Magnesium in PDB 1mbz: Beta-Lactam Synthetase with Trapped Intermediate

The structure of Beta-Lactam Synthetase with Trapped Intermediate, PDB code: 1mbz 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)	29.27 / 2.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.390, 97.154, 81.087, 90.00, 90.11, 90.00
R / Rfree (%)	21.4 / 27

The binding sites of Magnesium atom in the Beta-Lactam Synthetase with Trapped Intermediate (pdb code 1mbz). 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 Trapped Intermediate, PDB code: 1mbz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Beta-Lactam Synthetase with Trapped Intermediate


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 Trapped Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:10.7 occ:1.00 O1A A:IOT606 1.9 17.0 1.0 O A:HOH734 1.9 6.4 1.0 OD1 A:ASP351 2.1 7.2 1.0 OD2 A:ASP253 2.2 9.0 1.0 O6 A:POP605 2.3 16.5 1.0 O2 A:POP605 2.6 4.9 1.0 CG A:ASP351 3.2 8.0 1.0 CG A:ASP253 3.3 7.8 1.0 PA A:IOT606 3.4 16.1 1.0 NZ A:LYS443 3.5 18.0 1.0 P2 A:POP605 3.7 16.0 1.0 OD2 A:ASP351 3.8 8.3 1.0 CB A:ASP253 3.8 7.9 1.0 P1 A:POP605 3.8 7.8 1.0 O A:POP605 3.9 9.8 1.0 O A:IOT606 3.9 17.9 1.0 NZ A:LYS423 4.1 1.1 1.0 O A:GLY347 4.1 9.8 1.0 C A:IOT606 4.3 18.3 1.0 CB A:ASP351 4.3 7.8 1.0 N A:ASP351 4.3 6.5 1.0 O5' A:IOT606 4.3 17.2 1.0 OD1 A:ASP253 4.3 6.6 1.0 C5' A:IOT606 4.3 18.1 1.0 OX2 A:IOT606 4.4 18.7 1.0 O2A A:IOT606 4.4 15.8 1.0 OX3 A:IOT606 4.4 16.0 1.0 CB A:ALA350 4.5 7.4 1.0 O5 A:POP605 4.5 15.7 1.0 CE A:LYS443 4.6 17.0 1.0 O3 A:POP605 4.6 7.0 1.0 O4 A:POP605 4.7 15.1 1.0 O3' A:IOT606 4.7 17.0 1.0 MG A:MG604 4.7 14.8 1.0 CA A:ASP351 4.9 6.7 1.0 C3' A:IOT606 4.9 15.7 1.0 N A:ALA350 4.9 6.4 1.0 C4' A:IOT606 5.0 17.3 1.0 O1 A:POP605 5.0 8.0 1.0

Magnesium binding site 2 out of 4 in the Beta-Lactam Synthetase with Trapped Intermediate


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 Trapped Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:14.8 occ:1.00 O3 A:POP605 2.0 7.0 1.0 O5 A:POP605 2.0 15.7 1.0 O2A A:IOT606 2.1 15.8 1.0 O A:HOH608 2.1 9.0 1.0 O A:LEU444 2.4 14.3 1.0 O A:HOH788 2.4 11.2 1.0 P1 A:POP605 2.9 7.8 1.0 P2 A:POP605 2.9 16.0 1.0 O A:POP605 3.0 9.8 1.0 PA A:IOT606 3.2 16.1 1.0 C A:LEU444 3.5 13.6 1.0 O1A A:IOT606 3.5 17.0 1.0 O6 A:POP605 3.5 16.5 1.0 O2 A:POP605 3.5 4.9 1.0 O5' A:IOT606 3.7 17.2 1.0 NZ A:LYS443 3.8 18.0 1.0 OG A:SER249 3.9 15.3 1.0 O1 A:POP605 4.2 8.0 1.0 O4 A:POP605 4.2 15.1 1.0 N A:LEU444 4.3 14.9 1.0 N A:GLY445 4.3 12.5 1.0 CB A:SER249 4.3 15.1 1.0 CA A:GLY445 4.3 11.6 1.0 O A:HOH701 4.4 10.7 1.0 CA A:LEU444 4.4 13.3 1.0 N A:VAL446 4.4 11.8 1.0 C A:GLY445 4.4 11.2 1.0 OX2 A:IOT606 4.5 18.7 1.0 C8 A:IOT606 4.6 15.7 1.0 MG A:MG603 4.7 10.7 1.0 CB A:LEU444 4.7 12.6 1.0 OE1 A:GLU280 4.7 16.3 1.0 CA A:GLY251 4.8 11.4 1.0 OE2 A:GLU280 4.8 15.9 1.0 N7 A:IOT606 4.8 16.9 1.0 C5' A:IOT606 4.9 18.1 1.0 O A:GLY445 5.0 8.6 1.0

