Manganese in PDB 5krr: 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus in Complex with Mn(2+)

All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus in Complex with Mn(2+):
1.1.1.267;

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus in Complex with Mn(2+), PDB code: 5krr was solved by N.Ussin, R.W.Abdulsalam, L.R.Offermann, M.Perdue, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	64.840, 149.084, 242.512, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus in Complex with Mn(2+) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus in Complex with Mn(2+) (pdb code 5krr). 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 in Complex with Mn(2+), PDB code: 5krr:
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 in Complex with Mn(2+)


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 in Complex with Mn(2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn504 b:45.4 occ:0.75 O A:HOH661 1.9 40.6 1.0 O A:HOH603 1.9 33.6 1.0 OE2 A:GLU152 2.5 29.9 1.0 OE2 A:GLU231 2.5 26.6 1.0 O A:HOH679 2.7 29.4 0.8 O A:HOH629 2.7 33.3 1.0 OE1 A:GLU152 3.1 26.6 1.0 CD A:GLU152 3.1 26.8 1.0 O A:HOH653 3.5 40.8 1.0 CD A:GLU231 3.5 26.1 1.0 NZ A:LYS228 3.7 27.2 1.0 OE1 A:GLU231 3.8 26.4 1.0 ND2 A:ASN227 3.8 41.4 1.0 OD1 A:ASP150 4.1 30.9 1.0 O A:HOH680 4.2 28.5 1.0 O A:HOH667 4.6 39.2 1.0 CG A:GLU152 4.6 25.6 1.0 CE A:LYS228 4.7 27.7 1.0 CG A:GLU231 4.9 25.9 1.0

Manganese binding site 2 out of 2 in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From Vibrio Vulnificus in Complex with Mn(2+)


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 in Complex with Mn(2+) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn504 b:36.8 occ:0.50 OE1 B:GLU152 2.2 31.7 1.0 O B:HOH695 2.3 18.5 0.5 OD1 B:ASP150 2.3 37.4 1.0 OE2 B:GLU231 2.4 24.8 1.0 O B:HOH602 2.6 32.9 1.0 O B:HOH672 2.7 21.6 0.5 CD B:GLU152 3.0 29.4 1.0 OE2 B:GLU152 3.0 30.8 1.0 O B:HOH636 3.3 33.9 1.0 CG B:ASP150 3.4 32.7 1.0 CD B:GLU231 3.5 22.5 1.0 OD2 B:ASP150 3.7 35.3 1.0 O B:HOH604 3.7 44.5 1.0 OE1 B:GLU231 4.1 22.8 1.0 ND2 B:ASN227 4.2 38.5 1.0 CG B:GLU152 4.5 28.6 1.0 NZ B:LYS125 4.5 48.3 1.0 CG B:GLU231 4.6 21.0 1.0 CB B:SER151 4.6 21.6 1.0 N B:SER151 4.7 21.1 1.0 CB B:ASP150 4.8 27.3 1.0 N B:GLU152 4.8 22.3 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