Manganese in PDB 4yh5: Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Manganese

The structure of Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Manganese, PDB code: 4yh5 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)	47.21 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.440, 114.440, 232.484, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 17.4

The binding sites of Manganese atom in the Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Manganese (pdb code 4yh5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Manganese, PDB code: 4yh5:
Jump to Manganese binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:27.3 occ:1.00 O2B A:ADP601 2.0 14.2 1.0 O A:HOH1086 2.2 18.9 1.0 OE2 A:GLU362 2.2 13.0 1.0 O A:HOH724 2.3 10.1 1.0 OE1 A:GLU362 2.3 19.6 1.0 O A:HOH1060 2.3 24.3 1.0 CD A:GLU362 2.6 20.1 1.0 PB A:ADP601 3.3 15.4 1.0 O3B A:ADP601 3.7 17.7 1.0 O3A A:ADP601 3.9 15.9 1.0 O A:HOH1014 4.0 23.5 1.0 ND2 A:ASN186 4.0 15.8 1.0 O2A A:ADP601 4.1 15.9 1.0 CG A:GLU362 4.1 16.5 1.0 O A:HOH1016 4.3 24.8 1.0 OD1 A:ASN186 4.3 18.6 1.0 CA A:GLY188 4.3 13.8 1.0 O A:HOH1110 4.3 22.0 1.0 O A:HOH773 4.3 30.7 1.0 O A:HOH728 4.4 15.4 1.0 O A:HOH723 4.5 18.8 1.0 O A:HOH811 4.5 29.6 1.0 CA A:GLY22 4.5 16.8 1.0 O1B A:ADP601 4.5 15.4 1.0 CG A:ASN186 4.6 15.2 1.0 PA A:ADP601 4.6 16.5 1.0 ND2 A:ASN20 4.6 19.2 1.0 O A:HOH706 4.7 32.6 1.0 N A:GLY188 4.9 14.4 1.0 CB A:GLU362 4.9 15.4 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:28.3 occ:1.00 O1B A:ADP601 2.1 15.4 1.0 OD1 A:ASP26 2.2 15.9 1.0 O1A A:ADP601 2.2 16.7 1.0 O A:HOH728 2.3 15.4 1.0 O A:HOH726 2.3 16.2 1.0 O A:HOH810 2.3 16.4 1.0 PB A:ADP601 3.2 15.4 1.0 CG A:ASP26 3.2 20.6 1.0 PA A:ADP601 3.4 16.5 1.0 O3A A:ADP601 3.5 15.9 1.0 OD2 A:ASP26 3.6 22.5 1.0 O2B A:ADP601 3.7 14.2 1.0 OD2 A:ASP29 4.0 33.7 1.0 O A:HOH875 4.1 28.2 1.0 O A:GLY27 4.1 18.5 1.0 N A:GLY22 4.1 17.6 1.0 N A:GLY27 4.2 19.4 1.0 N A:ASP26 4.2 15.2 1.0 C5' A:ADP601 4.3 19.2 1.0 O5' A:ADP601 4.3 18.7 1.0 OE1 A:GLU53 4.4 32.7 1.0 O2A A:ADP601 4.5 15.9 1.0 CB A:ASP26 4.5 19.5 1.0 CB A:SER24 4.5 15.3 1.0 O3B A:ADP601 4.5 17.7 1.0 OD1 A:ASP29 4.6 32.1 1.0 CA A:GLY22 4.7 16.8 1.0 CG A:ASP29 4.7 27.8 1.0 N A:MET25 4.7 15.9 1.0 CA A:ASP26 4.8 17.6 1.0 O A:GLY22 4.8 16.6 1.0 C A:GLY27 4.9 19.6 1.0 C A:ASP26 4.9 23.6 1.0 CA A:GLY27 5.0 18.1 1.0 C A:GLY22 5.0 17.6 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:29.2 occ:1.00 O3B B:ADP501 2.1 18.6 1.0 OE2 B:GLU362 2.2 18.8 1.0 O B:HOH937 2.2 16.0 1.0 O B:HOH648 2.3 18.9 1.0 O B:HOH969 2.3 11.5 1.0 OE1 B:GLU362 2.3 16.5 1.0 CD B:GLU362 2.6 21.5 1.0 PB B:ADP501 3.4 16.1 1.0 O1B B:ADP501 3.7 20.0 1.0 O B:HOH923 3.9 28.1 1.0 O3A B:ADP501 4.0 19.7 1.0 CG B:GLU362 4.1 21.4 1.0 ND2 B:ASN186 4.1 16.9 1.0 O1A B:ADP501 4.1 20.2 1.0 O B:HOH933 4.2 29.5 1.0 O B:HOH620 4.2 12.9 1.0 O B:HOH962 4.3 25.4 1.0 O B:HOH945 4.3 30.8 1.0 O B:HOH846 4.3 34.8 1.0 OD1 B:ASN186 4.3 16.6 1.0 CA B:GLY188 4.3 15.5 1.0 CA B:GLY22 4.5 17.8 1.0 O B:HOH645 4.6 21.0 1.0 PA B:ADP501 4.6 17.6 1.0 O2B B:ADP501 4.6 11.9 1.0 CG B:ASN186 4.6 16.3 1.0 ND2 B:ASN20 4.7 17.7 1.0 O B:HOH604 4.8 33.7 1.0 CB B:GLU362 4.9 16.5 1.0 N B:GLY188 4.9 15.4 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Lipomyces Starkeyi Levoglucosan Kinase Bound to Adp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:29.5 occ:1.00 O2B B:ADP501 2.1 11.9 1.0 OD1 B:ASP26 2.1 23.2 1.0 O2A B:ADP501 2.2 17.6 1.0 O B:HOH650 2.3 26.3 1.0 O B:HOH620 2.3 12.9 1.0 O B:HOH688 2.3 15.8 1.0 PB B:ADP501 3.1 16.1 1.0 CG B:ASP26 3.2 25.9 1.0 PA B:ADP501 3.4 17.6 1.0 O3A B:ADP501 3.5 19.7 1.0 O3B B:ADP501 3.5 18.6 1.0 OD2 B:ASP26 3.6 25.9 1.0 O B:HOH665 4.0 29.9 1.0 OD2 B:ASP29 4.0 36.4 1.0 N B:GLY22 4.1 16.1 1.0 O B:GLY27 4.1 20.9 1.0 N B:GLY27 4.2 19.6 1.0 O B:HOH849 4.2 41.5 1.0 N B:ASP26 4.2 17.4 1.0 C5' B:ADP501 4.3 22.0 1.0 O5' B:ADP501 4.4 17.9 1.0 O1A B:ADP501 4.5 20.2 1.0 CB B:ASP26 4.5 17.7 1.0 CB B:SER24 4.5 20.3 1.0 O1B B:ADP501 4.5 20.0 1.0 OD1 B:ASP29 4.5 30.4 1.0 OE1 B:GLU53 4.6 38.6 1.0 CA B:GLY22 4.6 17.8 1.0 N B:MET25 4.6 17.5 1.0 CG B:ASP29 4.7 27.5 1.0 CA B:ASP26 4.8 20.2 1.0 O B:GLY22 4.8 17.4 1.0 C B:GLY27 4.9 21.6 1.0 C B:GLY22 4.9 16.5 1.0 C B:ASP26 4.9 24.5 1.0 CA B:GLY27 5.0 19.2 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