Atomistry » Iodine » PDB 6k9o-6nfk » 6kwg
Atomistry »
  Iodine »
    PDB 6k9o-6nfk »
      6kwg »

Iodine in PDB 6kwg: Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose

Enzymatic activity of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose

All present enzymatic activity of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose, PDB code: 6kwg was solved by C.Li, Q.Wan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.50 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.915, 58.533, 69.138, 90, 90, 90
R / Rfree (%) 20.9 / 24.4

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose (pdb code 6kwg). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose, PDB code: 6kwg:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 6kwg

Go back to Iodine Binding Sites List in 6kwg
Iodine binding site 1 out of 7 in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:166.2
occ:1.00
 HG3 A:MET169 2.9 39.7 0.3
HG2 A:MET169 2.9 40.0 0.7
H A:MET169 3.1 37.0 0.7
H A:MET169 3.1 37.1 0.3
HA A:THR168 3.4 36.3 1.0
HZ3 A:LYS56 3.5 68.1 1.0
CG A:MET169 3.8 33.3 0.7
CG A:MET169 3.8 33.0 0.3
N A:MET169 3.9 30.8 0.7
N A:MET169 3.9 30.9 0.3
HB2 A:MET169 4.1 36.1 0.3
HG3 A:MET169 4.1 40.0 0.7
HB2 A:MET169 4.1 36.0 0.7
O A:GLY167 4.2 32.1 1.0
HG2 A:MET169 4.2 39.7 0.3
HG23 A:THR168 4.2 46.0 1.0
CA A:THR168 4.3 30.2 1.0
NZ A:LYS56 4.3 56.7 1.0
HD3 A:LYS56 4.4 58.3 1.0
CB A:MET169 4.4 30.1 0.3
CB A:MET169 4.4 30.0 0.7
HZ2 A:LYS56 4.5 68.1 1.0
C A:THR168 4.6 28.6 1.0
O A:HOH458 4.6 47.3 1.0
HZ1 A:LYS56 4.7 68.1 1.0
HB3 A:LYS56 4.7 42.9 1.0
CA A:MET169 4.8 29.0 0.7
CA A:MET169 4.8 29.4 0.3
SD A:MET169 4.9 36.1 0.3
HG2 A:LYS56 4.9 54.5 1.0
O A:HOH344 4.9 39.2 1.0
CG2 A:THR168 5.0 38.3 1.0

Iodine binding site 2 out of 7 in 6kwg

Go back to Iodine Binding Sites List in 6kwg
Iodine binding site 2 out of 7 in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:64.6
occ:1.00
 HE A:ARG119 3.2 50.1 1.0
HE1 A:TYR135 3.3 35.5 1.0
HA A:THR120 3.3 34.1 1.0
HG2 A:ARG119 3.5 34.0 1.0
HB2 A:GLN121 3.6 36.6 1.0
HD1 A:TYR135 3.7 34.5 1.0
O A:ARG119 3.9 27.0 1.0
C A:THR120 4.0 28.1 1.0
CA A:THR120 4.0 28.4 1.0
CE1 A:TYR135 4.0 29.6 1.0
NE A:ARG119 4.0 41.7 1.0
O A:HOH331 4.0 50.2 1.0
C A:ARG119 4.2 23.3 1.0
O A:HOH383 4.2 36.9 1.0
N A:GLN121 4.2 31.2 1.0
CD1 A:TYR135 4.2 28.7 1.0
CG A:ARG119 4.3 28.3 1.0
HB3 A:ARG119 4.3 35.3 1.0
O A:THR120 4.3 26.6 1.0
N A:THR120 4.3 24.4 1.0
CB A:GLN121 4.4 30.5 1.0
H A:GLN121 4.4 37.4 1.0
HB3 A:GLN121 4.4 36.6 1.0
O A:HOH480 4.4 46.8 1.0
HD2 A:ARG119 4.5 39.5 1.0
HH21 A:ARG119 4.5 51.9 1.0
CD A:ARG119 4.5 32.9 1.0
O A:HOH450 4.7 36.9 1.0
CB A:ARG119 4.8 29.4 1.0
O A:HOH301 4.9 42.4 1.0
CA A:GLN121 4.9 27.6 1.0
H A:THR120 5.0 29.3 1.0

