Manganese in PDB 5ks1: 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus

All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus:
1.1.1.267;

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus, PDB code: 5ks1 was solved by N.Ussin, R.W.Abdulsalam, L.R.Offermann, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	64.063, 149.247, 243.768, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.9

The binding sites of Manganese atom in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus (pdb code 5ks1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus, PDB code: 5ks1:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn505 b:0.6 occ:1.00 O A:HOH652 2.1 96.0 1.0 O3 A:PO4504 2.3 0.1 1.0 OE2 A:GLU231 2.3 82.3 1.0 OE2 A:GLU152 2.6 69.1 1.0 OE1 A:GLU152 2.8 61.1 1.0 CD A:GLU152 3.0 62.5 1.0 O2 A:PO4504 3.2 98.2 1.0 O A:HOH658 3.3 78.8 1.0 P A:PO4504 3.3 0.1 1.0 CD A:GLU231 3.3 77.8 1.0 O A:HOH622 3.7 75.5 1.0 OE1 A:GLU231 3.7 76.6 1.0 OD1 A:ASP150 3.8 0.2 1.0 NZ A:LYS228 3.9 70.9 1.0 OD1 A:ASN227 3.9 99.1 1.0 O A:HOH602 4.2 77.5 1.0 O4 A:PO4504 4.3 84.9 1.0 O1 A:PO4504 4.4 0.3 1.0 CG A:GLU152 4.5 62.7 1.0 OD2 A:ASP150 4.6 90.9 1.0 CG A:ASP150 4.6 96.3 1.0 CG A:GLU231 4.6 69.6 1.0 O A:HOH628 4.7 72.5 1.0 CE A:LYS228 4.9 70.8 1.0

Manganese binding site 2 out of 2 in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn505 b:0.8 occ:0.50 O B:HOH620 1.3 83.3 0.5 O B:HOH618 1.6 75.3 0.5 OE2 B:GLU152 2.3 69.1 1.0 OE1 B:GLU152 2.4 68.8 1.0 OE2 B:GLU231 2.6 64.4 1.0 CD B:GLU152 2.6 70.9 1.0 CD B:GLU231 3.5 66.6 1.0 OD1 B:ASP150 3.7 96.1 1.0 OE1 B:GLU231 3.8 61.2 1.0 ND2 B:ASN227 3.9 89.2 1.0 NZ B:LYS228 4.0 54.3 1.0 O B:HOH633 4.1 66.7 1.0 O B:HOH601 4.2 74.5 1.0 CG B:GLU152 4.2 67.2 1.0 O4 B:PO4504 4.2 0.5 0.5 OD2 B:ASP150 4.3 91.5 1.0 O3 B:PO4504 4.4 97.1 0.5 CG B:ASP150 4.5 93.0 1.0 O1 B:PO4504 4.6 82.2 0.5 P B:PO4504 4.7 0.6 0.5 CG B:GLU231 4.8 58.6 1.0 CB B:SER151 4.9 53.0 1.0 N B:GLU152 5.0 53.8 1.0

N.K.Ussin, A.M.Bagnell, L.R.Offermann, R.Abdulsalam, M.L.Perdue, P.Magee, M.Chruszcz. Structural Characterization of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus. Biochim Biophys Acta V.1866 1209 2018PROTEINS Proteom.
ISSN: ISSN 1878-1454
PubMed: 30278288
DOI: 10.1016/J.BBAPAP.2018.09.008