Zinc in PDB 3h5n: Crystal Structure of E. Coli Mccb + Atp

The structure of Crystal Structure of E. Coli Mccb + Atp, PDB code: 3h5n was solved by C.A.Regni, R.F.Roush, D.Miller, A.Nourse, C.T.Walsh, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.64 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.847, 138.239, 80.224, 90.00, 92.62, 90.00
R / Rfree (%)	20.4 / 25.6

The structure of Crystal Structure of E. Coli Mccb + Atp also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of E. Coli Mccb + Atp (pdb code 3h5n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of E. Coli Mccb + Atp, PDB code: 3h5n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of E. Coli Mccb + Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of E. Coli Mccb + Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:33.5 occ:1.00 SG A:CYS343 2.3 40.5 1.0 SG A:CYS346 2.3 35.9 1.0 SG A:CYS260 2.3 33.9 1.0 SG A:CYS257 2.4 28.6 1.0 CB A:CYS343 3.0 40.9 1.0 CB A:CYS260 3.5 36.3 1.0 CB A:CYS257 3.5 29.4 1.0 CB A:CYS346 3.6 38.3 1.0 CA A:CYS260 3.6 36.4 1.0 N A:CYS260 3.6 36.1 1.0 N A:CYS257 3.8 29.7 1.0 N A:CYS346 3.8 38.7 1.0 CA A:CYS257 4.1 29.8 1.0 CA A:CYS346 4.2 38.4 1.0 C A:GLU259 4.3 35.4 1.0 C A:CYS257 4.4 30.2 1.0 O A:CYS257 4.5 29.8 1.0 CA A:CYS343 4.5 40.8 1.0 C A:CYS346 4.7 39.0 1.0 CB A:VAL345 4.7 39.3 1.0 N A:GLY347 4.8 39.5 1.0 N A:GLU259 4.8 33.5 1.0 C A:VAL345 4.9 39.1 1.0 O A:SER340 4.9 40.4 1.0 O A:GLU259 5.0 35.6 1.0 N A:VAL345 5.0 39.9 1.0 CA A:GLU259 5.0 34.9 1.0 C A:GLY256 5.0 29.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of E. Coli Mccb + Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of E. Coli Mccb + Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:24.4 occ:1.00 SG B:CYS260 2.2 23.0 1.0 SG B:CYS346 2.3 26.3 1.0 SG B:CYS257 2.3 21.5 1.0 SG B:CYS343 2.4 27.9 1.0 CB B:CYS257 3.2 22.2 1.0 CB B:CYS343 3.3 31.0 1.0 CB B:CYS260 3.5 26.1 1.0 CB B:CYS346 3.5 28.4 1.0 N B:CYS260 3.5 25.8 1.0 N B:CYS257 3.6 22.4 1.0 CA B:CYS260 3.6 26.6 1.0 N B:CYS346 3.8 28.4 1.0 CA B:CYS257 3.9 22.3 1.0 CA B:CYS346 4.2 28.7 1.0 C B:GLU259 4.3 25.5 1.0 C B:CYS257 4.3 22.3 1.0 O B:CYS257 4.4 22.7 1.0 N B:GLU259 4.7 24.3 1.0 O B:HOH373 4.7 18.4 1.0 C B:CYS346 4.7 29.7 1.0 CA B:CYS343 4.7 31.1 1.0 CB B:VAL345 4.8 28.6 1.0 CB B:GLU259 4.8 25.8 1.0 N B:GLY347 4.8 30.7 1.0 C B:GLY256 4.8 22.3 1.0 CA B:GLU259 4.8 25.6 1.0 C B:VAL345 4.9 28.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of E. Coli Mccb + Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of E. Coli Mccb + Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn500 b:20.1 occ:1.00 SG C:CYS346 2.2 23.4 1.0 SG C:CYS257 2.3 21.8 1.0 SG C:CYS343 2.3 23.4 1.0 SG C:CYS260 2.4 23.6 1.0 CB C:CYS343 3.2 26.1 1.0 CB C:CYS346 3.3 28.4 1.0 CB C:CYS257 3.4 19.3 1.0 N C:CYS260 3.5 27.4 1.0 CB C:CYS260 3.5 28.0 1.0 CA C:CYS260 3.6 28.4 1.0 N C:CYS257 3.7 19.0 1.0 N C:CYS346 3.8 28.3 1.0 CA C:CYS257 4.0 19.3 1.0 CA C:CYS346 4.1 28.7 1.0 C C:GLU259 4.2 26.4 1.0 O C:CYS257 4.3 19.1 1.0 C C:CYS257 4.3 19.6 1.0 CA C:CYS343 4.6 26.3 1.0 N C:GLU259 4.7 23.9 1.0 O C:HOH600 4.7 30.3 1.0 C C:GLY256 4.8 18.6 1.0 CA C:GLU259 4.8 25.9 1.0 O C:HOH400 4.8 29.5 1.0 CB C:GLU259 4.8 26.3 1.0 O C:GLU259 4.9 26.4 1.0 C C:CYS346 4.9 30.2 1.0 C C:VAL345 4.9 27.9 1.0 CB C:VAL345 5.0 28.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of E. Coli Mccb + Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of E. Coli Mccb + Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn500 b:33.3 occ:1.00 SG D:CYS346 2.1 33.2 1.0 SG D:CYS343 2.3 37.5 1.0 SG D:CYS257 2.4 28.2 1.0 SG D:CYS260 2.5 31.7 1.0 CB D:CYS343 3.2 38.4 1.0 CB D:CYS257 3.4 29.4 1.0 CB D:CYS346 3.5 35.4 1.0 N D:CYS260 3.5 33.4 1.0 CB D:CYS260 3.6 33.3 1.0 CA D:CYS260 3.7 33.6 1.0 N D:CYS346 3.8 35.8 1.0 N D:CYS257 3.8 29.4 1.0 CA D:CYS257 4.0 29.3 1.0 CA D:CYS346 4.1 35.8 1.0 C D:GLU259 4.3 33.6 1.0 CB D:GLU259 4.4 34.1 1.0 C D:CYS257 4.4 29.7 1.0 O D:CYS257 4.5 29.2 1.0 O D:CYS346 4.5 37.1 1.0 CA D:CYS343 4.6 38.4 1.0 C D:CYS346 4.7 36.5 1.0 N D:GLU259 4.7 32.5 1.0 CA D:GLU259 4.7 33.7 1.0 O D:HOH370 4.8 24.4 1.0 CB D:VAL345 4.8 36.4 1.0 C D:VAL345 4.9 36.1 1.0 N D:VAL345 4.9 37.0 1.0 C D:GLY256 4.9 29.3 1.0

C.A.Regni, R.F.Roush, D.J.Miller, A.Nourse, C.T.Walsh, B.A.Schulman. How the Mccb Bacterial Ancestor of Ubiquitin E1 Initiates Biosynthesis of the Microcin C7 Antibiotic. Embo J. V. 28 1953 2009.
ISSN: ISSN 0261-4189
PubMed: 19494832
DOI: 10.1038/EMBOJ.2009.146