Iodine binding site 3 out of 7 in 6kwg

Go back to Iodine Binding Sites List in 6kwg
Iodine binding site 3 out of 7 in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:65.7
occ:1.00
 HB3 A:PRO126 3.0 43.4 1.0
O A:HOH474 3.1 37.5 1.0
HA2 A:GLY130 3.2 30.5 1.0
H A:SER127 3.3 35.2 1.0
HA A:PRO126 3.4 39.1 1.0
O A:SER127 3.5 27.9 1.0
H1 B:XYP3 3.5 41.9 1.0
H51 B:XYP2 3.6 36.7 1.0
CB A:PRO126 3.9 36.1 1.0
H A:GLY130 3.9 34.8 1.0
N A:SER127 3.9 29.3 1.0
CA A:PRO126 4.0 32.6 1.0
CA A:GLY130 4.0 25.4 1.0
H3 B:XYP3 4.2 59.3 1.0
C A:GLY130 4.2 28.2 1.0
O2 B:XYP3 4.3 41.4 1.0
HB2 A:PRO126 4.4 43.4 1.0
N A:GLY130 4.4 29.0 1.0
C1 B:XYP3 4.4 34.9 1.0
C5 B:XYP2 4.4 30.6 1.0
H52 B:XYP2 4.5 36.7 1.0
C A:PRO126 4.5 31.0 1.0
N A:THR131 4.5 27.1 1.0
H A:THR131 4.5 32.6 1.0
C A:SER127 4.6 27.6 1.0
O A:GLY130 4.7 27.4 1.0
HG3 A:PRO126 4.7 40.6 1.0
C2 B:XYP3 4.7 34.5 1.0
HE1 A:TRP18 4.7 40.1 1.0
H51 B:XYP3 4.8 42.4 1.0
HA3 A:GLY130 4.8 30.5 1.0
HG1 A:THR131 4.8 38.3 1.0
CA A:SER127 4.9 28.5 1.0
C3 B:XYP3 4.9 49.4 1.0
CG A:PRO126 4.9 33.8 1.0

Iodine binding site 4 out of 7 in 6kwg

Go back to Iodine Binding Sites List in 6kwg
Iodine binding site 4 out of 7 in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:65.4
occ:1.00
 HD21 A:ASN19 3.0 45.0 1.0
HD3 A:PRO5 3.3 46.3 1.0
O A:HOH342 3.6 36.1 1.0
HD2 A:PRO5 3.8 46.3 1.0
ND2 A:ASN19 3.8 37.5 1.0
HE22 A:GLN4 3.8 38.0 1.0
CD A:PRO5 3.9 38.6 1.0
HG2 A:PRO5 3.9 44.5 1.0
O A:HOH464 4.0 35.1 1.0
HG3 A:PRO5 4.2 44.5 1.0
OE1 A:GLN4 4.2 36.3 1.0
CG A:PRO5 4.2 37.0 1.0
HD22 A:ASN19 4.3 45.0 1.0
NE2 A:GLN4 4.5 31.7 1.0
HH A:TYR17 4.5 42.0 1.0
OD1 A:ASN19 4.6 37.8 1.0
CG A:ASN19 4.7 37.5 1.0
CD A:GLN4 4.7 32.9 1.0
HA A:GLN4 4.8 39.4 1.0
HA2 A:GLY23 5.0 51.7 1.0
HA2 A:GLY21 5.0 54.6 1.0

Iodine binding site 5 out of 7 in 6kwg

Go back to Iodine Binding Sites List in 6kwg
Iodine binding site 5 out of 7 in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I208

