Magnesium in PDB 5jm8: The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae

The structure of The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae, PDB code: 5jm8 was solved by D.C.Bailey, E.J.Drake, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.57 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	170.850, 96.630, 173.230, 90.00, 90.02, 90.00
R / Rfree (%)	21.4 / 24.9

The binding sites of Magnesium atom in the The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae (pdb code 5jm8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae, PDB code: 5jm8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:19.0 occ:1.00 OD1 A:ASN428 2.0 22.7 1.0 OE1 A:GLN427 2.3 17.8 1.0 O3A A:ATP600 2.5 17.1 1.0 OD2 A:ASP445 2.6 22.1 1.0 O2G A:ATP600 2.8 21.0 1.0 CG A:ASN428 3.1 23.2 1.0 O2A A:ATP600 3.1 22.5 1.0 CG A:ASP445 3.4 22.7 1.0 CD A:GLN427 3.4 16.9 1.0 CB A:ASP445 3.4 17.2 1.0 PA A:ATP600 3.4 21.0 1.0 O3B A:ATP600 3.5 19.9 1.0 ND2 A:ASN428 3.5 21.1 1.0 PB A:ATP600 3.6 20.2 1.0 PG A:ATP600 3.7 22.4 1.0 NE2 A:GLN427 3.9 16.3 1.0 O2B A:ATP600 4.0 21.3 1.0 O3G A:ATP600 4.0 21.4 1.0 ND1 A:HIS425 4.2 36.5 1.0 C5' A:ATP600 4.2 18.2 1.0 CB A:ASN428 4.4 15.9 1.0 O5' A:ATP600 4.4 17.5 1.0 O1A A:ATP600 4.6 22.1 1.0 OD1 A:ASP445 4.6 18.5 1.0 N A:ASN428 4.6 15.0 1.0 CA A:ASN428 4.6 15.2 1.0 O A:GLN427 4.7 20.1 1.0 C A:GLN427 4.7 20.0 1.0 CG A:GLN427 4.7 16.7 1.0 CE1 A:HIS425 4.8 42.2 1.0 CB A:GLN427 4.8 15.8 1.0 O1B A:ATP600 4.9 18.4 1.0 O A:ARG444 4.9 26.6 1.0 CA A:ASP445 4.9 18.9 1.0 CG A:HIS425 5.0 30.8 1.0

Magnesium binding site 2 out of 8 in the The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:24.3 occ:1.00 OD1 B:ASN428 1.9 34.6 1.0 O2A B:ATP600 2.1 27.8 1.0 OE1 B:GLN427 2.2 20.5 1.0 O1G B:ATP600 2.4 14.5 1.0 OD2 B:ASP445 2.9 27.6 1.0 O3A B:ATP600 3.0 24.9 1.0 CG B:ASN428 3.0 29.5 1.0 PA B:ATP600 3.1 29.2 1.0 CD B:GLN427 3.3 24.5 1.0 ND2 B:ASN428 3.6 30.2 1.0 CG B:ASP445 3.8 25.3 1.0 C5' B:ATP600 3.8 24.2 1.0 PG B:ATP600 3.8 18.8 1.0 NE2 B:GLN427 3.8 24.2 1.0 CB B:ASP445 3.9 22.2 1.0 O5' B:ATP600 4.0 23.6 1.0 PB B:ATP600 4.0 28.4 1.0 ND1 B:HIS425 4.1 36.9 1.0 O3B B:ATP600 4.2 18.8 1.0 O2B B:ATP600 4.2 31.9 1.0 CB B:ASN428 4.3 21.5 1.0 O1A B:ATP600 4.4 27.5 1.0 N B:ASN428 4.4 20.6 1.0 CA B:ASN428 4.5 20.6 1.0 C B:GLN427 4.5 24.0 1.0 CG B:GLN427 4.5 19.7 1.0 O B:GLN427 4.6 21.8 1.0 O B:HOH706 4.6 26.5 1.0 C4' B:ATP600 4.7 27.1 1.0 CB B:GLN427 4.7 20.2 1.0 O3G B:ATP600 4.7 11.9 1.0 O2G B:ATP600 4.8 19.3 1.0 CE1 B:HIS425 4.8 44.9 1.0 O4' B:ATP600 5.0 27.1 1.0 OD1 B:ASP445 5.0 27.2 1.0

