Magnesium in PDB 6sum: Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami

All present enzymatic activity of Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami:
2.7.1.230;

The structure of Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami, PDB code: 6sum was solved by G.P.Bourenkov, Y.A.Mokrushina, S.S.Terekhov, I.V.Smirnov, A.G.Gabibov, S.Altman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 1.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.660, 66.000, 70.410, 112.29, 102.81, 94.79
R / Rfree (%)	14.5 / 17.6

The binding sites of Magnesium atom in the Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami (pdb code 6sum). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami, PDB code: 6sum:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:10.6 occ:1.00 O2G A:ANP403 2.0 10.7 1.0 O2B A:ANP403 2.0 10.4 1.0 O A:HOH574 2.1 12.2 1.0 O A:HOH564 2.1 10.6 1.0 OD2 A:ASP220 2.1 10.3 1.0 OD1 A:ASP220 2.2 10.3 1.0 CG A:ASP220 2.5 10.0 1.0 PG A:ANP403 3.1 12.6 1.0 PB A:ANP403 3.2 10.9 1.0 N3B A:ANP403 3.4 11.2 1.0 O1G A:ANP403 3.6 12.6 1.0 MG A:MG402 3.7 16.3 1.0 OD2 A:ASP223 3.8 12.7 1.0 CB A:ASP220 4.0 10.4 1.0 OD2 A:ASP203 4.1 12.0 1.0 NZ A:LYS53 4.2 14.3 0.5 O3A A:ANP403 4.2 11.4 1.0 NAD A:UAM404 4.2 14.7 1.0 CB A:ASP222 4.3 11.1 1.0 O1B A:ANP403 4.3 11.9 1.0 NZ A:LYS53 4.4 13.3 0.5 OD2 A:ASP222 4.4 12.2 1.0 O3G A:ANP403 4.4 13.0 1.0 ND2 A:ASN37 4.5 14.6 1.0 O2A A:ANP403 4.6 12.9 1.0 CB A:GLU36 4.6 20.2 1.0 O A:ASP220 4.6 10.9 1.0 PA A:ANP403 4.7 12.4 1.0 O1A A:ANP403 4.7 14.4 1.0 OAI A:UAM404 4.7 13.6 1.0 ND2 A:ASN208 4.8 10.7 1.0 CA A:ASP220 4.9 9.7 1.0 CG A:ASP223 4.9 11.1 1.0 CG A:ASP222 4.9 12.2 1.0

Magnesium binding site 2 out of 5 in the Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:16.3 occ:1.00 O2A A:ANP403 1.9 12.9 1.0 O1G A:ANP403 1.9 12.6 1.0 OD1 A:ASN208 2.0 11.0 1.0 OD2 A:ASP220 2.1 10.3 1.0 O A:HOH665 2.3 17.8 1.0 N3B A:ANP403 2.7 11.2 1.0 PG A:ANP403 2.9 12.6 1.0 CG A:ASN208 3.0 10.9 1.0 CG A:ASP220 3.1 10.0 1.0 PA A:ANP403 3.2 12.4 1.0 ND2 A:ASN208 3.4 10.7 1.0 CB A:ASP220 3.6 10.4 1.0 O2G A:ANP403 3.6 10.7 1.0 O3A A:ANP403 3.7 11.4 1.0 PB A:ANP403 3.7 10.9 1.0 MG A:MG401 3.7 10.6 1.0 CE1 A:HIS205 3.8 12.9 1.0 O2B A:ANP403 3.9 10.4 1.0 NE2 A:HIS205 3.9 13.3 1.0 O1A A:ANP403 4.0 14.4 1.0 O3G A:ANP403 4.1 13.0 1.0 OD1 A:ASP220 4.2 10.3 1.0 O A:GLY207 4.4 13.9 1.0 O5' A:ANP403 4.4 11.9 1.0 CB A:ASN208 4.4 11.1 1.0 O A:HOH790 4.4 16.8 1.0 O3' A:ANP403 4.5 15.6 1.0 O A:HOH578 4.6 19.2 1.0 O A:HOH564 4.6 10.6 1.0 C A:GLY207 4.7 13.4 1.0 C5' A:ANP403 4.7 13.1 1.0 OD2 A:ASP203 4.7 12.0 1.0 CA A:ASN208 4.8 11.5 1.0 C3' A:ANP403 4.8 13.0 1.0 N A:ASN208 4.9 12.9 1.0

