T.M.Swayne, K.R.Schmitz. Clps Directs Degradation of N-Degron Substrates with Primary Destabilizing Residues in Mycolicibacterium Smegmatis. Mol.Microbiol. 2024.
ISSN: ESSN 1365-2958
PubMed: 39626090
DOI: 10.1111/MMI.15334