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Iodine in PDB 4hko: Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form

Enzymatic activity of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form

All present enzymatic activity of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form, PDB code: 4hko was solved by P.Langan, Q.Wan, L.Coates, A.Kovalevsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.216, 59.209, 69.718, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 18.6

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form (pdb code 4hko). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form, PDB code: 4hko:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 4hko

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Iodine binding site 1 out of 6 in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form


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 (E177Q) in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I500

b:5.7
occ:0.90
 O A:HOH613 3.4 8.5 1.0
O A:HOH603 3.5 6.7 1.0
N A:SER146 3.6 5.8 1.0
OG A:SER146 3.9 8.2 1.0
O A:HOH620 4.0 12.0 1.0
CA A:ARG145 4.1 7.6 1.0
CB A:ARG145 4.1 5.1 1.0
N A:SER147 4.2 7.1 1.0
C A:ARG145 4.3 8.8 1.0
CA A:SER146 4.5 7.2 1.0
O A:HOH726 4.6 15.8 1.0
C A:SER146 4.7 6.5 1.0
CB A:SER146 4.8 8.1 1.0

Iodine binding site 2 out of 6 in 4hko

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Iodine binding site 2 out of 6 in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form


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 (E177Q) in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:16.3
occ:0.70
 O A:HOH765 3.8 28.0 1.0
NE A:ARG119 3.8 18.2 1.0
O A:ARG119 3.9 8.3 1.0
C A:THR120 3.9 5.5 1.0
CA A:THR120 4.0 6.2 1.0
O A:HOH624 4.1 13.0 1.0
N A:GLN121 4.1 6.8 1.0
CE1 A:TYR135 4.1 9.6 1.0
CG A:ARG119 4.2 8.9 1.0
C A:ARG119 4.2 8.7 1.0
CB A:GLN121 4.2 9.4 1.0
O A:THR120 4.3 7.4 1.0
CD A:ARG119 4.3 13.2 1.0
CD1 A:TYR135 4.3 8.3 1.0
N A:THR120 4.3 7.0 1.0
O A:HOH618 4.5 13.2 1.0
O A:HOH774 4.6 29.5 1.0
CA A:GLN121 4.8 6.1 1.0
CB A:ARG119 4.8 8.4 1.0
CZ A:ARG119 4.8 25.0 1.0
O A:HOH744 4.9 21.5 1.0
NH2 A:ARG119 4.9 21.6 1.0

Iodine binding site 3 out of 6 in 4hko

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Iodine binding site 3 out of 6 in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form


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 (E177Q) in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:23.9
occ:0.61
 HG2 A:MET169 3.1 11.1 1.0
N A:MET169 3.6 5.8 1.0
CA A:THR168 3.9 7.0 1.0
CG A:MET169 4.0 9.3 1.0
CE A:LYS56 4.1 12.6 1.0
O A:HOH649 4.1 15.2 1.0
HB A:THR168 4.2 12.5 1.0
O A:HOH745 4.2 27.7 1.0
C A:THR168 4.2 6.4 1.0
HG22 A:THR168 4.3 8.6 1.0
O A:GLY167 4.3 11.1 1.0
HG3 A:MET169 4.4 11.1 1.0
CB A:MET169 4.4 8.3 1.0
CB A:THR168 4.5 10.4 1.0
NZ A:LYS56 4.5 15.6 1.0
CD A:LYS56 4.6 11.2 1.0
CA A:MET169 4.6 5.5 1.0
CG A:LYS56 4.8 8.4 1.0
N A:THR168 4.9 7.2 1.0
CG2 A:THR168 4.9 7.2 1.0

Iodine binding site 4 out of 6 in 4hko

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Iodine binding site 4 out of 6 in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form


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 (E177Q) in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:24.8
occ:0.39
 O A:HOH805 3.3 30.4 1.0
O A:PRO68 3.3 12.2 1.0
N A:GLY70 3.6 6.2 1.0
CA A:GLY94 3.9 8.4 1.0
CG2 A:THR95 3.9 8.1 1.0
C A:PRO68 4.0 9.5 1.0
C A:GLY94 4.0 8.2 1.0
CA A:ASN69 4.1 10.2 1.0
N A:THR95 4.1 6.4 1.0
O A:GLY70 4.1 6.9 1.0
O A:HOH718 4.2 25.7 1.0
N A:ASN69 4.4 11.6 1.0
C A:ASN69 4.4 9.2 1.0
CG A:PRO68 4.5 11.5 1.0
CA A:GLY70 4.6 6.8 1.0
O A:GLY94 4.7 9.7 1.0
CB A:PRO68 4.7 10.5 1.0
CA A:THR95 4.7 5.8 1.0
C A:GLY70 4.8 6.9 1.0
CB A:THR95 4.9 7.1 1.0
CA A:PRO68 5.0 10.7 1.0

Iodine binding site 5 out of 6 in 4hko

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Iodine binding site 5 out of 6 in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:27.3
occ:0.43
 O A:HOH784 3.1 37.5 1.0
NE2 A:GLN125 3.4 18.9 1.0
N A:VAL123 3.5 7.1 1.0
O A:HOH761 3.9 24.6 1.0
NH1 A:ARG122 3.9 13.3 1.0
CG A:GLN125 4.0 10.4 1.0
CA A:ARG122 4.0 6.2 1.0
CD A:GLN125 4.2 12.9 1.0
O A:VAL123 4.2 10.3 1.0
C A:ARG122 4.3 8.0 1.0
O A:GLN121 4.3 9.7 1.0
CA A:VAL123 4.4 8.6 1.0
CB A:VAL123 4.4 10.6 1.0
CD A:ARG122 4.5 8.2 1.0
CZ A:ARG122 4.7 10.6 1.0
C A:VAL123 4.8 8.7 1.0
CG2 A:VAL123 4.8 11.0 1.0
CB A:ARG122 4.8 6.8 1.0
NE A:ARG122 4.9 9.3 1.0

Iodine binding site 6 out of 6 in 4hko

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Iodine binding site 6 out of 6 in the Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structures of Mutant Endo-Beta-1,4-Xylanase II (E177Q) in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:37.9
occ:0.40
 O A:HOH648 3.2 15.3 1.0
C A:ASP111 3.8 5.7 1.0
CA A:ASP111 3.8 6.2 1.0
N A:GLY112 3.9 7.3 1.0
O A:ASP111 4.2 6.2 1.0
CA A:GLY112 4.4 7.7 1.0
CB A:ASP111 4.8 7.2 1.0
N A:ASP111 4.8 7.0 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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