Magnesium in PDB 1mc1: Beta-Lactam Synthetase with Product (Dgpc), Amp and Ppi

The structure of Beta-Lactam Synthetase with Product (Dgpc), Amp and Ppi, PDB code: 1mc1 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)	29.10 / 2.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.038, 96.570, 80.912, 90.00, 90.54, 90.00
R / Rfree (%)	20.8 / 24.7

The binding sites of Magnesium atom in the Beta-Lactam Synthetase with Product (Dgpc), Amp and Ppi (pdb code 1mc1). 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 with Product (Dgpc), Amp and Ppi, PDB code: 1mc1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Beta-Lactam Synthetase with Product (Dgpc), Amp and Ppi


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 with Product (Dgpc), Amp and Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:32.5 occ:1.00 O1P A:AMP702 1.9 48.7 1.0 O A:HOH812 1.9 17.7 1.0 OD2 A:ASP253 2.0 24.4 1.0 OD1 A:ASP351 2.2 24.4 1.0 O3 A:POP701 2.3 30.4 1.0 O5 A:POP701 2.7 24.7 1.0 P A:AMP702 3.1 49.7 1.0 CG A:ASP253 3.1 23.2 1.0 CG A:ASP351 3.3 24.8 1.0 O A:POP701 3.3 28.4 1.0 P1 A:POP701 3.4 28.8 1.0 O5' A:AMP702 3.5 48.1 1.0 P2 A:POP701 3.5 23.4 1.0 O2P A:AMP702 3.6 50.0 1.0 NZ A:LYS443 3.6 34.0 1.0 CB A:ASP253 3.6 22.1 1.0 O2 A:PCX703 3.8 46.1 1.0 OD2 A:ASP351 3.9 24.0 1.0 O A:GLY347 4.0 15.5 1.0 NZ A:LYS423 4.1 22.5 1.0 OD1 A:ASP253 4.2 22.3 1.0 O1 A:POP701 4.3 31.3 1.0 O6 A:POP701 4.3 24.5 1.0 O3' A:AMP702 4.4 35.6 1.0 O3P A:AMP702 4.4 51.0 1.0 N A:ASP351 4.4 20.8 1.0 O2 A:POP701 4.4 28.7 1.0 CB A:ASP351 4.5 22.8 1.0 C3 A:PCX703 4.6 46.2 1.0 CB A:ALA350 4.6 20.4 1.0 O4 A:POP701 4.7 27.1 1.0 O4 A:PCX703 4.7 51.0 1.0 C5' A:AMP702 4.8 43.2 1.0 CE A:LYS443 4.9 37.7 1.0 N A:ALA350 4.9 19.8 1.0 C8 A:PCX703 4.9 49.2 1.0 MG A:MG603 4.9 36.0 1.0 C3' A:AMP702 4.9 36.2 1.0

Magnesium binding site 2 out of 4 in the Beta-Lactam Synthetase with Product (Dgpc), Amp and Ppi


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 with Product (Dgpc), Amp and Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:36.0 occ:1.00 O A:HOH813 1.9 26.1 1.0 O6 A:POP701 2.0 24.5 1.0 O A:LEU444 2.2 48.5 1.0 O A:HOH814 2.3 28.7 1.0 O2P A:AMP702 2.4 50.0 1.0 O2 A:POP701 2.5 28.7 1.0 P2 A:POP701 3.4 23.4 1.0 C A:LEU444 3.4 47.4 1.0 P1 A:POP701 3.5 28.8 1.0 O A:POP701 3.6 28.4 1.0 OG A:SER249 3.8 29.4 1.0 P A:AMP702 3.8 49.7 1.0 O3 A:POP701 3.9 30.4 1.0 O5 A:POP701 4.1 24.7 1.0 CA A:LEU444 4.1 46.1 1.0 NZ A:LYS443 4.1 34.0 1.0 OE2 A:GLU280 4.2 36.8 1.0 N A:LEU444 4.2 45.0 1.0 OE1 A:GLU280 4.3 35.3 1.0 CG2 A:VAL446 4.3 57.5 1.0 O1P A:AMP702 4.3 48.7 1.0 N A:GLY445 4.3 49.0 1.0 CB A:LEU444 4.4 45.8 1.0 O4 A:POP701 4.4 27.1 1.0 CB A:SER249 4.5 28.5 1.0 O3P A:AMP702 4.5 51.0 1.0 N A:VAL446 4.6 54.5 1.0 CA A:GLY445 4.6 51.2 1.0 CD A:GLU280 4.7 34.4 1.0 O1 A:POP701 4.8 31.3 1.0 CA A:GLY251 4.9 23.6 1.0 O5' A:AMP702 4.9 48.1 1.0 C8 A:AMP702 4.9 39.1 1.0 C A:GLY445 4.9 53.3 1.0 MG A:MG601 4.9 32.5 1.0

