Magnesium in PDB 1mb9: Beta-Lactam Synthetase Complexed with Atp

The structure of Beta-Lactam Synthetase Complexed with Atp, PDB code: 1mb9 was solved by M.T.Miller, B.O.Bachmann, C.A.Townsend, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.78 / 2.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.252, 97.571, 81.313, 90.00, 90.69, 90.00
R / Rfree (%)	21 / 25.1

The binding sites of Magnesium atom in the Beta-Lactam Synthetase Complexed with Atp (pdb code 1mb9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Beta-Lactam Synthetase Complexed with Atp, PDB code: 1mb9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Beta-Lactam Synthetase Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beta-Lactam Synthetase Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:26.8 occ:1.00 O3A A:ATP701 1.8 23.9 0.5 O3G A:ATP701 2.1 21.2 0.5 O5 A:POP705 2.3 8.9 0.5 O A:HOH801 2.3 18.3 1.0 O3 A:POP705 2.5 6.3 0.5 O A:HOH884 2.6 15.1 1.0 PA A:ATP701 2.9 24.8 0.5 O2A A:ATP701 2.9 22.3 0.5 PB A:ATP701 3.2 23.3 0.5 PG A:ATP701 3.2 20.8 0.5 O A:POP705 3.3 8.4 0.5 P2 A:POP705 3.4 7.5 0.5 O3B A:ATP701 3.5 22.5 0.5 P1 A:POP705 3.5 7.5 0.5 O A:HOH886 3.6 41.5 1.0 O1G A:ATP701 3.7 21.1 0.5 O1A A:ATP701 3.7 20.7 0.5 O1B A:ATP701 3.8 23.4 0.5 NZ A:LYS443 3.9 26.8 1.0 O6 A:POP705 3.9 8.8 0.5 OG A:SER249 4.0 17.1 1.0 O A:HOH802 4.2 33.5 1.0 O A:HOH897 4.2 31.6 1.0 OE2 A:GLU280 4.2 23.5 1.0 O2B A:ATP701 4.2 24.3 0.5 O5' A:ATP701 4.3 23.3 0.5 O2 A:POP705 4.4 8.2 0.5 O2P A:AMP706 4.5 27.3 0.5 OE1 A:GLU280 4.5 24.9 1.0 O2G A:ATP701 4.5 22.5 0.5 O1 A:POP705 4.6 4.5 0.5 O4 A:POP705 4.6 11.3 0.5 CB A:SER249 4.8 18.8 1.0 CD A:GLU280 4.8 21.7 1.0 CA A:GLY251 4.9 14.5 1.0 MG A:MG604 5.0 18.9 1.0

Magnesium binding site 2 out of 4 in the Beta-Lactam Synthetase Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beta-Lactam Synthetase Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:18.9 occ:1.00 O A:HOH885 1.9 9.5 1.0 OD2 A:ASP253 1.9 18.2 1.0 O6 A:POP705 2.0 8.8 0.5 OD1 A:ASP351 2.1 14.2 1.0 O2B A:ATP701 2.2 24.3 0.5 O1A A:ATP701 2.3 20.7 0.5 O2 A:POP705 2.3 8.2 0.5 O1G A:ATP701 2.4 21.1 0.5 O2P A:AMP706 3.0 27.3 0.5 CG A:ASP253 3.1 14.5 1.0 CG A:ASP351 3.2 13.8 1.0 PA A:ATP701 3.3 24.8 0.5 PB A:ATP701 3.3 23.3 0.5 O A:POP705 3.3 8.4 0.5 P1 A:POP705 3.4 7.5 0.5 P2 A:POP705 3.4 7.5 0.5 O3B A:ATP701 3.5 22.5 0.5 PG A:ATP701 3.6 20.8 0.5 O5' A:ATP701 3.6 23.3 0.5 O3A A:ATP701 3.7 23.9 0.5 OD2 A:ASP351 3.7 14.3 1.0 CB A:ASP253 3.7 13.3 1.0 OD1 A:ASP253 4.1 12.8 1.0 O A:GLY347 4.1 13.2 1.0 O A:HOH724 4.2 32.3 1.0 O3 A:POP705 4.2 6.3 0.5 NZ A:LYS443 4.3 26.8 1.0 NZ A:LYS423 4.3 11.9 1.0 O5 A:POP705 4.3 8.9 0.5 O4 A:POP705 4.3 11.3 0.5 CB A:ASP351 4.4 13.6 1.0 P A:AMP706 4.4 28.4 0.5 N A:ASP351 4.4 10.3 1.0 C5' A:ATP701 4.4 23.9 0.5 O2G A:ATP701 4.5 22.5 0.5 O3' A:AMP706 4.5 21.2 0.5 O3' A:ATP701 4.5 22.1 0.5 O1 A:POP705 4.6 4.5 0.5 O2A A:ATP701 4.6 22.3 0.5 O1B A:ATP701 4.6 23.4 0.5 O3G A:ATP701 4.6 21.2 0.5 O1P A:AMP706 4.7 29.2 0.5 CE A:LYS443 4.8 28.5 1.0 CB A:ALA350 4.8 13.9 1.0 C3' A:ATP701 4.8 21.6 0.5 N A:ALA350 4.9 13.1 1.0 MG A:MG603 5.0 26.8 1.0 CA A:ASP351 5.0 12.1 1.0

