Cobalt in PDB 4zcm: Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp

The structure of Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp, PDB code: 4zcm was solved by H.T.Fan, J.Hahm, S.Diggs, G.Blaha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.47 / 3.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.821, 160.125, 89.718, 90.00, 98.04, 90.00
R / Rfree (%)	23.3 / 29.1

The structure of Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Cobalt atom in the Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp (pdb code 4zcm). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp, PDB code: 4zcm:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1001 b:0.3 occ:1.00 CO A:NCO1001 0.0 0.3 1.0 N1 A:NCO1001 2.0 0.6 1.0 N3 A:NCO1001 2.0 0.1 1.0 N4 A:NCO1001 2.0 0.2 1.0 N2 A:NCO1001 2.0 0.1 1.0 N6 A:NCO1001 2.0 0.8 1.0 N5 A:NCO1001 2.0 0.0 1.0 O A:SER530 4.4 0.6 1.0 OE1 A:GLN482 4.5 0.1 1.0 OD2 A:ASP573 4.6 75.5 1.0 O A:ASN485 4.7 0.1 1.0 N A:GLN484 4.9 92.6 1.0 O A:GLN484 4.9 0.0 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1002 b:92.7 occ:1.00 CO A:NCO1002 0.0 92.7 1.0 N2 A:NCO1002 2.0 0.5 1.0 N4 A:NCO1002 2.0 80.0 1.0 N3 A:NCO1002 2.0 97.7 1.0 N6 A:NCO1002 2.0 0.4 1.0 N1 A:NCO1002 2.0 0.1 1.0 N5 A:NCO1002 2.0 95.7 1.0 OD1 A:ASP159 4.3 0.2 1.0 CA A:ASP159 5.0 0.3 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1001 b:0.8 occ:1.00 CO B:NCO1001 0.0 0.8 1.0 N1 B:NCO1001 2.0 66.3 1.0 N3 B:NCO1001 2.0 75.2 1.0 N4 B:NCO1001 2.0 82.1 1.0 N6 B:NCO1001 2.0 71.4 1.0 N2 B:NCO1001 2.0 76.7 1.0 N5 B:NCO1001 2.0 0.3 1.0 O B:SER530 4.3 85.2 1.0 OE1 B:GLN482 4.5 1.0 1.0 OD2 B:ASP573 4.6 76.0 1.0 N B:GLN484 4.8 81.2 1.0 O B:ASN485 4.9 0.7 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Escherichia Coli Gtpase Bipa/Typa Complexed with Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1002 b:0.8 occ:1.00 CO B:NCO1002 0.0 0.8 1.0 N4 B:NCO1002 2.0 0.4 1.0 N3 B:NCO1002 2.0 0.8 1.0 N6 B:NCO1002 2.0 0.8 1.0 N2 B:NCO1002 2.0 0.0 1.0 N1 B:NCO1002 2.0 0.5 1.0 N5 B:NCO1002 2.0 0.5 1.0 OD1 B:ASP159 4.2 0.7 1.0 CA B:ASP159 4.7 0.2 1.0

H.Fan, J.Hahm, S.Diggs, J.J.Perry, G.Blaha. Structural and Functional Analysis of Bipa, A Regulator of Virulence in Enteropathogenic Escherichia Coli. J.Biol.Chem. V. 290 20856 2015.
ISSN: ESSN 1083-351X
PubMed: 26163516
DOI: 10.1074/JBC.M115.659136