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Iodine in PDB 4s2d: Joint X-Ray/Neutron Structure of Trichoderma Reesei Xylanase II in Complex with Mes at pH 5.7

Enzymatic activity of Joint X-Ray/Neutron Structure of Trichoderma Reesei Xylanase II in Complex with Mes at pH 5.7

All present enzymatic activity of Joint X-Ray/Neutron Structure of Trichoderma Reesei Xylanase II in Complex with Mes at pH 5.7:
3.2.1.8;

Protein crystallography data

The structure of Joint X-Ray/Neutron Structure of Trichoderma Reesei Xylanase II in Complex with Mes at pH 5.7, PDB code: 4s2d was solved by A.Y.Kovalevsky, Q.Wan, P.Langan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.174, 60.214, 70.434, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 27.9

Iodine Binding Sites:

The binding sites of Iodine atom in the Joint X-Ray/Neutron Structure of Trichoderma Reesei Xylanase II in Complex with Mes at pH 5.7 (pdb code 4s2d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total only one binding site of Iodine was determined in the Joint X-Ray/Neutron Structure of Trichoderma Reesei Xylanase II in Complex with Mes at pH 5.7, PDB code: 4s2d:

Iodine binding site 1 out of 1 in 4s2d

Go back to Iodine Binding Sites List in 4s2d
Iodine binding site 1 out of 1 in the Joint X-Ray/Neutron Structure of Trichoderma Reesei Xylanase II in Complex with Mes at pH 5.7


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Joint X-Ray/Neutron Structure of Trichoderma Reesei Xylanase II in Complex with Mes at pH 5.7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:18.2
occ:1.00
 D2 A:DOD1005 2.4 21.8 1.0
H A:SER146 2.6 14.6 0.3
D A:SER146 2.6 14.6 0.7
D1 A:DOD1085 3.0 60.6 1.0
D1 A:DOD1077 3.1 29.5 1.0
D2 A:DOD1077 3.2 28.8 1.0
O A:DOD1005 3.2 25.0 1.0
HB2 A:ARG145 3.4 12.5 1.0
HA A:ARG145 3.4 13.9 1.0
N A:SER146 3.6 14.1 1.0
O A:DOD1077 3.6 29.0 1.0
D2 A:DOD1085 3.7 61.3 1.0
D1 A:DOD1005 3.7 22.3 1.0
H A:SER147 3.8 14.6 0.7
D A:SER147 3.8 14.6 0.3
O A:DOD1085 3.8 60.7 1.0
HB2 A:SER146 3.9 18.2 1.0
HB2 A:SER147 4.0 16.6 1.0
CA A:ARG145 4.1 13.8 1.0
CB A:ARG145 4.1 12.3 1.0
N A:SER147 4.3 14.2 1.0
C A:ARG145 4.4 14.1 1.0
HB3 A:ARG145 4.5 13.5 1.0
CA A:SER146 4.5 14.7 1.0
DG A:SER147 4.5 17.8 1.0
CB A:SER146 4.6 17.3 1.0
C A:SER146 4.8 15.2 1.0
CB A:SER147 4.8 16.7 1.0
OG A:SER146 4.9 21.4 1.0
OG A:SER147 5.0 16.5 1.0

Reference:

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: ISSN 0027-8424
PubMed: 26392527
DOI: 10.1073/PNAS.1504986112
Page generated: Sun Aug 11 19:48:27 2024

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