Magnesium in PDB 7w15: Crystal Structure of Mph-E in Complex with Gtp and Erythromycin

The structure of Crystal Structure of Mph-E in Complex with Gtp and Erythromycin, PDB code: 7w15 was solved by Q.Qi, L.Kuang, Y.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.85 / 1.77
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.62, 50.278, 97.396, 90, 115.41, 90
R / Rfree (%)	18.8 / 19.6

The binding sites of Magnesium atom in the Crystal Structure of Mph-E in Complex with Gtp and Erythromycin (pdb code 7w15). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Mph-E in Complex with Gtp and Erythromycin, PDB code: 7w15:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Mph-E in Complex with Gtp and Erythromycin


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 Mph-E in Complex with Gtp and Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:12.5 occ:1.00 O2A B:GTP402 1.9 13.1 1.0 O B:HOH675 2.1 13.1 1.0 O1G B:GTP402 2.1 14.6 1.0 OD2 B:ASP213 2.2 15.1 1.0 NE2 B:HIS199 2.2 14.5 1.0 O3B B:GTP402 2.2 13.8 1.0 PG B:GTP402 2.7 16.9 1.0 CE1 B:HIS199 3.1 14.5 1.0 CD2 B:HIS199 3.2 14.1 1.0 PA B:GTP402 3.2 15.8 1.0 CG B:ASP213 3.2 15.1 1.0 PB B:GTP402 3.4 13.8 1.0 O3A B:GTP402 3.4 14.7 1.0 O2G B:GTP402 3.6 16.2 1.0 O B:HOH545 3.6 17.4 1.0 CB B:ASP213 3.6 13.5 1.0 MG B:MG404 3.7 16.3 1.0 O2B B:GTP402 3.8 13.2 1.0 O3G B:GTP402 3.9 17.4 1.0 O3' B:GTP402 4.2 12.9 1.0 ND1 B:HIS199 4.2 12.4 1.0 O1A B:GTP402 4.2 14.0 1.0 O5' B:GTP402 4.3 14.2 1.0 OD1 B:ASP213 4.3 12.0 1.0 CG B:HIS199 4.3 14.9 1.0 C5' B:GTP402 4.3 15.5 1.0 C3' B:GTP402 4.6 14.7 1.0 O1B B:GTP402 4.6 15.3 1.0 O B:HOH571 4.8 15.5 1.0 OD2 B:ASP194 4.8 15.6 1.0 CA B:GLY27 4.9 21.4 1.0 O8 B:ERY401 4.9 15.7 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Mph-E in Complex with Gtp and Erythromycin


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 Mph-E in Complex with Gtp and Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:16.3 occ:1.00 O2G B:GTP402 2.0 16.2 1.0 O B:HOH563 2.0 17.0 1.0 OD2 B:ASP213 2.1 15.1 1.0 O2B B:GTP402 2.1 13.2 1.0 O B:HOH571 2.1 15.5 1.0 OD1 B:ASP213 2.1 12.0 1.0 CG B:ASP213 2.4 15.1 1.0 PG B:GTP402 3.1 16.9 1.0 PB B:GTP402 3.2 13.8 1.0 O3B B:GTP402 3.2 13.8 1.0 O1G B:GTP402 3.7 14.6 1.0 MG B:MG403 3.7 12.5 1.0 CB B:ASP213 3.9 13.5 1.0 NH2 B:ARG46 4.0 15.8 1.0 OG B:SER215 4.1 14.9 1.0 OD2 B:ASP194 4.2 15.6 1.0 N1 B:ERY401 4.2 19.3 1.0 O B:HOH569 4.2 14.3 1.0 O1B B:GTP402 4.2 15.3 1.0 OD2 B:ASP29 4.3 17.7 1.0 O3A B:GTP402 4.3 14.7 1.0 O3G B:GTP402 4.4 17.4 1.0 C28 B:ERY401 4.4 19.0 1.0 O2A B:GTP402 4.5 13.1 1.0 C29 B:ERY401 4.6 17.7 1.0 PA B:GTP402 4.7 15.8 1.0 CB B:ASP29 4.8 16.6 1.0 O1A B:GTP402 4.8 14.0 1.0 CA B:ASP213 4.8 16.5 1.0 CE1 B:HIS199 4.9 14.5 1.0 CG B:ASP29 4.9 18.8 1.0 O8 B:ERY401 4.9 15.7 1.0 C B:ASP213 4.9 14.0 1.0 NE2 B:HIS199 4.9 14.5 1.0 O B:ASP213 5.0 14.4 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Mph-E in Complex with Gtp and Erythromycin


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 Mph-E in Complex with Gtp and Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:30.9 occ:1.00 O B:HOH922 1.9 41.5 1.0 O B:HOH553 2.0 24.4 1.0 O B:HOH774 2.1 24.5 1.0 O B:ASP181 3.9 17.4 1.0 O B:HOH757 4.0 30.2 1.0 CB B:ASP181 4.4 18.5 1.0 C B:ASP181 4.5 16.5 1.0 O B:TRP184 4.6 20.0 1.0 OD2 B:ASP181 4.6 25.7 1.0 O B:HOH513 4.9 30.9 1.0 NH1 B:ARG150 4.9 20.3 1.0 CA B:ASP181 5.0 16.6 1.0 O B:HOH767 5.0 28.9 1.0 NH2 B:ARG150 5.0 17.9 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Mph-E in Complex with Gtp and Erythromycin


