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Iodine in PDB 1wnw: D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)

Enzymatic activity of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)

All present enzymatic activity of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo):
1.14.99.3;

Protein crystallography data

The structure of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo), PDB code: 1wnw was solved by M.Unno, T.Matsui, M.Ikeda-Saito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.059, 63.101, 107.164, 90.00, 101.03, 90.00
R / Rfree (%) 19.6 / 23.3

Other elements in 1wnw:

The structure of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) also contains other interesting chemical elements:

Iron (Fe) 3 atoms
Sodium (Na) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) (pdb code 1wnw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo), PDB code: 1wnw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 1wnw

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Iodine binding site 1 out of 9 in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1006

b:77.6
occ:1.00
O A:HOH2132 2.2 29.6 1.0
O A:HOH2083 2.8 34.4 1.0
O A:HOH2032 3.5 29.1 1.0
I A:IOD1007 3.5 54.1 1.0
NH2 A:ARG132 3.8 27.1 1.0
CB A:ALA49 4.0 19.7 1.0
CZ A:PHE52 4.1 20.3 1.0
CD1 A:LEU45 4.3 22.4 1.0
CZ A:PHE160 4.4 19.1 1.0
CE1 A:PHE52 4.4 20.8 1.0
CE2 A:TYR53 4.5 17.6 1.0
OE1 A:GLN46 4.6 25.4 1.0
CZ A:ARG132 4.6 26.3 1.0
CE2 A:PHE160 4.7 21.9 1.0
CG A:LEU45 4.8 18.8 1.0
NE A:ARG132 4.9 23.7 1.0
CD2 A:LEU45 4.9 23.1 1.0

Iodine binding site 2 out of 9 in 1wnw

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Iodine binding site 2 out of 9 in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1007

b:54.1
occ:1.00
O A:HOH2032 2.8 29.1 1.0
CAB A:HEM901 3.4 36.2 1.0
I A:IOD1006 3.5 77.6 1.0
O A:HOH2127 3.8 42.3 1.0
O A:HOH2083 3.8 34.4 1.0
CZ A:PHE208 3.8 38.9 1.0
I A:IOD1008 4.0 57.0 1.0
NH2 A:ARG132 4.1 27.1 1.0
C3B A:HEM901 4.2 25.5 1.0
CE1 A:PHE208 4.3 34.5 1.0
CD1 A:ILE143 4.4 29.8 1.0
CBB A:HEM901 4.5 40.8 1.0
C4B A:HEM901 4.7 23.6 1.0
CHC A:HEM901 4.8 28.5 1.0
O A:HOH2132 4.9 29.6 1.0
OD1 A:ASN204 4.9 28.6 1.0
CE2 A:PHE208 4.9 37.5 1.0
C2B A:HEM901 5.0 23.1 1.0

Iodine binding site 3 out of 9 in 1wnw

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Iodine binding site 3 out of 9 in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1008

b:57.0
occ:1.00
O A:HOH2127 2.6 42.3 1.0
O A:HOH2083 3.4 34.4 1.0
O A:HOH2032 3.5 29.1 1.0
CA A:ASN136 3.8 19.7 1.0
O A:HOH2050 3.9 27.5 1.0
I A:IOD1007 4.0 54.1 1.0
CD1 A:ILE143 4.0 29.8 1.0
N A:ASN136 4.1 19.2 1.0
CB A:ASN136 4.1 18.0 1.0
CE2 A:TYR161 4.2 18.9 1.0
O A:HOH2138 4.3 27.8 1.0
CA A:GLY140 4.3 20.4 1.0
CG A:ASN136 4.3 21.1 1.0
OD1 A:ASN136 4.4 25.6 1.0
C A:GLY135 4.4 20.9 1.0
O A:GLY135 4.5 22.1 1.0
CE2 A:PHE160 4.5 21.9 1.0
N A:GLY140 4.7 24.7 1.0
CD2 A:TYR161 4.8 18.8 1.0

Iodine binding site 4 out of 9 in 1wnw

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Iodine binding site 4 out of 9 in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1009

b:49.6
occ:1.00
O A:HOH2048 3.8 30.3 1.0
O A:ARG36 4.2 24.6 1.0
CA A:ARG36 4.5 25.4 1.0
C A:ARG36 4.7 24.3 1.0
O A:GLY35 4.9 25.1 1.0

Iodine binding site 5 out of 9 in 1wnw

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Iodine binding site 5 out of 9 in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1002

b:45.8
occ:1.00
O B:HOH4097 2.5 33.6 1.0
O B:HOH4090 3.3 26.3 1.0
CE B:MET29 3.7 39.8 1.0
CAB B:HEM902 3.7 30.1 1.0
I B:IOD1004 3.9 74.2 1.0
CZ B:PHE208 4.0 23.7 1.0
CHC B:HEM902 4.1 22.9 1.0
C3B B:HEM902 4.2 23.3 1.0
CD1 B:ILE143 4.3 27.4 1.0
C4B B:HEM902 4.3 22.2 1.0
O B:HOH4102 4.3 40.2 1.0
O B:HOH4072 4.4 31.4 1.0
NH2 B:ARG132 4.5 32.6 1.0
O B:HOH4046 4.6 32.2 1.0
CE1 B:PHE208 4.8 26.2 1.0
CBB B:HEM902 4.8 37.3 1.0
CMC B:HEM902 4.8 31.8 1.0
C1C B:HEM902 4.9 22.9 1.0
CE2 B:PHE208 5.0 27.1 1.0