b:26.0
occ:1.00
 H A:ASN82 2.8 26.4 1.0
HD13 A:ILE129 2.8 49.8 1.0
HD12 A:ILE129 2.9 49.8 1.0
HB2 A:LEU84 3.1 29.2 0.0
HB2 A:LEU84 3.1 30.1 1.0
HD23 A:LEU84 3.2 29.6 0.0
CD1 A:ILE129 3.2 41.5 1.0
HB3 A:ARG81 3.5 28.1 1.0
HD11 A:ILE129 3.5 49.8 1.0
HA A:ARG81 3.5 30.2 1.0
N A:ASN82 3.5 22.0 1.0
HD13 A:LEU84 3.5 29.8 1.0
HG2 A:ARG81 3.8 31.9 1.0
CB A:LEU84 4.0 24.3 0.0
CB A:LEU84 4.0 25.1 1.0
CD2 A:LEU84 4.1 24.6 0.0
CB A:ARG81 4.1 23.4 1.0
CA A:ARG81 4.1 25.2 1.0
H A:LEU84 4.2 31.4 1.0
HA A:ASN82 4.2 33.5 1.0
H A:LEU84 4.2 30.5 0.0
HB2 A:ASN82 4.2 28.9 1.0
HG21 A:ILE129 4.2 47.4 1.0
HA A:LEU84 4.2 30.3 1.0
HA A:LEU84 4.2 29.6 0.0
C A:ARG81 4.3 27.1 1.0
HD22 A:LEU84 4.4 31.5 1.0
CD1 A:LEU84 4.4 24.8 1.0
N A:LEU84 4.4 26.2 1.0
N A:LEU84 4.4 25.4 0.0
CA A:ASN82 4.4 27.9 1.0
HD22 A:LEU84 4.4 29.6 0.0
HG A:LEU84 4.4 31.3 0.0
CG A:LEU84 4.4 26.0 0.0
CA A:LEU84 4.5 24.6 0.0
CG A:ARG81 4.5 26.6 1.0
CA A:LEU84 4.5 25.2 1.0
HD12 A:LEU84 4.6 29.8 1.0
CG1 A:ILE129 4.6 31.0 1.0
HB A:ILE129 4.6 37.7 1.0
HB3 A:LEU84 4.6 30.1 1.0
HB3 A:LEU84 4.7 29.2 0.0
CG A:LEU84 4.7 25.5 1.0
HD21 A:LEU84 4.8 29.6 0.0
CB A:ASN82 4.8 24.1 1.0
HH11 A:ARG81 4.9 44.2 1.0
HD3 A:ARG81 5.0 36.6 1.0
HB2 A:ARG81 5.0 28.1 1.0
CB A:ILE129 5.0 31.4 1.0

Iodine binding site 6 out of 7 in 6kwg

Go back to Iodine Binding Sites List in 6kwg
Iodine binding site 6 out of 7 in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I209

b:142.5
occ:1.00
 O A:HOH502 2.7 36.3 1.0
HA A:ARG145 2.8 31.9 1.0
O A:HIS144 2.8 26.6 1.0
O A:HOH466 3.3 51.2 1.0
CA A:ARG145 3.7 26.6 1.0
O A:HOH315 3.7 31.3 1.0
C A:HIS144 3.7 27.4 1.0
O A:HOH349 3.9 35.6 1.0
HB3 A:ARG145 4.0 28.6 1.0
N A:ARG145 4.1 25.7 1.0
CB A:ARG145 4.2 23.8 1.0
HB2 A:ARG145 4.3 28.6 1.0
H A:SER146 4.3 29.4 1.0
O A:HOH354 4.6 37.4 1.0
HB2 A:HIS144 4.7 33.7 1.0
C A:ARG145 4.7 24.6 1.0
N A:SER146 4.8 24.5 1.0
HD21 A:ASN92 4.8 35.6 1.0
H A:ARG145 4.9 30.9 1.0
CA A:HIS144 5.0 26.9 1.0

Iodine binding site 7 out of 7 in 6kwg

Go back to Iodine Binding Sites List in 6kwg
Iodine binding site 7 out of 7 in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I210

b:86.8
occ:1.00
 HG23 A:THR2 3.1 54.2 1.0
N A:THR2 3.6 45.6 1.0
O A:HOH312 3.7 46.7 1.0
OG1 A:THR2 3.8 47.4 1.0
CG2 A:THR2 4.0 45.1 1.0
HG1 A:THR2 4.0 56.9 1.0
O A:HOH305 4.3 51.9 1.0
HG21 A:THR2 4.3 54.2 1.0
CB A:THR2 4.4 37.5 1.0
CA A:THR2 4.6 40.4 1.0
HG22 A:THR2 4.7 54.2 1.0

Reference:

Z.Li, X.Zhang, C.Li, A.Kovalevsky, Q.Wan. Studying the Role of A Single Mutation of A Family 11 Glycoside Hydrolase Using High-Resolution X-Ray Crystallography. Protein J. V. 39 671 2020.
ISSN: ISSN 1572-3887
PubMed: 33128114
DOI: 10.1007/S10930-020-09938-5
Page generated: Sun Aug 11 23:30:20 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy