Magnesium in PDB 3jz0: Linb Complexed with Clindamycin and Ampcpp

The structure of Linb Complexed with Clindamycin and Ampcpp, PDB code: 3jz0 was solved by M.Morar, G.D.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.689, 96.064, 102.708, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 22.1

The structure of Linb Complexed with Clindamycin and Ampcpp also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Linb Complexed with Clindamycin and Ampcpp (pdb code 3jz0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Linb Complexed with Clindamycin and Ampcpp, PDB code: 3jz0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Linb Complexed with Clindamycin and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Linb Complexed with Clindamycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg300 b:10.3 occ:1.00 OD1 A:ASP40 2.0 10.8 1.0 O2B A:APC738 2.1 11.6 1.0 OE1 A:GLU42 2.1 10.0 1.0 O A:HOH322 2.1 8.4 1.0 O1G A:APC738 2.2 13.4 1.0 O1A A:APC738 2.2 10.7 1.0 CD A:GLU42 3.0 11.6 1.0 CG A:ASP40 3.1 10.8 1.0 PB A:APC738 3.2 12.8 1.0 OE2 A:GLU42 3.2 13.4 1.0 PG A:APC738 3.3 13.4 1.0 PA A:APC738 3.4 11.2 1.0 OD2 A:ASP40 3.5 11.4 1.0 MG A:MG303 3.5 12.5 1.0 O3B A:APC738 3.7 12.3 1.0 C3A A:APC738 3.7 11.0 1.0 C5' A:APC738 3.9 10.8 1.0 O A:HOH424 3.9 9.4 1.0 O A:ASP40 4.0 10.3 1.0 OG A:SER29 4.1 11.2 1.0 O2G A:APC738 4.1 13.8 1.0 O5' A:APC738 4.1 10.6 1.0 N A:SER29 4.2 10.3 1.0 O A:HOH276 4.3 5.3 1.0 N A:ASP40 4.3 9.5 1.0 C A:ASP40 4.4 10.2 1.0 CG A:GLU42 4.4 11.3 1.0 CB A:ASP40 4.4 9.6 1.0 CA A:GLY28 4.5 10.4 1.0 O1B A:APC738 4.6 9.6 1.0 CA A:ASP40 4.6 10.1 1.0 O3G A:APC738 4.6 13.4 1.0 O2A A:APC738 4.7 11.2 1.0 O A:HOH470 4.7 13.9 1.0 CB A:SER29 4.8 10.4 1.0 C A:GLY28 4.9 10.6 1.0

Magnesium binding site 2 out of 5 in the Linb Complexed with Clindamycin and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Linb Complexed with Clindamycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:12.5 occ:1.00 O A:HOH470 2.0 13.9 1.0 OE2 A:GLU42 2.0 13.4 1.0 OE1 A:GLU89 2.1 19.8 1.0 OD2 A:ASP40 2.1 11.4 1.0 O1A A:APC738 2.2 10.7 1.0 O6 A:CLY900 2.6 22.8 1.0 CG A:ASP40 3.1 10.8 1.0 CD A:GLU42 3.2 11.6 1.0 PA A:APC738 3.2 11.2 1.0 CD A:GLU89 3.3 17.4 1.0 OD1 A:ASP40 3.3 10.8 1.0 O2A A:APC738 3.4 11.2 1.0 MG A:MG300 3.5 10.3 1.0 OE1 A:GLU42 3.6 10.0 1.0 C2 A:CLY900 3.9 22.1 1.0 O4 A:CLY900 3.9 24.8 1.0 O5' A:APC738 3.9 10.6 1.0 OE2 A:GLU89 4.0 21.0 1.0 O A:HOH424 4.1 9.4 1.0 C5' A:APC738 4.1 10.8 1.0 C1 A:CLY900 4.2 22.9 1.0 CG A:GLU89 4.3 15.1 1.0 CG A:GLU42 4.4 11.3 1.0 NH1 A:ARG87 4.5 8.2 1.0 CB A:ASP40 4.5 9.6 1.0 NH2 A:ARG87 4.6 10.5 1.0 CB A:GLU42 4.6 11.4 1.0 O1G A:APC738 4.7 13.4 1.0 C3A A:APC738 4.8 11.0 1.0 CB A:GLU89 4.8 13.0 1.0 O2B A:APC738 4.8 11.6 1.0 O7 A:CLY900 4.9 20.1 1.0 C3 A:CLY900 5.0 21.1 1.0