Magnesium binding site 3 out of 4 in the Beta-Lactam Synthetase with Product (Dgpc), Amp and Ppi


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 with Product (Dgpc), Amp and Ppi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:38.4 occ:1.00 O B:HOH844 2.0 45.5 1.0 O B:HOH842 2.1 34.3 1.0 O B:HOH843 2.2 24.6 1.0 O3 B:POP704 2.4 22.1 1.0 O5 B:POP704 2.4 21.7 1.0 O2P B:AMP705 3.3 60.3 1.0 P2 B:POP704 3.4 20.2 1.0 P1 B:POP704 3.5 23.6 1.0 O B:POP704 3.6 20.3 1.0 OG B:SER249 3.7 27.4 1.0 O B:HOH864 3.8 36.5 1.0 O6 B:POP704 3.8 19.2 1.0 OE1 B:GLU280 4.0 38.3 1.0 O2 B:POP704 4.2 19.9 1.0 OE2 B:GLU280 4.3 40.0 1.0 CB B:SER249 4.4 27.9 1.0 P B:AMP705 4.5 61.6 1.0 CD B:GLU280 4.6 37.3 1.0 NZ B:LYS443 4.7 38.2 1.0 O1 B:POP704 4.7 22.5 1.0 O4 B:POP704 4.7 20.9 1.0 O1P B:AMP705 4.8 59.3 1.0 CA B:GLY251 4.9 23.6 1.0 MG B:MG605 4.9 29.4 1.0 O B:LYS443 5.0 46.0 1.0

Magnesium binding site 4 out of 4 in the Beta-Lactam Synthetase with Product (Dgpc), Amp and Ppi


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 with Product (Dgpc), Amp and Ppi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:29.4 occ:1.00 O6 B:POP704 2.0 19.2 1.0 OD1 B:ASP253 2.1 25.2 1.0 O2 B:POP704 2.1 19.9 1.0 O B:HOH727 2.2 17.7 1.0 O1P B:AMP705 2.3 59.3 1.0 OD1 B:ASP351 2.3 20.6 1.0 CG B:ASP253 3.1 22.3 1.0 P2 B:POP704 3.2 20.2 1.0 P1 B:POP704 3.2 23.6 1.0 O B:POP704 3.2 20.3 1.0 CG B:ASP351 3.4 21.1 1.0 P B:AMP705 3.5 61.6 1.0 CB B:ASP253 3.6 20.8 1.0 O2P B:AMP705 3.7 60.3 1.0 NZ B:LYS443 3.9 38.2 1.0 OD2 B:ASP351 3.9 17.3 1.0 O2 B:PCX706 3.9 28.9 1.0 NZ B:LYS423 4.0 24.8 1.0 O4 B:POP704 4.0 20.9 1.0 OD2 B:ASP253 4.1 23.6 1.0 O5' B:AMP705 4.1 56.4 1.0 O3 B:POP704 4.1 22.1 1.0 O5 B:POP704 4.2 21.7 1.0 O1 B:POP704 4.4 22.5 1.0 O B:GLY347 4.4 13.3 1.0 O3' B:AMP705 4.5 43.1 1.0 C3 B:PCX706 4.5 29.1 1.0 CB B:ASP351 4.6 17.0 1.0 O3P B:AMP705 4.7 61.2 1.0 O4 B:PCX706 4.7 39.0 1.0 C8 B:PCX706 4.8 36.8 1.0 N B:ASP351 4.8 14.5 1.0 MG B:MG602 4.9 38.4 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