Magnesium in PDB 4zfv: Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium.

The structure of Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium., PDB code: 4zfv was solved by J.P.Bacik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.20 / 1.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.399, 114.399, 232.499, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 17.4

The binding sites of Magnesium atom in the Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium. (pdb code 4zfv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium., PDB code: 4zfv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:12.6 occ:1.00 O1B A:ADP601 2.0 11.5 1.0 O A:HOH730 2.1 14.1 1.0 O A:HOH819 2.1 13.3 1.0 OD1 A:ASP26 2.1 13.8 1.0 O A:HOH835 2.1 13.7 1.0 O1A A:ADP601 2.1 13.2 1.0 PB A:ADP601 3.1 11.6 1.0 CG A:ASP26 3.1 17.5 1.0 PA A:ADP601 3.3 12.5 1.0 O3A A:ADP601 3.5 11.4 1.0 OD2 A:ASP26 3.6 20.4 1.0 O2B A:ADP601 3.6 12.2 1.0 OD2 A:ASP29 3.8 26.9 1.0 O A:HOH725 3.9 27.1 1.0 N A:GLY22 4.0 11.6 1.0 O A:GLY27 4.1 15.7 1.0 N A:ASP26 4.2 12.6 1.0 N A:GLY27 4.2 15.0 1.0 C5' A:ADP601 4.3 13.2 1.0 O5' A:ADP601 4.3 12.8 1.0 OE1 A:GLU53 4.3 33.8 1.0 O3B A:ADP601 4.4 12.4 1.0 O2A A:ADP601 4.4 12.8 1.0 CB A:ASP26 4.4 13.2 1.0 CB A:SER24 4.5 12.2 1.0 CA A:GLY22 4.6 11.0 1.0 N A:MET25 4.7 12.2 1.0 CA A:ASP26 4.7 12.5 1.0 CG A:ASP29 4.8 22.7 1.0 O A:GLY22 4.8 13.3 1.0 C A:GLY27 4.9 15.2 1.0 C A:ASP26 4.9 19.4 1.0 C A:GLY22 4.9 12.4 1.0 CA A:GLY27 5.0 14.5 1.0 C A:SER21 5.0 11.6 1.0

Magnesium binding site 2 out of 4 in the Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:12.4 occ:1.00 O2B A:ADP601 2.0 12.2 1.0 O A:HOH896 2.1 16.0 1.0 O A:HOH1057 2.1 15.0 1.0 O A:HOH805 2.1 12.8 1.0 OE2 A:GLU362 2.1 11.9 1.0 OE1 A:GLU362 2.2 14.3 1.0 CD A:GLU362 2.4 13.4 1.0 PB A:ADP601 3.3 11.6 1.0 O3B A:ADP601 3.8 12.4 1.0 O A:HOH1143 3.8 21.3 1.0 O3A A:ADP601 3.9 11.4 1.0 CG A:GLU362 3.9 11.1 1.0 ND2 A:ASN186 4.0 11.6 1.0 O2A A:ADP601 4.1 12.8 1.0 C3 A:TRS604 4.1 27.8 1.0 O A:HOH1027 4.2 16.3 1.0 O A:HOH872 4.2 28.4 1.0 O A:HOH819 4.2 13.3 1.0 OD1 A:ASN186 4.3 12.7 1.0 CA A:GLY188 4.3 12.3 1.0 O A:HOH894 4.4 19.5 1.0 O3 A:TRS604 4.4 29.6 1.0 CA A:GLY22 4.4 11.0 1.0 O1B A:ADP601 4.5 11.5 1.0 O A:HOH762 4.5 15.6 1.0 CG A:ASN186 4.5 12.2 1.0 PA A:ADP601 4.6 12.5 1.0 ND2 A:ASN20 4.6 14.6 1.0 O A:HOH721 4.7 28.6 1.0 CB A:GLU362 4.8 11.5 1.0 N A:GLY188 5.0 9.6 1.0

Magnesium binding site 3 out of 4 in the Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:13.6 occ:1.00 O2B B:ADP501 2.0 13.1 1.0 OD1 B:ASP26 2.1 16.1 1.0 O B:HOH638 2.1 15.5 1.0 O B:HOH770 2.1 14.1 1.0 O B:HOH648 2.1 15.9 1.0 O2A B:ADP501 2.1 15.6 1.0 CG B:ASP26 3.1 19.0 1.0 PB B:ADP501 3.1 12.8 1.0 PA B:ADP501 3.4 14.1 1.0 O3A B:ADP501 3.5 13.2 1.0 OD2 B:ASP26 3.5 21.4 1.0 O1B B:ADP501 3.6 14.4 1.0 O B:HOH623 3.7 28.0 1.0 OD2 B:ASP29 3.9 31.6 1.0 N B:GLY22 4.0 13.8 1.0 O B:GLY27 4.1 17.7 1.0 N B:GLY27 4.2 15.5 1.0 N B:ASP26 4.2 14.7 1.0 C5' B:ADP501 4.3 11.6 1.0 O5' B:ADP501 4.3 12.7 1.0 OE1 B:GLU53 4.4 32.3 1.0 CB B:ASP26 4.4 17.8 1.0 O1A B:ADP501 4.4 15.0 1.0 O3B B:ADP501 4.5 15.6 1.0 CB B:SER24 4.5 15.6 1.0 O B:HOH645 4.5 36.5 1.0 CA B:GLY22 4.6 13.8 1.0 CG B:ASP29 4.6 24.4 1.0 N B:MET25 4.6 14.1 1.0 OD1 B:ASP29 4.7 34.8 1.0 CA B:ASP26 4.7 14.5 1.0 O B:GLY22 4.8 14.5 1.0 C B:GLY27 4.9 16.8 1.0 C B:GLY22 4.9 15.3 1.0 C B:ASP26 4.9 19.5 1.0 CA B:GLY27 4.9 16.2 1.0 C B:SER21 5.0 13.7 1.0

Magnesium binding site 4 out of 4 in the Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Magnesium. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:13.7 occ:1.00 O1B B:ADP501 2.0 14.4 1.0 O B:HOH1012 2.1 15.8 1.0 OE2 B:GLU362 2.1 15.2 1.0 O B:HOH669 2.1 15.2 1.0 O B:HOH875 2.1 17.4 1.0 OE1 B:GLU362 2.1 15.6 1.0 CD B:GLU362 2.4 14.5 1.0 PB B:ADP501 3.3 12.8 1.0 O3B B:ADP501 3.8 15.6 1.0 CG B:GLU362 3.9 13.6 1.0 O3A B:ADP501 3.9 13.2 1.0 O B:HOH1024 3.9 23.1 1.0 ND2 B:ASN186 4.1 14.5 1.0 O1A B:ADP501 4.1 15.0 1.0 O B:HOH845 4.1 29.1 1.0 O B:HOH1073 4.1 16.6 1.0 O B:HOH966 4.2 29.3 1.0 O B:HOH648 4.2 15.9 1.0 OD1 B:ASN186 4.3 14.6 1.0 CA B:GLY188 4.4 11.9 1.0 O B:HOH709 4.4 21.7 1.0 CA B:GLY22 4.5 13.8 1.0 O2B B:ADP501 4.5 13.1 1.0 PA B:ADP501 4.5 14.1 1.0 O B:HOH677 4.5 17.1 1.0 CG B:ASN186 4.6 14.4 1.0 ND2 B:ASN20 4.6 15.1 1.0 CB B:GLU362 4.7 11.3 1.0 O B:HOH605 4.8 28.1 1.0 N B:GLY188 5.0 13.6 1.0

J.P.Bacik, J.R.Klesmith, T.A.Whitehead, L.R.Jarboe, C.J.Unkefer, B.L.Mark, R.Michalczyk. Producing Glucose 6-Phosphate From Cellulosic Biomass: Structural Insights Into Levoglucosan Bioconversion. J.Biol.Chem. V. 290 26638 2015.
ISSN: ESSN 1083-351X
PubMed: 26354439
DOI: 10.1074/JBC.M115.674614