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Iodine in PDB 1fz9: Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane

Enzymatic activity of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane

All present enzymatic activity of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane:
1.14.13.25;

Protein crystallography data

The structure of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane, PDB code: 1fz9 was solved by D.A.Whittington, A.C.Rosenzweig, C.A.Frederick, S.J.Lippard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.220, 172.220, 221.190, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26

Other elements in 1fz9:

The structure of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Calcium (Ca) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane (pdb code 1fz9). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane, PDB code: 1fz9:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 1fz9

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Iodine binding site 1 out of 8 in the Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I9003

b:40.0
occ:0.87
 I A:ETI9003 0.0 40.0 0.9
C1 A:ETI9003 2.2 40.0 0.9
C2 A:ETI9003 3.0 40.0 0.9
CA A:GLY293 3.7 31.7 1.0
CD2 A:LEU361 3.7 32.3 1.0
N A:GLY293 3.8 28.7 1.0
CE1 A:TYR347 3.9 40.9 1.0
CD1 A:LEU289 3.9 33.2 1.0
O A:MET288 3.9 38.4 1.0
C A:TYR292 4.1 32.1 1.0
O A:TYR292 4.2 34.1 1.0
CA A:LEU289 4.2 37.5 1.0
CB A:TYR292 4.4 31.3 1.0
CD1 A:TYR347 4.5 35.7 1.0
C A:MET288 4.5 39.8 1.0
CG A:MET288 4.6 40.2 1.0
O A:HOH9073 4.6 22.6 1.0
OG1 A:THR102 4.6 30.6 1.0
O A:LEU289 4.6 39.2 1.0
N A:LEU289 4.7 38.1 1.0
CA A:TYR292 4.9 31.8 1.0
CZ A:TYR347 4.9 40.8 1.0
C A:LEU289 4.9 39.3 1.0

Iodine binding site 2 out of 8 in 1fz9

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Iodine binding site 2 out of 8 in the Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I9004

b:40.0
occ:0.52
 I A:ETI9004 0.0 40.0 0.5
C1 A:ETI9004 2.1 40.0 0.5
C2 A:ETI9004 3.0 40.0 0.5
CD2 A:LEU289 3.8 31.0 1.0
CB A:PHE109 4.1 28.8 1.0
CD2 A:LEU286 4.4 53.3 1.0
SD A:MET184 4.4 41.8 1.0
CD2 A:PHE109 4.5 24.1 1.0
CA A:VAL106 4.6 32.4 1.0
CG1 A:VAL285 4.7 22.9 1.0
CG A:PHE109 4.8 30.4 1.0
O A:VAL105 4.8 35.6 1.0
O A:VAL106 4.8 33.5 1.0

Iodine binding site 3 out of 8 in 1fz9

Go back to Iodine Binding Sites List in 1fz9
Iodine binding site 3 out of 8 in the Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I9005

b:40.0
occ:0.50
 I B:ETI9005 0.0 40.0 0.5
C1 B:ETI9005 2.1 40.0 0.5
C2 B:ETI9005 3.0 40.0 0.5
CD1 B:LEU289 3.6 27.1 1.0
CD2 B:LEU286 4.1 47.2 1.0
CB B:PHE109 4.2 36.2 1.0
SD B:MET184 4.3 40.5 1.0
CA B:VAL106 4.5 30.9 1.0
CG1 B:VAL285 4.6 28.9 1.0
CD2 B:PHE109 4.7 36.1 1.0
O B:VAL106 4.8 33.4 1.0
CE1 B:PHE282 4.8 49.7 1.0
O B:VAL105 4.8 33.3 1.0
CG1 B:VAL105 4.9 30.0 1.0
CG B:PHE109 4.9 33.6 1.0

