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Iodine in PDB 2oyy: Hthp: A Hexameric Tyrosine-Coordinated Heme Protein

Protein crystallography data

The structure of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein, PDB code: 2oyy was solved by H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.71 / 2.50
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 173.710, 173.710, 45.880, 90.00, 90.00, 120.00
R / Rfree (%) 23.4 / 26.9

Other elements in 2oyy:

The structure of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein (pdb code 2oyy). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein, PDB code: 2oyy:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 2oyy

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Iodine binding site 1 out of 12 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I9001

b:10.5
occ:1.00
 O A:ARG23 3.5 2.0 1.0
NE A:ARG23 3.7 2.3 1.0
NH2 A:ARG23 3.7 2.0 1.0
CB A:ARG23 3.9 2.0 1.0
CG1 A:VAL26 4.0 2.0 1.0
NE A:ARG36 4.0 2.0 1.0
C4C A:HEM201 4.1 2.0 1.0
CD A:ARG36 4.1 2.0 1.0
NC A:HEM201 4.1 2.0 1.0
CB A:VAL26 4.2 2.0 1.0
CHD A:HEM201 4.2 2.0 1.0
CZ A:ARG23 4.2 3.0 1.0
C A:ARG23 4.3 2.0 1.0
N A:LYS27 4.3 2.0 1.0
CA A:ARG23 4.3 2.0 1.0
CB A:LYS27 4.5 2.4 1.0
C1D A:HEM201 4.5 2.0 1.0
C3C A:HEM201 4.6 2.0 1.0
C1C A:HEM201 4.6 2.0 1.0
CG A:ARG23 4.6 2.0 1.0
CA A:LYS27 4.7 2.1 1.0
ND A:HEM201 4.8 2.0 1.0
CD A:ARG23 4.8 2.2 1.0
FE A:HEM201 4.9 2.0 1.0
C2C A:HEM201 4.9 2.0 1.0
C A:VAL26 4.9 2.0 1.0

Iodine binding site 2 out of 12 in 2oyy

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Iodine binding site 2 out of 12 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I9001

b:12.2
occ:1.00
 NH2 B:ARG23 3.5 4.8 1.0
NE B:ARG23 3.6 4.3 1.0
NE B:ARG36 3.8 2.9 1.0
CHD B:HEM201 4.0 4.9 1.0
O B:ARG23 4.0 2.0 1.0
CZ B:ARG23 4.0 3.8 1.0
C4C B:HEM201 4.0 4.2 1.0
CD B:ARG36 4.0 2.0 1.0
NC B:HEM201 4.1 3.6 1.0
CG1 B:VAL26 4.2 2.0 1.0
C1D B:HEM201 4.2 4.3 1.0
CB B:ARG23 4.3 2.0 1.0
ND B:HEM201 4.5 4.5 1.0
CB B:LYS27 4.6 3.1 1.0
C B:ARG23 4.7 2.0 1.0
CZ B:ARG36 4.7 3.9 1.0
C3C B:HEM201 4.7 3.2 1.0
CA B:ARG23 4.7 2.0 1.0
CG B:ARG23 4.8 2.5 1.0
CD B:ARG23 4.8 3.6 1.0
C1C B:HEM201 4.8 2.9 1.0
FE B:HEM201 4.8 3.8 1.0
I B:IOD9005 4.8 29.8 1.0
N B:LYS27 4.9 2.2 1.0
C2D B:HEM201 4.9 5.2 1.0
CD B:LYS27 4.9 5.8 1.0
CA B:LYS27 5.0 2.5 1.0

Iodine binding site 3 out of 12 in 2oyy

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Iodine binding site 3 out of 12 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I9005

