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Iodine in PDB 4hkl: Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A)

Enzymatic activity of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A)

All present enzymatic activity of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A):
3.2.1.8;

Protein crystallography data

The structure of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A), PDB code: 4hkl was solved by P.Langan, Q.Wan, L.Coates, A.Kovalevsky, Oak Ridge National Lab, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.307, 59.032, 69.717, 90.00, 90.00, 90.00
R / Rfree (%) 11.9 / 12.9

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A) (pdb code 4hkl). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A), PDB code: 4hkl:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 4hkl

Go back to Iodine Binding Sites List in 4hkl
Iodine binding site 1 out of 4 in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I500

b:13.5
occ:0.33
 H A:SER146 2.4 11.9 0.2
HG A:SER146 2.7 13.1 0.2
O A:HOH604 3.1 9.7 0.9
O A:HOH647 3.3 12.4 0.6
N A:SER146 3.3 9.9 1.0
HA A:ARG145 3.4 11.3 1.0
HB2 A:SER146 3.4 14.3 0.8
OG A:SER146 3.4 10.9 0.2
O A:HOH801 3.4 14.5 0.3
H A:SER147 3.5 12.9 1.0
HB2 A:ARG145 3.5 11.1 1.0
CA A:ARG145 4.0 9.4 1.0
CA A:SER146 4.1 10.8 0.8
CB A:SER146 4.1 12.0 0.8
N A:SER147 4.1 10.8 1.0
CA A:SER146 4.1 10.6 0.2
C A:ARG145 4.1 9.4 1.0
CB A:ARG145 4.2 9.2 1.0
CB A:SER146 4.3 10.9 0.2
C A:SER146 4.4 10.8 1.0
HB2 A:SER147 4.5 12.1 1.0
OG A:SER146 4.5 12.6 0.8
HB3 A:ARG145 4.5 11.1 1.0
HG A:SER146 4.6 15.1 0.8
HB3 A:SER146 4.6 13.1 0.2
HB3 A:SER146 4.9 14.3 0.8
HA A:SER146 5.0 13.0 0.2
HG A:SER147 5.0 12.3 1.0

Iodine binding site 2 out of 4 in 4hkl

Go back to Iodine Binding Sites List in 4hkl
Iodine binding site 2 out of 4 in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:22.1
occ:0.14
 HH21 A:ARG119 2.7 23.4 0.2
HH22 A:ARG119 2.9 23.4 0.2
NH2 A:ARG119 2.9 19.5 0.2
HB2 A:GLN121 3.2 14.7 1.0
HE1 A:TYR135 3.2 16.8 1.0
HG2 A:ARG119 3.2 16.3 0.2
HA A:THR120 3.2 10.7 1.0
HG2 A:ARG119 3.3 14.8 0.8
HE A:ARG119 3.3 22.8 0.8
O A:HOH858 3.4 29.3 0.6
HD1 A:TYR135 3.5 15.0 1.0
C A:THR120 3.6 8.9 1.0
CA A:THR120 3.8 8.9 1.0
N A:GLN121 3.8 10.1 1.0
CZ A:ARG119 3.8 18.9 0.2
O A:ARG119 3.9 10.1 1.0
CE1 A:TYR135 3.9 14.0 1.0
CB A:GLN121 4.0 12.2 1.0
H A:GLN121 4.0 12.1 1.0
O A:THR120 4.0 9.3 1.0
NE A:ARG119 4.0 19.0 0.8
HD2 A:ARG119 4.0 19.1 0.8
CD1 A:TYR135 4.0 12.5 1.0
HB3 A:GLN121 4.1 14.7 1.0
HD2 A:ARG119 4.1 19.1 0.2
CG A:ARG119 4.1 13.6 0.2
CG A:ARG119 4.1 12.3 0.8
C A:ARG119 4.1 9.0 1.0
N A:THR120 4.2 9.0 1.0
O A:HOH622 4.2 11.4 0.7
CD A:ARG119 4.3 15.9 0.8
HB3 A:ARG119 4.3 12.3 0.8
CD A:ARG119 4.4 15.9 0.2
NE A:ARG119 4.4 17.9 0.2
CA A:GLN121 4.5 10.9 1.0
HB3 A:ARG119 4.5 13.8 0.2
O A:HOH651 4.5 20.6 1.0
HH12 A:ARG119 4.6 23.0 0.2
NH1 A:ARG119 4.6 19.2 0.2
CB A:ARG119 4.7 10.2 0.8
HG3 A:ARG119 4.7 16.3 0.2
H A:THR120 4.7 10.8 1.0
CB A:ARG119 4.8 11.5 0.2
HA A:GLN121 4.8 13.1 1.0
HH21 A:ARG119 4.8 24.8 0.8
HG3 A:ARG119 4.9 14.8 0.8