Iodine binding site 4 out of 8 in 1fz9

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Iodine binding site 4 out of 8 in the Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I9006

b:40.0
occ:0.97
 I B:ETI9006 0.0 40.0 1.0
C1 B:ETI9006 2.2 40.0 1.0
C2 B:ETI9006 3.0 40.0 1.0
CD2 B:LEU361 3.7 23.5 1.0
N B:GLY293 3.7 37.4 1.0
CA B:GLY293 3.7 35.5 1.0
O B:MET288 3.9 36.4 1.0
CE1 B:TYR347 4.0 30.5 1.0
CD2 B:LEU289 4.0 25.3 1.0
C B:TYR292 4.1 34.7 1.0
CA B:LEU289 4.3 30.0 1.0
CB B:TYR292 4.3 36.4 1.0
O B:HOH9028 4.3 24.2 1.0
O B:TYR292 4.4 35.6 1.0
CG B:MET288 4.5 31.2 1.0
OG1 B:THR102 4.5 23.9 1.0
CD1 B:TYR347 4.5 31.2 1.0
C B:MET288 4.6 33.6 1.0
O B:LEU289 4.7 29.7 1.0
N B:LEU289 4.7 30.7 1.0
CA B:TYR292 4.8 36.9 1.0
O B:HOH9029 4.8 21.2 1.0
CE B:MET288 4.9 33.6 1.0
CZ B:TYR347 4.9 31.0 1.0
C B:LEU289 4.9 30.0 1.0

Iodine binding site 5 out of 8 in 1fz9

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Iodine binding site 5 out of 8 in the Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I9007

b:40.0
occ:0.27
 I C:ETI9007 0.0 40.0 0.3
C1 C:ETI9007 2.2 40.0 0.3
C2 C:ETI9007 3.0 40.0 0.3
NE2 D:GLN293 3.8 57.4 1.0
CD1 D:ILE290 3.9 50.3 1.0
CB D:GLN289 3.9 42.6 1.0
CB C:GLN125 4.2 48.3 1.0
N C:GLY126 4.2 45.5 1.0
C C:GLN125 4.3 45.8 1.0
CA C:GLY126 4.3 45.8 1.0
C D:GLN289 4.3 47.3 1.0
O C:GLN125 4.4 45.4 1.0
O D:GLN289 4.4 46.6 1.0
N D:ILE290 4.5 48.4 1.0
O D:THR286 4.6 34.5 1.0
CG1 D:ILE290 4.7 49.1 1.0
CA D:ILE290 4.8 47.8 1.0
CA D:GLN289 4.8 44.5 1.0
CG A:PRO20 4.8 67.3 1.0
CA C:GLN125 4.9 46.2 1.0
CB C:ALA129 5.0 44.8 1.0

Iodine binding site 6 out of 8 in 1fz9

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Iodine binding site 6 out of 8 in the Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I9001

b:40.0
occ:0.60
 I D:ETI9001 0.0 40.0 0.6
C1 D:ETI9001 2.1 40.0 0.6
C2 D:ETI9001 3.0 40.0 0.6
OE2 D:GLU116 3.3 39.7 1.0
CD D:GLU116 3.7 33.4 1.0
CG2 D:THR286 3.8 38.4 1.0
CB D:THR286 3.9 40.0 1.0
OG1 D:THR286 4.0 41.3 1.0
CG D:GLU116 4.0 37.6 1.0
CZ C:TYR119 4.2 46.6 1.0
CE1 C:TYR119 4.3 44.6 1.0
CB C:ARG122 4.3 42.7 1.0
CE2 D:TYR287 4.3 33.3 1.0
OE1 D:GLU116 4.4 38.1 1.0
NE C:ARG122 4.4 33.0 1.0
CE2 C:TYR119 4.4 44.1 1.0
CD1 C:TYR119 4.6 44.6 1.0
CA D:GLN283 4.6 41.2 1.0
OH C:TYR119 4.6 47.8 1.0
CD2 C:TYR119 4.7 39.1 1.0
NH2 C:ARG122 4.8 37.4 1.0
CG C:TYR119 4.8 41.7 1.0
CG C:ARG122 4.9 41.2 1.0
O C:TYR119 4.9 33.6 1.0
CD2 D:TYR287 4.9 33.2 1.0
CG D:GLN283 4.9 34.0 1.0
CB D:GLN283 5.0 35.5 1.0

