Iodine in PDB 4xpv: Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6

All present enzymatic activity of Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6:
3.2.1.8;

The structure of Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6, PDB code: 4xpv was solved by Q.Wan, J.M.Park, D.M.Riccardi, L.B.Hanson, Z.Fisher, J.C.Smith, A.Ostermann, T.Schrader, D.E.Graham, L.Coates, P.Langan, A.Y.Kovalevsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.194, 60.287, 70.520, 90.00, 90.00, 90.00
R / Rfree (%)	26.4 / 30.4

The binding sites of Iodine atom in the Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6 (pdb code 4xpv). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6, PDB code: 4xpv:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6 within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:14.7 occ:1.00 H A:SER146 2.8 12.9 0.2 D A:SER146 2.8 12.9 0.8 D1 A:DOD321 3.0 13.9 1.0 D1 A:DOD400 3.1 19.6 1.0 D2 A:DOD343 3.4 19.2 1.0 O A:DOD321 3.5 13.2 1.0 HB2 A:ARG145 3.5 13.1 1.0 HA A:ARG145 3.6 14.7 1.0 N A:SER146 3.6 11.4 1.0 O A:DOD400 3.7 24.4 1.0 D A:SER147 3.7 12.9 0.5 H A:SER147 3.7 12.9 0.5 D2 A:DOD400 3.7 21.0 1.0 HB2 A:SER146 3.8 10.9 1.0 HB2 A:SER147 4.2 13.8 1.0 O A:DOD343 4.2 34.4 1.0 CA A:ARG145 4.2 10.0 1.0 CB A:ARG145 4.2 9.6 1.0 N A:SER147 4.3 11.1 1.0 D2 A:DOD321 4.3 16.6 1.0 D1 A:DOD343 4.4 21.2 1.0 C A:ARG145 4.4 10.5 1.0 CA A:SER146 4.5 8.1 1.0 HB3 A:ARG145 4.5 11.3 1.0 CB A:SER146 4.5 16.5 1.0 DG A:SER147 4.7 14.5 1.0 HG A:SER147 4.7 14.5 0.0 C A:SER146 4.7 11.6 1.0 CB A:SER147 4.9 13.6 1.0 OG A:SER146 5.0 23.1 1.0

Iodine binding site 2 out of 3 in the Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6 within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:35.7 occ:0.39 D A:MET169 2.7 17.6 0.8 H A:MET169 2.7 17.6 0.2 HG2 A:MET169 3.1 18.8 1.0 HE3 A:LYS56 3.2 20.0 1.0 HA A:THR168 3.3 17.6 1.0 D1 A:DOD386 3.4 22.1 1.0 O A:DOD352 3.4 30.1 1.0 D1 A:DOD352 3.5 21.6 1.0 N A:MET169 3.5 13.2 1.0 HG23 A:THR168 3.6 18.2 1.0 HB2 A:MET169 3.8 15.4 1.0 O A:DOD386 3.9 27.1 1.0 CG A:MET169 4.0 17.1 1.0 CE A:LYS56 4.1 21.3 1.0 CA A:THR168 4.1 11.1 1.0 HG3 A:LYS56 4.1 19.0 1.0 D2 A:DOD352 4.2 23.0 1.0 CB A:MET169 4.2 13.9 1.0 HG3 A:MET169 4.3 17.9 1.0 C A:THR168 4.3 14.3 1.0 DZ1 A:LYS56 4.4 22.2 0.7 HZ1 A:LYS56 4.4 22.2 0.3 D2 A:DOD386 4.4 19.8 1.0 CG2 A:THR168 4.4 26.7 1.0 HG22 A:THR168 4.5 21.7 1.0 O A:GLY167 4.5 19.6 1.0 CA A:MET169 4.5 11.7 1.0 DZ3 A:LYS56 4.5 21.6 0.9 HZ3 A:LYS56 4.5 21.6 0.1 HD2 A:LYS56 4.6 20.5 1.0 NZ A:LYS56 4.6 24.1 1.0 HE2 A:LYS56 4.7 19.4 1.0 CD A:LYS56 4.8 19.6 1.0 CB A:THR168 4.9 18.1 1.0 HA A:THR55 4.9 18.4 1.0 CG A:LYS56 4.9 17.2 1.0

Iodine binding site 3 out of 3 in the Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Neutron and X-Ray Structure Analysis of Xylanase: N44D at PH6 within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:45.3 occ:0.25 D A:VAL123 2.4 21.8 0.9 H A:VAL123 2.4 21.8 0.1 HA A:ARG122 2.9 20.6 1.0 N A:VAL123 3.2 19.7 1.0 HE21 A:GLN125 3.5 26.4 0.3 DE21 A:GLN125 3.5 26.4 0.7 HB A:VAL123 3.5 21.9 1.0 HD2 A:ARG122 3.7 27.0 1.0 CA A:ARG122 3.8 16.1 1.0 HG2 A:GLN125 3.8 23.6 1.0 HG23 A:VAL123 3.9 21.7 1.0 DH11 A:ARG122 3.9 34.1 1.0 HH11 A:ARG122 3.9 34.1 0.0 HG3 A:GLN125 3.9 25.4 1.0 C A:ARG122 4.0 19.7 1.0 O A:VAL123 4.0 19.2 1.0 O A:GLN121 4.0 20.3 1.0 NE2 A:GLN125 4.0 29.2 1.0 CA A:VAL123 4.1 15.9 1.0 CB A:VAL123 4.2 21.2 1.0 CG A:GLN125 4.3 25.1 1.0 HB3 A:ARG122 4.3 20.9 1.0 NH1 A:ARG122 4.4 40.1 1.0 CG2 A:VAL123 4.5 21.1 1.0 HE22 A:GLN125 4.5 28.6 0.3 DE22 A:GLN125 4.5 28.6 0.7 CD A:GLN125 4.5 25.5 1.0 C A:VAL123 4.5 18.6 1.0 CB A:ARG122 4.6 20.7 1.0 CD A:ARG122 4.6 27.1 1.0 HH12 A:ARG122 4.6 35.4 0.3 DH12 A:ARG122 4.6 35.4 0.7 N A:ARG122 4.7 14.7 1.0 C A:GLN121 4.8 20.1 1.0 HG21 A:VAL123 4.9 23.3 1.0 HA A:VAL123 5.0 20.0 1.0

Q.Wan, J.M.Parks, B.L.Hanson, S.Z.Fisher, A.Ostermann, T.E.Schrader, D.E.Graham, L.Coates, P.Langan, A.Kovalevsky. Direct Determination of Protonation States and Visualization of Hydrogen Bonding in A Glycoside Hydrolase with Neutron Crystallography. Proc.Natl.Acad.Sci.Usa V. 112 12384 2015.
ISSN: ESSN 1091-6490
PubMed: 26392527
DOI: 10.1073/PNAS.1504986112