Magnesium binding site 3 out of 8 in the The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:14.5 occ:1.00 O1G C:ATP600 2.1 14.0 1.0 OE1 C:GLN427 2.3 14.6 1.0 OD1 C:ASN428 2.4 12.6 1.0 O3A C:ATP600 2.5 13.6 1.0 OD2 C:ASP445 2.6 13.8 1.0 O2A C:ATP600 2.8 20.2 1.0 CD C:GLN427 3.2 14.0 1.0 PA C:ATP600 3.2 23.2 1.0 CG C:ASP445 3.3 16.6 1.0 PG C:ATP600 3.3 20.7 1.0 NE2 C:GLN427 3.4 11.6 1.0 CB C:ASP445 3.4 16.9 1.0 PB C:ATP600 3.5 19.8 1.0 CG C:ASN428 3.5 16.1 1.0 O3B C:ATP600 3.6 11.9 1.0 O3G C:ATP600 3.8 20.2 1.0 O2B C:ATP600 3.8 17.0 1.0 ND2 C:ASN428 4.1 13.5 1.0 CE1 C:HIS425 4.2 13.7 1.0 O5' C:ATP600 4.3 15.9 1.0 OD1 C:ASP445 4.3 16.1 1.0 C5' C:ATP600 4.3 14.2 1.0 NE2 C:HIS425 4.3 15.6 1.0 O1A C:ATP600 4.4 20.8 1.0 O2G C:ATP600 4.6 18.7 1.0 CG C:GLN427 4.6 16.7 1.0 O C:GLN427 4.8 21.4 1.0 CB C:ASN428 4.8 12.4 1.0 O C:HOH714 4.8 18.4 1.0 CA C:ASP445 4.8 19.9 1.0 O1B C:ATP600 4.8 13.2 1.0 CA C:ASN428 4.9 11.8 1.0 C C:GLN427 4.9 11.4 1.0 N C:ASN428 4.9 11.7 1.0 O C:ARG444 4.9 19.5 1.0

Magnesium binding site 4 out of 8 in the The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:21.7 occ:1.00 OE1 D:GLN427 2.0 16.6 1.0 O1G D:ATP600 2.2 15.0 1.0 OD1 D:ASN428 2.3 16.9 1.0 O2A D:ATP600 2.5 20.7 1.0 O3A D:ATP600 2.6 20.7 1.0 OD2 D:ASP445 2.9 31.1 1.0 CD D:GLN427 2.9 16.0 1.0 PA D:ATP600 3.1 25.0 1.0 NE2 D:GLN427 3.3 15.8 1.0 CG D:ASN428 3.4 17.1 1.0 PG D:ATP600 3.5 16.1 1.0 CG D:ASP445 3.5 29.1 1.0 CB D:ASP445 3.6 21.8 1.0 CE1 D:HIS425 3.6 17.6 1.0 PB D:ATP600 3.8 20.8 1.0 O3B D:ATP600 3.9 15.8 1.0 NE2 D:HIS425 3.9 18.3 1.0 ND2 D:ASN428 4.0 17.9 1.0 O3G D:ATP600 4.1 15.5 1.0 O5' D:ATP600 4.1 22.2 1.0 O2B D:ATP600 4.2 20.5 1.0 C5' D:ATP600 4.3 18.2 1.0 CG D:GLN427 4.3 15.7 1.0 O1A D:ATP600 4.3 27.9 1.0 OD1 D:ASP445 4.5 32.1 1.0 N D:ASN428 4.6 15.9 1.0 CB D:ASN428 4.6 16.6 1.0 C D:GLN427 4.6 19.4 1.0 CB D:GLN427 4.6 15.9 1.0 CA D:ASN428 4.6 22.2 1.0 O D:GLN427 4.7 20.5 1.0 O2G D:ATP600 4.7 16.2 1.0 O D:HOH721 4.7 15.2 1.0 ND1 D:HIS425 4.8 17.5 1.0 O D:ARG444 5.0 23.2 1.0