Magnesium binding site 3 out of 4 in the Beta-Lactam Synthetase Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Beta-Lactam Synthetase Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:17.8 occ:1.00 O2G B:ATP702 2.1 12.8 1.0 O3A B:ATP702 2.1 22.8 1.0 OD1 B:ASP253 2.1 17.1 1.0 OD2 B:ASP351 2.2 10.1 1.0 O B:HOH946 2.2 15.9 1.0 O2A B:ATP702 2.3 25.9 1.0 PA B:ATP702 2.5 33.7 1.0 O3B B:ATP702 2.9 16.9 1.0 PG B:ATP702 3.0 13.0 1.0 CG B:ASP253 3.1 15.0 1.0 CG B:ASP351 3.2 12.6 1.0 PB B:ATP702 3.3 18.2 1.0 O5' B:ATP702 3.5 31.2 1.0 OD1 B:ASP351 3.6 10.5 1.0 O1A B:ATP702 3.7 28.4 1.0 CB B:ASP253 3.7 14.2 1.0 O2B B:ATP702 3.9 18.4 1.0 O1G B:ATP702 3.9 15.4 1.0 NZ B:LYS423 3.9 14.5 1.0 NZ B:LYS443 3.9 21.3 1.0 OD2 B:ASP253 4.1 15.6 1.0 C5' B:ATP702 4.2 29.6 1.0 O3G B:ATP702 4.2 14.6 1.0 O1B B:ATP702 4.3 19.2 1.0 O B:HOH949 4.4 22.2 1.0 O B:GLY347 4.5 7.4 1.0 CB B:ASP351 4.5 10.7 1.0 O3' B:ATP702 4.6 24.9 1.0 O B:HOH948 4.7 20.7 1.0 CE B:LYS443 4.7 24.4 1.0 N B:ASP351 4.8 8.4 1.0 MG B:MG602 4.9 18.1 1.0

Magnesium binding site 4 out of 4 in the Beta-Lactam Synthetase Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Beta-Lactam Synthetase Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:18.1 occ:1.00 O B:HOH903 2.0 24.8 1.0 O2B B:ATP702 2.0 18.4 1.0 O1G B:ATP702 2.1 15.4 1.0 O B:HOH792 2.1 11.3 1.0 O B:HOH793 2.2 22.0 1.0 O1A B:ATP702 2.5 28.4 1.0 PB B:ATP702 3.3 18.2 1.0 PG B:ATP702 3.4 13.0 1.0 OG B:SER249 3.6 20.5 1.0 PA B:ATP702 3.6 33.7 1.0 O3A B:ATP702 3.7 22.8 1.0 O3B B:ATP702 3.8 16.9 1.0 OE2 B:GLU280 4.0 28.9 1.0 O B:HOH751 4.0 36.6 1.0 O5' B:ATP702 4.1 31.2 1.0 O2G B:ATP702 4.1 12.8 1.0 CB B:SER249 4.3 20.0 1.0 OE1 B:GLU280 4.3 32.2 1.0 O B:HOH741 4.4 29.9 1.0 O B:HOH824 4.5 32.5 1.0 O1B B:ATP702 4.5 19.2 1.0 O3G B:ATP702 4.6 14.6 1.0 CA B:GLY251 4.6 16.1 1.0 CD B:GLU280 4.6 30.2 1.0 NZ B:LYS443 4.7 21.3 1.0 N B:GLY251 4.9 20.2 1.0 MG B:MG601 4.9 17.8 1.0 O2A B:ATP702 5.0 25.9 1.0

M.T.Miller, B.O.Bachmann, C.A.Townsend, A.C.Rosenzweig. The Catalytic Cycle of Beta -Lactam Synthetase Observed By X-Ray Crystallographic Snapshots Proc.Natl.Acad.Sci.Usa V. 99 14752 2002.
ISSN: ISSN 0027-8424
PubMed: 12409610
DOI: 10.1073/PNAS.232361199