Magnesium binding site 3 out of 5 in the Linb Complexed with Clindamycin and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Linb Complexed with Clindamycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:18.3 occ:1.00 O A:HOH1033 1.9 8.1 1.0 O A:HOH1031 2.0 14.0 1.0 OD1 A:ASP63 2.0 13.9 1.0 O A:HOH1032 2.2 9.7 1.0 O A:HOH1034 2.2 8.7 1.0 CG A:ASP63 3.0 14.5 1.0 OD2 A:ASP63 3.3 14.8 1.0 O A:ASN59 4.1 13.7 1.0 O A:HOH351 4.2 20.0 1.0 CB A:ASP63 4.4 13.1 1.0 CD2 A:PHE62 4.6 14.5 1.0 N A:ASP63 4.6 13.0 1.0 CA A:ASP63 4.7 13.2 1.0 C A:ASN59 5.0 14.4 1.0

Magnesium binding site 4 out of 5 in the Linb Complexed with Clindamycin and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Linb Complexed with Clindamycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:11.1 occ:1.00 O2B B:APC738 2.0 10.6 1.0 O1G B:APC738 2.1 11.8 1.0 OD1 B:ASP40 2.1 10.3 1.0 O B:HOH307 2.1 6.2 1.0 OE1 B:GLU42 2.1 11.2 1.0 O1A B:APC738 2.3 9.7 1.0 CD B:GLU42 3.1 11.3 1.0 PB B:APC738 3.1 11.0 1.0 CG B:ASP40 3.2 9.6 1.0 PG B:APC738 3.2 12.6 1.0 OE2 B:GLU42 3.4 13.0 1.0 PA B:APC738 3.5 9.1 1.0 O3B B:APC738 3.5 10.6 1.0 OD2 B:ASP40 3.6 11.2 1.0 C3A B:APC738 3.7 10.2 1.0 MG B:MG302 3.7 13.4 1.0 O B:HOH297 3.9 4.6 1.0 O2G B:APC738 4.0 11.2 1.0 C5' B:APC738 4.0 9.9 1.0 OG B:SER29 4.0 10.1 1.0 O B:ASP40 4.1 8.9 1.0 N B:SER29 4.1 9.6 1.0 O5' B:APC738 4.2 9.5 1.0 N B:ASP40 4.2 9.0 1.0 O B:HOH275 4.2 7.1 1.0 C B:ASP40 4.4 9.2 1.0 CG B:GLU42 4.4 11.0 1.0 CB B:ASP40 4.4 9.3 1.0 O1B B:APC738 4.5 11.4 1.0 CA B:GLY28 4.5 9.5 1.0 O3G B:APC738 4.5 10.5 1.0 CA B:ASP40 4.6 9.2 1.0 CB B:SER29 4.7 9.5 1.0 O2A B:APC738 4.8 7.9 1.0 C B:GLY28 4.9 9.9 1.0 O B:HOH401 4.9 8.4 1.0

Magnesium binding site 5 out of 5 in the Linb Complexed with Clindamycin and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Linb Complexed with Clindamycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:13.4 occ:1.00 OE1 B:GLU89 1.9 17.7 1.0 OE2 B:GLU42 2.0 13.0 1.0 OD2 B:ASP40 2.1 11.2 1.0 O B:HOH401 2.1 8.4 1.0 O1A B:APC738 2.2 9.7 1.0 O6 B:CLY900 2.5 15.3 1.0 CG B:ASP40 3.1 9.6 1.0 CD B:GLU89 3.1 15.6 1.0 CD B:GLU42 3.2 11.3 1.0 PA B:APC738 3.2 9.1 1.0 OD1 B:ASP40 3.3 10.3 1.0 O2A B:APC738 3.5 7.9 1.0 O4 B:CLY900 3.6 17.7 1.0 OE1 B:GLU42 3.6 11.2 1.0 MG B:MG301 3.7 11.1 1.0 C2 B:CLY900 3.7 15.8 1.0 OE2 B:GLU89 3.8 19.0 1.0 O5' B:APC738 4.0 9.5 1.0 C1 B:CLY900 4.0 16.7 1.0 O B:HOH297 4.0 4.6 1.0 CG B:GLU89 4.2 14.5 1.0 C5' B:APC738 4.2 9.9 1.0 NH1 B:ARG87 4.4 8.9 1.0 CG B:GLU42 4.4 11.0 1.0 CB B:ASP40 4.4 9.3 1.0 NH2 B:ARG87 4.4 10.2 1.0 CB B:GLU42 4.6 10.2 1.0 O1G B:APC738 4.7 11.8 1.0 CB B:GLU89 4.8 12.3 1.0 C3A B:APC738 4.8 10.2 1.0 O7 B:CLY900 4.8 14.7 1.0 C3 B:CLY900 4.9 15.9 1.0 O2B B:APC738 4.9 10.6 1.0 CZ B:ARG87 4.9 9.7 1.0

M.Morar, K.Bhullar, D.W.Hughes, M.Junop, G.D.Wright. Structure and Mechanism of the Lincosamide Antibiotic Adenylyltransferase Linb. Structure V. 17 1649 2009.
ISSN: ISSN 0969-2126
PubMed: 20004168
DOI: 10.1016/J.STR.2009.10.013