Iodine binding site 7 out of 8 in 1fz9

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Iodine binding site 7 out of 8 in the Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I9002

b:40.0
occ:0.73
 I D:ETI9002 0.0 40.0 0.7
C1 D:ETI9002 2.2 40.0 0.7
C2 D:ETI9002 3.0 40.0 0.7
OE2 C:GLU116 3.4 35.4 1.0
CD C:GLU116 3.6 38.4 1.0
CG2 C:THR286 3.7 32.0 1.0
CG C:GLU116 3.7 36.5 1.0
CB C:THR286 3.9 30.6 1.0
OG1 C:THR286 4.1 33.5 1.0
CE1 D:TYR119 4.1 42.0 1.0
O C:HOH9069 4.2 25.6 1.0
CE2 C:TYR287 4.2 22.8 1.0
OE1 C:GLU116 4.3 33.1 1.0
CZ D:TYR119 4.4 39.3 1.0
CD1 D:TYR119 4.4 41.7 1.0
NE D:ARG122 4.4 37.5 1.0
CA C:GLN283 4.5 34.0 1.0
CG C:GLN283 4.6 32.8 1.0
CB D:ARG122 4.6 44.4 1.0
OH D:TYR119 4.7 42.7 1.0
CB C:GLN283 4.8 30.8 1.0
CE2 D:TYR119 4.9 39.1 1.0
CD2 C:TYR287 4.9 19.6 1.0
CG D:TYR119 4.9 40.7 1.0
OH C:TYR287 4.9 21.0 1.0
O D:TYR119 5.0 36.0 1.0

Iodine binding site 8 out of 8 in 1fz9

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Iodine binding site 8 out of 8 in the Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Methane Monooxygenase Hydroxylase, Form II Cocrystallized with Iodoethane within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I9008

b:40.0
occ:0.35
 I D:ETI9008 0.0 40.0 0.3
C1 D:ETI9008 2.2 40.0 0.3
C2 D:ETI9008 3.0 40.0 0.3
NE2 C:GLN293 3.5 40.9 1.0
O D:GLN125 3.7 46.7 1.0
CB C:GLN289 3.7 30.7 1.0
C D:GLN125 3.9 43.9 1.0
O C:HOH9086 3.9 29.9 1.0
CB D:GLN125 4.0 45.4 1.0
N D:GLY126 4.2 45.8 1.0
C C:GLN289 4.3 30.2 1.0
CA D:GLY126 4.3 47.6 1.0
CB B:PRO20 4.4 54.5 1.0
O C:GLN289 4.4 29.6 1.0
CG1 C:ILE290 4.4 24.2 1.0
N C:ILE290 4.4 30.5 1.0
O D:HOH9051 4.4 47.8 1.0
CA D:GLN125 4.6 45.0 1.0
OE1 D:GLN125 4.7 56.6 1.0
CA C:GLN289 4.7 30.2 1.0
CA C:ILE290 4.8 26.8 1.0
CG C:GLN289 4.8 31.7 1.0
CB D:ALA129 4.8 39.8 1.0
CD C:GLN293 4.8 39.5 1.0
O C:THR286 4.8 30.9 1.0

Reference:

D.A.Whittington, A.C.Rosenzweig, C.A.Frederick, S.J.Lippard. Xenon and Halogenated Alkanes Track Putative Substrate Binding Cavities in the Soluble Methane Monooxygenase Hydroxylase. Biochemistry V. 40 3476 2001.
ISSN: ISSN 0006-2960
PubMed: 11297413
DOI: 10.1021/BI0022487
Page generated: Sun Aug 11 09:38:30 2024

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