Magnesium 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:

Zinc

(Zn)

4 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of E. Coli Mccb + Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:46.5 occ:1.00 O2A A:ATP502 2.1 23.9 1.0 O2B A:ATP502 2.5 31.9 1.0 O3G A:ATP502 2.5 38.1 1.0 PA A:ATP502 3.4 24.9 1.0 PB A:ATP502 3.5 31.2 1.0 O3A A:ATP502 3.7 29.1 1.0 O A:HOH513 3.8 25.1 1.0 PG A:ATP502 3.8 39.5 1.0 O3B A:ATP502 3.9 35.4 1.0 OD2 A:ASP214 3.9 36.0 1.0 OD1 A:ASP214 4.0 33.0 1.0 C5' A:ATP502 4.1 23.4 1.0 O5' A:ATP502 4.2 25.4 1.0 CG A:ASP214 4.4 32.2 1.0 O1A A:ATP502 4.6 23.3 1.0 O1G A:ATP502 4.7 38.3 1.0 C3' A:ATP502 4.8 24.1 1.0 O A:HOH388 4.8 38.3 1.0 O2G A:ATP502 4.8 39.6 1.0 O1B A:ATP502 4.9 32.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of E. Coli Mccb + Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:21.0 occ:1.00 O2B B:ATP502 2.0 21.6 1.0 O2A B:ATP502 2.1 19.2 1.0 O B:HOH362 2.1 21.0 1.0 O B:HOH385 2.1 26.0 1.0 O3G B:ATP502 2.2 23.7 1.0 O B:HOH396 2.3 22.1 1.0 PB B:ATP502 3.1 21.7 1.0 PG B:ATP502 3.3 21.9 1.0 PA B:ATP502 3.4 20.2 1.0 O3B B:ATP502 3.4 21.3 1.0 O3A B:ATP502 3.6 20.6 1.0 O B:HOH526 3.8 21.1 1.0 OD1 B:ASP214 4.0 22.9 1.0 O1G B:ATP502 4.0 23.6 1.0 C5' B:ATP502 4.1 19.3 1.0 O B:HOH510 4.1 24.3 1.0 O B:HOH417 4.2 21.4 1.0 O5' B:ATP502 4.2 19.5 1.0 OD2 B:ASP214 4.3 25.5 1.0 O B:HOH463 4.3 25.1 1.0 O B:HOH378 4.3 21.5 1.0 O B:HOH404 4.4 31.9 1.0 O1B B:ATP502 4.5 21.9 1.0 O2G B:ATP502 4.5 19.0 1.0 CG B:ASP214 4.6 24.8 1.0 O1A B:ATP502 4.6 16.5 1.0 O B:HOH462 4.6 26.9 1.0 C3' B:ATP502 4.9 16.8 1.0

Magnesium 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 Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of E. Coli Mccb + Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:28.0 occ:1.00 O2A C:ATP502 1.9 21.1 1.0 O3G C:ATP502 2.1 24.9 1.0 O C:HOH378 2.1 17.6 1.0 O C:HOH367 2.1 21.2 1.0 O2B C:ATP502 2.1 22.3 1.0 O C:HOH391 2.3 34.0 1.0 PB C:ATP502 3.1 23.4 1.0 PG C:ATP502 3.2 27.1 1.0 PA C:ATP502 3.3 22.6 1.0 O3B C:ATP502 3.4 24.2 1.0 O3A C:ATP502 3.5 23.1 1.0 O C:HOH543 3.6 21.7 1.0 O1G C:ATP502 3.9 27.8 1.0 C5' C:ATP502 4.1 22.5 1.0 OD2 C:ASP214 4.1 27.2 1.0 O5' C:ATP502 4.1 23.8 1.0 OD1 C:ASP214 4.2 22.8 1.0 O1A C:ATP502 4.4 22.0 1.0 O2G C:ATP502 4.5 26.6 1.0 O C:HOH398 4.5 26.8 1.0 O1B C:ATP502 4.5 25.1 1.0 CG C:ASP214 4.6 23.9 1.0 C3' C:ATP502 4.9 21.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of E. Coli Mccb + Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:34.2 occ:1.00 O D:HOH373 1.9 27.3 1.0 O2A D:ATP502 2.0 24.1 1.0 O2B D:ATP502 2.1 24.9 1.0 O3G D:ATP502 2.5 32.4 1.0 O D:HOH389 2.5 33.0 1.0 PB D:ATP502 3.2 28.8 1.0 PA D:ATP502 3.3 24.5 1.0 O D:HOH618 3.5 28.3 1.0 O3A D:ATP502 3.6 26.8 1.0 O3B D:ATP502 3.6 30.3 1.0 PG D:ATP502 3.6 33.1 1.0 OD2 D:ASP214 4.0 33.5 1.0 OD1 D:ASP214 4.0 32.8 1.0 C5' D:ATP502 4.1 23.6 1.0 O5' D:ATP502 4.1 25.8 1.0 O D:HOH360 4.3 28.1 1.0 O D:HOH411 4.3 28.5 1.0 CG D:ASP214 4.4 30.8 1.0 O1A D:ATP502 4.4 24.5 1.0 O1G D:ATP502 4.5 34.2 1.0 O1B D:ATP502 4.6 29.1 1.0 O2G D:ATP502 4.8 34.0 1.0 C3' D:ATP502 4.9 24.1 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