Magnesium binding site 3 out of 4 in the Beta-Lactam Synthetase with Trapped Intermediate


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 Trapped Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:23.9 occ:1.00 O1A B:IOT603 1.8 31.9 1.0 OD1 B:ASP351 1.9 13.4 1.0 O4 B:POP604 2.0 19.9 1.0 OD1 B:ASP253 2.2 11.6 1.0 O B:HOH615 2.4 2.5 1.0 O2 B:POP604 2.5 20.4 1.0 NZ B:LYS443 2.8 33.5 1.0 CG B:ASP351 3.0 12.6 1.0 CG B:ASP253 3.3 13.2 1.0 PA B:IOT603 3.3 35.2 1.0 P2 B:POP604 3.3 19.7 1.0 OD2 B:ASP351 3.5 13.3 1.0 P1 B:POP604 3.6 20.4 1.0 O B:POP604 3.6 20.2 1.0 CB B:ASP253 3.9 13.4 1.0 NZ B:LYS423 3.9 0.0 1.0 CE B:LYS443 3.9 33.4 1.0 O2A B:IOT603 4.0 33.3 1.0 O5 B:POP604 4.1 20.6 1.0 OX2 B:IOT603 4.1 36.1 1.0 OD2 B:ASP253 4.2 12.3 1.0 O B:IOT603 4.2 28.4 1.0 O3 B:POP604 4.3 21.2 1.0 CB B:ASP351 4.3 11.5 1.0 O6 B:POP604 4.4 22.3 1.0 O5' B:IOT603 4.4 33.6 1.0 CD B:LYS443 4.5 33.0 1.0 O B:GLY347 4.5 11.9 1.0 C B:IOT603 4.6 29.1 1.0 N B:ASP351 4.7 13.6 1.0 C5' B:IOT603 4.7 29.3 1.0 O1 B:POP604 4.8 18.4 1.0 CG B:LYS443 4.9 33.2 1.0 OX3 B:IOT603 4.9 27.5 1.0

Magnesium binding site 4 out of 4 in the Beta-Lactam Synthetase with Trapped Intermediate


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 Trapped Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:18.7 occ:1.00 O B:HOH766 2.2 34.0 1.0 O B:HOH767 2.4 21.3 1.0 O B:HOH765 2.5 18.3 1.0 O6 B:POP604 2.5 22.3 1.0 O3 B:POP604 2.7 21.2 1.0 O2A B:IOT603 2.8 33.3 1.0 OE1 B:GLU280 3.6 34.2 1.0 P2 B:POP604 3.7 19.7 1.0 O B:POP604 3.8 20.2 1.0 P1 B:POP604 3.9 20.4 1.0 O4 B:POP604 4.1 19.9 1.0 OG B:SER249 4.1 13.2 1.0 PA B:IOT603 4.2 35.2 1.0 CD B:GLU280 4.5 34.4 1.0 OE2 B:GLU280 4.6 35.4 1.0 O5' B:IOT603 4.7 33.6 1.0 NZ B:LYS443 4.7 33.5 1.0 O1A B:IOT603 4.8 31.9 1.0 O2 B:POP604 4.8 20.4 1.0 CB B:SER249 4.8 14.5 1.0 O1 B:POP604 4.9 18.4 1.0 O5 B:POP604 5.0 20.6 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