Iodine binding site 3 out of 4 in 4hkl

Go back to Iodine Binding Sites List in 4hkl
Iodine binding site 3 out of 4 in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:20.7
occ:0.25
 H A:MET169 2.3 11.6 1.0
HG2 A:MET169 2.7 15.5 1.0
HA A:THR168 3.0 12.5 0.3
HA A:THR168 3.0 13.2 0.7
HE3 A:LYS56 3.1 16.2 1.0
O A:HOH789 3.1 20.1 0.5
N A:MET169 3.2 9.7 1.0
O A:HOH655 3.2 14.5 0.7
HB2 A:MET169 3.5 13.4 1.0
CG A:MET169 3.5 12.9 1.0
HG23 A:THR168 3.6 17.2 0.7
CA A:THR168 3.8 10.4 0.3
HG3 A:LYS56 3.8 13.8 1.0
CA A:THR168 3.9 11.0 0.7
CB A:MET169 3.9 11.2 1.0
HG3 A:MET169 3.9 15.5 1.0
O A:HOH660 3.9 19.7 0.9
HB A:THR168 4.0 13.7 0.3
CE A:LYS56 4.0 13.5 1.0
C A:THR168 4.0 9.9 1.0
HD2 A:LYS56 4.1 15.2 1.0
CA A:MET169 4.1 9.8 1.0
HZ2 A:LYS56 4.2 17.2 1.0
HG22 A:THR168 4.2 17.2 0.7
CG2 A:THR168 4.3 14.4 0.7
HG22 A:THR168 4.3 14.1 0.3
O A:GLY167 4.3 12.8 1.0
CB A:THR168 4.4 11.4 0.3
CD A:LYS56 4.5 12.7 1.0
NZ A:LYS56 4.5 14.3 1.0
HZ1 A:LYS56 4.6 17.2 1.0
CG A:LYS56 4.6 11.5 1.0
HA A:THR55 4.6 11.3 1.0
HE2 A:LYS56 4.6 16.2 1.0
CB A:THR168 4.6 13.2 0.7
HA A:MET169 4.8 11.8 1.0
O A:HOH776 4.8 27.0 0.5
HB3 A:MET169 4.8 13.4 1.0
CG2 A:THR168 4.9 11.7 0.3
SD A:MET169 4.9 13.3 1.0
N A:THR168 4.9 10.1 1.0
O A:GLY54 5.0 10.4 1.0

Iodine binding site 4 out of 4 in 4hkl

Go back to Iodine Binding Sites List in 4hkl
Iodine binding site 4 out of 4 in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II Complexed with Substrate (1.15 A) and Products (1.6 A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:22.4
occ:0.19
 H A:VAL123 2.3 14.7 1.0
HE21 A:GLN125 2.4 25.4 1.0
HA A:ARG122 2.9 13.1 1.0
N A:VAL123 3.2 12.2 1.0
NE2 A:GLN125 3.3 21.2 1.0
HG3 A:GLN125 3.3 19.3 1.0
HD2 A:ARG122 3.4 16.8 1.0
HH11 A:ARG122 3.5 21.6 1.0
HB A:VAL123 3.5 18.0 1.0
HG2 A:GLN125 3.5 19.3 1.0
CA A:ARG122 3.7 10.9 1.0
CG A:GLN125 3.8 16.1 1.0
HE22 A:GLN125 3.8 25.4 1.0
NH1 A:ARG122 3.9 18.0 1.0
C A:ARG122 3.9 11.1 1.0
O A:VAL123 4.0 14.3 1.0
CD A:GLN125 4.0 19.1 1.0
HG23 A:VAL123 4.0 19.2 1.0
CA A:VAL123 4.1 13.3 1.0
HH12 A:ARG122 4.2 21.6 1.0
HB3 A:ARG122 4.2 14.0 1.0
O A:GLN121 4.2 12.6 1.0
CB A:VAL123 4.2 15.0 1.0
CD A:ARG122 4.4 14.0 1.0
C A:VAL123 4.5 13.7 1.0
CB A:ARG122 4.5 11.7 1.0
CG2 A:VAL123 4.6 16.0 1.0
CZ A:ARG122 4.6 16.9 1.0
O A:HOH844 4.7 29.8 0.7
NE A:ARG122 4.8 15.2 1.0
N A:ARG122 4.8 10.4 1.0
C A:GLN121 4.9 11.0 1.0
HD3 A:ARG122 5.0 16.8 1.0
HA A:VAL123 5.0 15.9 1.0

Reference:

Q.Wan, Q.Zhang, S.Hamilton-Brehm, K.Weiss, M.Mustyakimov, L.Coates, P.Langan, D.Graham, A.Kovalevsky. X-Ray Crystallographic Studies of Family 11 Xylanase Michaelis and Product Complexes: Implications For the Catalytic Mechanism. Acta Crystallogr.,Sect.D V. 70 11 2014.
ISSN: ISSN 0907-4449
PubMed: 24419374
DOI: 10.1107/S1399004713023626
Page generated: Sun Aug 11 18:04:21 2024

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