Magnesium binding site 3 out of 5 in the Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:10.9 occ:1.00 O1G B:ANP403 2.0 10.9 1.0 O B:HOH546 2.0 11.7 1.0 O2B B:ANP403 2.0 10.7 1.0 O B:HOH538 2.1 11.1 1.0 OD2 B:ASP220 2.2 10.7 1.0 OD1 B:ASP220 2.3 10.4 1.0 CG B:ASP220 2.5 11.2 1.0 PG B:ANP403 3.1 14.4 1.0 PB B:ANP403 3.2 11.3 1.0 N3B B:ANP403 3.4 12.3 1.0 O2G B:ANP403 3.6 16.7 1.0 OD2 B:ASP223 3.8 12.6 1.0 MG B:MG402 3.8 16.6 1.0 CB B:ASP220 4.1 11.2 1.0 OD2 B:ASP203 4.1 11.4 1.0 NAD B:UAM404 4.2 14.6 1.0 NZ B:LYS53 4.2 16.3 0.5 NZ B:LYS53 4.2 14.8 0.5 O3A B:ANP403 4.2 11.7 1.0 CB B:ASP222 4.3 12.3 1.0 O1B B:ANP403 4.3 12.3 1.0 O3G B:ANP403 4.4 13.8 1.0 OD2 B:ASP222 4.4 12.7 1.0 ND2 B:ASN37 4.5 15.1 1.0 O1A B:ANP403 4.6 14.2 1.0 O2A B:ANP403 4.6 14.8 1.0 O B:ASP220 4.7 11.3 1.0 PA B:ANP403 4.7 12.8 1.0 OAI B:UAM404 4.7 13.3 1.0 ND2 B:ASN208 4.9 11.2 1.0 CA B:ASP220 4.9 11.2 1.0 CG B:ASP222 4.9 12.0 1.0 CG B:ASP223 4.9 11.7 1.0 OE1 B:GLU36 4.9 26.7 1.0

Magnesium binding site 4 out of 5 in the Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:16.6 occ:1.00 O2G B:ANP403 1.9 16.7 1.0 O1A B:ANP403 2.0 14.2 1.0 OD1 B:ASN208 2.1 11.7 1.0 OD2 B:ASP220 2.1 10.7 1.0 O B:HOH689 2.3 19.5 1.0 N3B B:ANP403 2.9 12.3 1.0 PG B:ANP403 2.9 14.4 1.0 CG B:ASN208 3.1 11.2 1.0 CG B:ASP220 3.2 11.2 1.0 PA B:ANP403 3.2 12.8 1.0 ND2 B:ASN208 3.4 11.2 1.0 CB B:ASP220 3.6 11.2 1.0 O1G B:ANP403 3.7 10.9 1.0 O3A B:ANP403 3.7 11.7 1.0 PB B:ANP403 3.8 11.3 1.0 MG B:MG401 3.8 10.9 1.0 CE1 B:HIS205 3.8 14.3 1.0 NE2 B:HIS205 3.9 13.9 1.0 O2A B:ANP403 4.0 14.8 1.0 O2B B:ANP403 4.0 10.7 1.0 O3G B:ANP403 4.1 13.8 1.0 OD1 B:ASP220 4.2 10.4 1.0 O B:HOH748 4.2 20.2 1.0 O B:GLY207 4.3 14.6 1.0 O3' B:ANP403 4.4 15.2 1.0 CB B:ASN208 4.4 12.2 1.0 O5' B:ANP403 4.5 13.0 1.0 O B:HOH558 4.6 17.5 1.0 C B:GLY207 4.7 13.1 1.0 O B:HOH538 4.7 11.1 1.0 OD2 B:ASP203 4.7 11.4 1.0 CA B:ASN208 4.7 11.4 1.0 C5' B:ANP403 4.8 13.5 1.0 C3' B:ANP403 4.8 13.6 1.0 N B:ASN208 5.0 12.7 1.0 ND1 B:HIS205 5.0 13.2 1.0

Magnesium binding site 5 out of 5 in the Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Amicoumacin Kinase Hamin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:25.9 occ:1.00 O A:HOH763 2.1 23.1 1.0 O B:HOH506 2.1 25.7 1.0 O B:HOH516 2.1 24.7 1.0 O A:HOH838 2.1 26.6 1.0 O B:HOH872 2.2 25.4 1.0 O B:HOH557 2.2 27.1 1.0 O A:HOH590 3.7 33.2 1.0 O A:HOH657 4.0 38.3 1.0 OE1 B:GLU4 4.0 27.8 1.0 OE2 B:GLU4 4.2 27.1 1.0 O A:HOH857 4.2 31.2 1.0 OE2 A:GLU4 4.2 27.4 1.0 O B:HOH649 4.3 35.0 1.0 OE1 A:GLU4 4.4 30.9 1.0 CD B:GLU4 4.6 26.5 1.0 O B:ILE58 4.6 16.5 1.0 O B:HOH673 4.7 32.4 1.0 CD A:GLU4 4.8 26.8 1.0

S.S.Terekhov, Y.A.Mokrushina, A.S.Nazarov, A.Zlobin, A.Zalevsky, G.Bourenkov, A.Golovin, A.Belogurov Jr., I.A.Osterman, A.A.Kulikova, V.A.Mitkevich, H.J.Lou, B.E.Turk, M.Wilmanns, I.V.Smirnov, S.Altman, A.G.Gabibov. A Kinase Bioscavenger Provides Antibiotic Resistance By Extremely Tight Substrate Binding. Sci Adv V. 6 Z9861 2020.
ISSN: ESSN 2375-2548
PubMed: 32637600
DOI: 10.1126/SCIADV.AAZ9861