b:29.8
occ:1.00
 O B:SER22 2.8 2.0 1.0
CA B:ARG23 2.9 2.0 1.0
CB B:VAL26 2.9 2.0 1.0
O B:ARG23 3.1 2.0 1.0
C B:ARG23 3.3 2.0 1.0
C B:SER22 3.4 2.0 1.0
CBB B:HEM201 3.4 4.4 1.0
N B:VAL26 3.5 2.0 1.0
CG2 B:VAL26 3.5 2.0 1.0
N B:ARG23 3.5 2.0 1.0
CHC B:HEM201 3.6 2.7 1.0
CG1 B:VAL26 3.7 2.0 1.0
CA B:VAL26 3.8 2.0 1.0
C4B B:HEM201 3.9 2.7 1.0
CB B:ARG23 4.0 2.0 1.0
C1C B:HEM201 4.0 2.9 1.0
CAB B:HEM201 4.0 3.6 1.0
C3B B:HEM201 4.1 3.5 1.0
CG B:ARG23 4.3 2.5 1.0
N B:ILE24 4.5 2.0 1.0
C2C B:HEM201 4.6 4.0 1.0
C B:ALA25 4.6 2.0 1.0
N B:ALA25 4.7 2.0 1.0
NC B:HEM201 4.7 3.6 1.0
NB B:HEM201 4.7 3.6 1.0
C B:VAL26 4.8 2.0 1.0
CA B:SER22 4.8 2.0 1.0
CMC B:HEM201 4.8 4.7 1.0
N B:LYS27 4.8 2.2 1.0
I B:IOD9001 4.8 12.2 1.0
C2B B:HEM201 5.0 3.8 1.0

Iodine binding site 4 out of 12 in 2oyy

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Iodine binding site 4 out of 12 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I9001

b:9.9
occ:1.00
 NE C:ARG36 3.7 2.2 1.0
O C:ARG23 3.7 2.0 1.0
NH2 C:ARG23 3.8 2.6 1.0
NE C:ARG23 3.8 2.0 1.0
CD C:ARG36 3.9 2.3 1.0
C4C C:HEM201 4.0 6.1 1.0
CHD C:HEM201 4.0 6.4 1.0
CB C:VAL26 4.1 2.0 1.0
NC C:HEM201 4.1 5.6 1.0
CG1 C:VAL26 4.2 2.0 1.0
CZ C:ARG23 4.3 2.9 1.0
CB C:ARG23 4.3 2.0 1.0
N C:LYS27 4.4 2.5 1.0
C1D C:HEM201 4.4 6.7 1.0
C C:ARG23 4.5 2.0 1.0
C3C C:HEM201 4.6 4.8 1.0
CA C:ARG23 4.7 2.0 1.0
CZ C:ARG36 4.7 2.0 1.0
CB C:LYS27 4.7 3.5 1.0
ND C:HEM201 4.7 6.4 1.0
C1C C:HEM201 4.7 5.3 1.0
CG2 C:VAL26 4.8 2.0 1.0
CA C:LYS27 4.8 3.0 1.0
CG C:ARG23 4.8 2.0 1.0
FE C:HEM201 4.9 6.0 1.0
CD C:ARG23 5.0 2.0 1.0

Iodine binding site 5 out of 12 in 2oyy

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Iodine binding site 5 out of 12 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I9003

b:18.0
occ:1.00
 CD C:ARG23 3.8 2.0 1.0
NH1 C:ARG23 3.9 3.0 1.0
CA C:LYS20 3.9 2.0 1.0
CB C:LYS20 4.1 2.0 1.0
CG C:LYS20 4.3 2.1 1.0
N C:LYS20 4.4 2.0 1.0
NE C:ARG23 4.5 2.0 1.0
CZ C:ARG23 4.5 2.9 1.0
O C:VAL19 4.7 2.1 1.0
CG C:ARG23 4.7 2.0 1.0
CG A:PRO4 4.7 6.2 1.0
C C:VAL19 4.8 2.0 1.0
CG1 C:VAL19 4.8 2.0 1.0
CB C:ARG23 4.8 2.0 1.0

Iodine binding site 6 out of 12 in 2oyy

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Iodine binding site 6 out of 12 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I9001