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 Mph-E in Complex with Gtp and Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:16.9 occ:1.00 O2A A:GTP402 2.0 16.6 1.0 O3G A:GTP402 2.1 19.3 1.0 O A:HOH619 2.1 17.8 1.0 NE2 A:HIS199 2.2 19.9 1.0 OD2 A:ASP213 2.2 19.4 1.0 O3B A:GTP402 2.2 19.1 1.0 PG A:GTP402 2.7 27.5 1.0 CE1 A:HIS199 3.0 18.2 1.0 CD2 A:HIS199 3.2 17.0 1.0 CG A:ASP213 3.2 17.8 1.0 PA A:GTP402 3.2 18.5 1.0 PB A:GTP402 3.3 19.7 1.0 O3A A:GTP402 3.4 20.1 1.0 O A:HOH534 3.5 25.2 1.0 O1G A:GTP402 3.5 23.8 1.0 CB A:ASP213 3.7 17.0 1.0 O1B A:GTP402 3.7 20.2 1.0 MG A:MG404 3.8 21.5 1.0 O2G A:GTP402 3.8 26.5 1.0 ND1 A:HIS199 4.1 16.8 1.0 O3' A:GTP402 4.2 18.2 1.0 CG A:HIS199 4.2 18.3 1.0 O1A A:GTP402 4.2 20.6 1.0 OD1 A:ASP213 4.3 18.6 1.0 O5' A:GTP402 4.3 17.8 1.0 C5' A:GTP402 4.4 17.2 1.0 O2B A:GTP402 4.6 22.0 1.0 C3' A:GTP402 4.7 17.6 1.0 O A:HOH579 4.7 22.4 1.0 O8 A:ERY401 4.7 24.8 1.0 OD2 A:ASP194 4.7 21.5 1.0 CA A:GLY27 4.8 25.5 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Mph-E in Complex with Gtp and Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Mph-E in Complex with Gtp and Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:21.5 occ:1.00 O A:HOH560 2.0 21.6 1.0 O1G A:GTP402 2.1 23.8 1.0 O1B A:GTP402 2.1 20.2 1.0 OD2 A:ASP213 2.1 19.4 1.0 O A:HOH579 2.2 22.4 1.0 OD1 A:ASP213 2.2 18.6 1.0 CG A:ASP213 2.5 17.8 1.0 PG A:GTP402 3.1 27.5 1.0 PB A:GTP402 3.2 19.7 1.0 O3B A:GTP402 3.2 19.1 1.0 O3G A:GTP402 3.7 19.3 1.0 MG A:MG403 3.8 16.9 1.0 NH2 A:ARG46 3.9 19.6 1.0 OG A:SER215 4.0 20.1 1.0 CB A:ASP213 4.0 17.0 1.0 N1 A:ERY401 4.2 27.9 1.0 O2B A:GTP402 4.2 22.0 1.0 OD2 A:ASP29 4.2 23.9 1.0 O A:HOH581 4.2 19.4 1.0 OD2 A:ASP194 4.3 21.5 1.0 O3A A:GTP402 4.3 20.1 1.0 C28 A:ERY401 4.4 25.9 1.0 O2G A:GTP402 4.4 26.5 1.0 O2A A:GTP402 4.6 16.6 1.0 C29 A:ERY401 4.6 27.5 1.0 CB A:ASP29 4.7 24.1 1.0 CG A:ASP29 4.7 25.1 1.0 PA A:GTP402 4.8 18.5 1.0 O8 A:ERY401 4.8 24.8 1.0 O1A A:GTP402 4.8 20.6 1.0 CE1 A:HIS199 4.8 18.2 1.0 CA A:ASP213 4.9 18.7 1.0 CB A:SER215 5.0 20.5 1.0 C A:ASP213 5.0 18.4 1.0 O A:ASP213 5.0 19.3 1.0 NE2 A:HIS199 5.0 19.9 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Mph-E in Complex with Gtp and Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Mph-E in Complex with Gtp and Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:34.7 occ:1.00 O A:HOH720 2.6 37.4 1.0 O A:HOH696 2.7 34.8 1.0 OD1 A:ASP220 2.8 24.2 1.0 NH2 A:ARG263 3.0 27.3 1.0 CG A:ASP220 3.6 24.7 1.0 OD2 A:ASP220 3.6 27.2 1.0 NH1 A:ARG263 3.7 28.4 1.0 CZ A:ARG263 3.7 25.0 1.0 CD2 A:LEU149 3.9 31.8 1.0 CD1 A:ILE224 4.1 22.2 1.0 CB A:LEU149 4.2 31.3 1.0 CD1 A:ILE153 4.2 31.9 1.0 CG A:LEU149 4.5 32.1 1.0 CA A:LEU149 4.6 32.1 1.0 CG1 A:ILE153 4.6 36.4 1.0 CB A:ASP221 4.7 22.8 1.0 CE A:MET144 4.8 36.5 1.0 CD1 A:LEU149 4.9 29.6 1.0 O A:LEU149 4.9 31.6 1.0 N A:ASP221 5.0 23.1 1.0 NE A:ARG263 5.0 27.1 1.0

Q.Qi, L.Kuang, Y.Jiang. Crystal Structure of the Acinetobacter Baumannii Macrolide Phosphotransferases E Reveal the Novel Catalysis Mechanism To Be Published.