Iodine binding site 6 out of 9 in 1wnw

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Iodine binding site 6 out of 9 in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1003

b:64.1
occ:1.00
N B:ASP154 3.6 23.8 1.0
CB B:ASP154 4.0 25.0 1.0
CD2 B:LEU90 4.1 22.4 1.0
CG1 B:VAL153 4.1 23.8 1.0
CB B:ALA157 4.2 25.1 1.0
CA B:VAL153 4.2 23.9 1.0
CA B:ASP154 4.4 24.6 1.0
C B:VAL153 4.4 23.6 1.0
CB B:VAL153 4.7 24.2 1.0
CA B:LEU90 5.0 21.7 1.0
O B:ASP154 5.0 21.6 1.0

Iodine binding site 7 out of 9 in 1wnw

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Iodine binding site 7 out of 9 in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1004

b:74.2
occ:1.00
O B:HOH4102 3.4 40.2 1.0
CA B:ASN136 3.8 19.0 1.0
O B:HOH4011 3.8 24.7 1.0
CD1 B:ILE143 3.8 27.4 1.0
O B:HOH4097 3.9 33.6 1.0
I B:IOD1002 3.9 45.8 1.0
OD1 B:ASN136 4.0 32.7 1.0
CB B:ASN136 4.1 20.3 1.0
CG B:ASN136 4.1 28.2 1.0
N B:ASN136 4.1 18.4 1.0
CE2 B:TYR161 4.1 22.2 1.0
O B:HOH4159 4.3 27.2 1.0
CE2 B:PHE160 4.3 20.9 1.0
O B:GLY135 4.3 23.3 1.0
C B:GLY135 4.4 20.4 1.0
CA B:GLY140 4.5 26.2 1.0
CD2 B:TYR161 4.5 21.6 1.0
ND2 B:ASN136 4.7 25.9 1.0
CZ B:PHE160 4.8 23.2 1.0
N B:GLY140 4.8 24.5 1.0

Iodine binding site 8 out of 9 in 1wnw

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Iodine binding site 8 out of 9 in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1005

b:44.6
occ:1.00
NH1 B:ARG145 3.7 49.6 1.0
CD B:ARG145 3.7 36.8 1.0
CG B:MET146 3.9 27.9 1.0
CG B:ARG145 3.9 29.9 1.0
CB B:ARG145 4.2 25.0 1.0
NH2 B:ARG149 4.3 46.0 0.5
CZ B:ARG149 4.4 45.5 0.5
NE B:ARG149 4.5 42.1 0.5
N B:MET146 4.6 23.5 1.0
NE B:ARG145 4.7 41.2 1.0
CZ B:ARG145 4.7 46.8 1.0
C B:ARG145 4.7 22.4 1.0
O B:VAL142 4.8 26.8 1.0
CA B:MET146 4.8 24.3 1.0
CB B:MET146 5.0 25.6 1.0
NH1 B:ARG149 5.0 48.4 0.5

Iodine binding site 9 out of 9 in 1wnw

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Iodine binding site 9 out of 9 in the D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of D136N Mutant of Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1001

b:41.4
occ:1.00
N C:TRP96 3.7 24.2 1.0
CA C:TRP96 4.0 22.7 1.0
C C:GLU95 4.0 26.8 1.0
CB C:ASN91 4.2 32.8 1.0
CB C:TRP96 4.2 23.1 1.0
CD C:ARG99 4.4 46.2 1.0
O C:GLU95 4.4 30.7 1.0
CG C:ASN91 4.5 33.8 1.0
CB C:GLU95 4.5 27.6 1.0
CB C:SER93 4.6 22.1 1.0
CA C:GLU95 4.6 24.9 1.0
N C:GLU95 4.7 22.4 1.0
OG C:SER93 4.7 23.8 1.0
OD1 C:ASN91 4.9 40.1 1.0
NH1 C:ARG99 4.9 47.8 1.0
ND2 C:ASN91 5.0 31.1 1.0
O C:ASN91 5.0 33.7 1.0

Reference:

T.Matsui, M.Furukawa, M.Unno, T.Tomita, M.Ikeda-Saito. Roles of Distal Asp in Heme Oxygenase From Corynebacterium Diphtheriae, Hmuo: A Water-Driven Oxygen Activation Mechanism J.Biol.Chem. V. 280 2981 2005.
ISSN: ISSN 0021-9258
PubMed: 15528205
DOI: 10.1074/JBC.M410263200
Page generated: Sun Dec 13 19:22:00 2020

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