Magnesium binding site 5 out of 8 in the The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:21.6 occ:1.00 O3G E:ATP600 1.9 16.4 1.0 OE1 E:GLN427 2.2 21.2 1.0 OD1 E:ASN428 2.3 12.5 1.0 O3A E:ATP600 2.7 17.7 1.0 O1A E:ATP600 2.8 13.0 1.0 OD2 E:ASP445 3.1 26.3 1.0 CD E:GLN427 3.2 21.4 1.0 PG E:ATP600 3.3 22.2 1.0 CG E:ASP445 3.3 19.0 1.0 CB E:ASP445 3.4 14.5 1.0 PA E:ATP600 3.4 20.4 1.0 CG E:ASN428 3.5 12.6 1.0 NE2 E:GLN427 3.6 22.9 1.0 PB E:ATP600 3.8 23.2 1.0 O3B E:ATP600 3.8 19.5 1.0 O1G E:ATP600 3.9 23.5 1.0 ND2 E:ASN428 4.1 13.0 1.0 CE1 E:HIS425 4.1 13.4 1.0 OD1 E:ASP445 4.2 17.4 1.0 O1B E:ATP600 4.2 25.6 1.0 O5' E:ATP600 4.3 20.3 1.0 C5' E:ATP600 4.3 18.7 1.0 O E:GLN427 4.3 15.1 1.0 NE2 E:HIS425 4.4 13.7 1.0 O2G E:ATP600 4.5 22.4 1.0 CG E:GLN427 4.6 19.7 1.0 O2A E:ATP600 4.6 23.3 1.0 C E:GLN427 4.6 13.9 1.0 O E:ARG444 4.6 12.1 1.0 CA E:ASP445 4.7 16.1 1.0 CB E:ASN428 4.7 12.3 1.0 CA E:ASN428 4.7 16.1 1.0 N E:ASN428 4.8 15.5 1.0 CB E:GLN427 4.9 16.9 1.0 NE2 E:GLN447 5.0 26.6 1.0

Magnesium binding site 6 out of 8 in the The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:27.2 occ:1.00 O2G F:ATP600 1.8 16.1 1.0 OE1 F:GLN427 2.0 31.2 1.0 OD1 F:ASN428 2.3 31.0 1.0 O3A F:ATP600 2.7 21.2 1.0 CD F:GLN427 2.9 35.3 1.0 O1A F:ATP600 2.9 23.6 1.0 OD2 F:ASP445 3.0 32.7 1.0 NE2 F:GLN427 3.2 31.2 1.0 PG F:ATP600 3.2 18.0 1.0 PA F:ATP600 3.4 23.0 1.0 CB F:ASP445 3.4 31.0 1.0 CG F:ASP445 3.5 32.0 1.0 CG F:ASN428 3.5 31.3 1.0 O3B F:ATP600 3.8 23.6 1.0 PB F:ATP600 3.9 21.0 1.0 O1G F:ATP600 4.0 22.9 1.0 C5' F:ATP600 4.0 25.1 1.0 ND2 F:ASN428 4.1 32.3 1.0 CE1 F:HIS425 4.1 33.1 1.0 O3G F:ATP600 4.3 19.0 1.0 NE2 F:HIS425 4.3 33.8 1.0 O5' F:ATP600 4.3 22.9 1.0 O1B F:ATP600 4.3 24.1 1.0 CG F:GLN427 4.3 39.0 1.0 OD1 F:ASP445 4.4 32.2 1.0 N F:ASN428 4.6 30.1 1.0 O2A F:ATP600 4.7 22.9 1.0 CB F:ASN428 4.7 30.6 1.0 CA F:ASN428 4.7 29.7 1.0 CB F:GLN427 4.7 30.8 1.0 C F:GLN427 4.8 30.7 1.0 CA F:ASP445 4.8 30.4 1.0 O F:GLN427 5.0 32.2 1.0 O F:ARG444 5.0 29.7 1.0

Magnesium binding site 7 out of 8 in the The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg601 b:17.1 occ:1.00 OD1 G:ASN428 2.1 25.8 1.0 OD2 G:ASP445 2.4 13.3 1.0 OE1 G:GLN427 2.5 22.1 1.0 O1A G:ATP600 2.5 13.2 1.0 O3G G:ATP600 2.5 5.7 1.0 O3A G:ATP600 2.8 7.1 1.0 CG G:ASN428 3.2 24.7 1.0 CG G:ASP445 3.2 13.3 1.0 PA G:ATP600 3.2 22.5 1.0 CB G:ASP445 3.3 11.6 1.0 CE1 G:HIS425 3.4 15.2 1.0 CD G:GLN427 3.6 21.0 1.0 ND2 G:ASN428 3.6 9.6 1.0 PG G:ATP600 3.7 8.6 1.0 NE2 G:HIS425 3.7 14.8 1.0 PB G:ATP600 3.8 9.3 1.0 O3B G:ATP600 3.9 16.4 1.0 O1B G:ATP600 3.9 17.8 1.0 NE2 G:GLN427 4.1 21.4 1.0 O1G G:ATP600 4.1 18.9 1.0 O5' G:ATP600 4.3 13.0 1.0 O2A G:ATP600 4.3 24.9 1.0 C5' G:ATP600 4.4 14.5 1.0 OD1 G:ASP445 4.4 17.0 1.0 CB G:ASN428 4.5 16.1 1.0 ND1 G:HIS425 4.6 13.9 1.0 O G:GLN427 4.6 12.5 1.0 N G:ASN428 4.7 12.3 1.0 CA G:ASN428 4.7 13.3 1.0 C G:GLN427 4.7 11.6 1.0 O G:HOH767 4.8 7.6 1.0 CA G:ASP445 4.8 13.5 1.0 O G:ARG444 4.8 18.1 1.0 CG G:GLN427 4.8 20.6 1.0 CB G:GLN427 4.9 18.9 1.0 O2G G:ATP600 5.0 14.3 1.0

Magnesium binding site 8 out of 8 in the The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of Atp-Bound Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg601 b:30.6 occ:1.00 OD1 H:ASN428 1.9 43.1 1.0 O1A H:ATP600 2.1 33.6 1.0 OE1 H:GLN427 2.4 27.3 1.0 OD2 H:ASP445 2.6 26.6 1.0 O3G H:ATP600 2.8 13.3 1.0 CE1 H:HIS425 2.9 37.1 1.0 CG H:ASN428 3.0 31.7 1.0 CD H:GLN427 3.2 26.5 1.0 CG H:ASP445 3.3 28.4 1.0 PA H:ATP600 3.3 32.8 1.0 NE2 H:HIS425 3.4 38.1 1.0 O3A H:ATP600 3.4 22.1 1.0 CB H:ASP445 3.4 29.5 1.0 ND2 H:ASN428 3.6 26.4 1.0 NE2 H:GLN427 3.7 23.7 1.0 O1B H:ATP600 3.8 28.7 1.0 PG H:ATP600 3.8 23.0 1.0 O3B H:ATP600 3.9 23.3 1.0 PB H:ATP600 4.0 25.9 1.0 O2G H:ATP600 4.2 23.8 1.0 ND1 H:HIS425 4.2 34.0 1.0 N H:ASN428 4.3 24.0 1.0 CB H:ASN428 4.3 24.5 1.0 OD1 H:ASP445 4.3 31.6 1.0 C5' H:ATP600 4.4 31.5 1.0 O5' H:ATP600 4.4 32.9 1.0 CA H:ASN428 4.4 24.1 1.0 CG H:GLN427 4.4 26.5 1.0 O2A H:ATP600 4.4 37.7 1.0 CB H:GLN427 4.5 27.4 1.0 C H:GLN427 4.5 23.4 1.0 O H:GLN427 4.7 22.6 1.0 CD2 H:HIS425 4.7 36.4 1.0 CA H:ASP445 4.9 24.4 1.0

D.C.Bailey, E.J.Drake, T.D.Grant, A.M.Gulick. Structural and Functional Characterization of Aerobactin Synthetase Iuca From A Hypervirulent Pathotype of Klebsiella Pneumoniae. Biochemistry V. 55 3559 2016.
ISSN: ISSN 0006-2960
PubMed: 27253399
DOI: 10.1021/ACS.BIOCHEM.6B00409