b:12.6
occ:1.00
 NE D:ARG23 3.5 2.9 1.0
NH2 D:ARG23 3.7 3.3 1.0
C4C D:HEM201 3.8 7.1 1.0
NC D:HEM201 3.8 7.2 1.0
O D:ARG23 3.8 2.0 1.0
CHD D:HEM201 3.8 8.5 1.0
CB D:ARG23 4.0 2.0 1.0
CD D:ARG36 4.0 2.3 1.0
CZ D:ARG23 4.1 3.5 1.0
NE D:ARG36 4.1 2.5 1.0
C1D D:HEM201 4.2 9.2 1.0
CB D:VAL26 4.2 2.0 1.0
CA D:ARG23 4.3 2.0 1.0
C D:ARG23 4.4 2.0 1.0
ND D:HEM201 4.4 9.2 1.0
FE D:HEM201 4.4 8.0 1.0
C1C D:HEM201 4.5 6.2 1.0
CG D:ARG23 4.5 2.0 1.0
C3C D:HEM201 4.5 6.9 1.0
CG1 D:VAL26 4.5 2.0 1.0
N D:LYS27 4.5 2.3 1.0
CD D:ARG23 4.6 2.5 1.0
CB D:LYS27 4.8 3.1 1.0
CA D:LYS27 4.8 2.8 1.0
C2C D:HEM201 4.8 6.3 1.0
CG2 D:VAL26 4.9 2.0 1.0

Iodine binding site 7 out of 12 in 2oyy

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Iodine binding site 7 out of 12 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I9002

b:13.2
occ:1.00
 CB D:ARG23 4.1 2.0 1.0
CD D:ARG23 4.3 2.5 1.0
CG D:LYS20 4.3 2.7 1.0
NE D:ARG23 4.5 2.9 1.0
O D:LYS20 4.5 2.0 1.0
CA D:LYS20 4.6 2.0 1.0
NH1 D:ARG23 4.6 3.3 1.0
CZ D:ARG23 4.7 3.5 1.0
CG2 D:ILE24 4.8 2.0 1.0
CG D:ARG23 4.8 2.0 1.0
CB D:LYS20 4.9 2.0 1.0

Iodine binding site 8 out of 12 in 2oyy

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Iodine binding site 8 out of 12 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I9001

b:9.6
occ:1.00
 NE E:ARG36 3.5 2.0 1.0
CD E:ARG36 3.7 2.0 1.0
O E:ARG23 3.7 2.1 1.0
NE E:ARG23 3.9 3.3 1.0
C4C E:HEM201 4.0 3.8 1.0
NC E:HEM201 4.0 3.5 1.0
CB E:ARG23 4.1 2.0 1.0
CHD E:HEM201 4.1 4.2 1.0
CB E:VAL26 4.1 2.0 1.0
CG1 E:VAL26 4.1 2.0 1.0
NH2 E:ARG23 4.2 2.3 1.0
N E:LYS27 4.3 2.4 1.0
C E:ARG23 4.3 2.1 1.0
CA E:ARG23 4.4 2.0 1.0
C1D E:HEM201 4.5 5.0 1.0
CZ E:ARG23 4.5 3.4 1.0
C1C E:HEM201 4.6 2.2 1.0
CG E:ARG23 4.6 2.0 1.0
C3C E:HEM201 4.6 3.2 1.0
CZ E:ARG36 4.6 2.0 1.0
CB E:LYS27 4.7 3.5 1.0
CA E:LYS27 4.7 3.0 1.0
ND E:HEM201 4.8 4.7 1.0
C E:VAL26 4.8 2.0 1.0
CD E:ARG23 4.8 3.1 1.0
FE E:HEM201 4.9 3.3 1.0
C2C E:HEM201 4.9 2.0 1.0

Iodine binding site 9 out of 12 in 2oyy

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Iodine binding site 9 out of 12 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I9004

b:34.0
occ:1.00
 CE E:LYS20 3.8 5.3 1.0
CB E:TRP2 3.8 8.8 1.0
NZ E:LYS20 4.4 6.2 1.0
CA E:TRP2 4.8 8.6 1.0
CG E:TRP2 4.8 9.3 1.0
O E:TRP2 4.8 8.1 1.0

Iodine binding site 10 out of 12 in 2oyy

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Iodine binding site 10 out of 12 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I9001

b:14.7
occ:1.00
 NE F:ARG23 3.6 4.1 1.0
NH2 F:ARG23 3.7 3.8 1.0
O F:ARG23 4.0 2.0 1.0
C4C F:HEM201 4.1 6.4 1.0
CZ F:ARG23 4.1 4.4 1.0
NC F:HEM201 4.1 5.9 1.0
CHD F:HEM201 4.2 7.7 1.0
CD F:ARG36 4.2 2.0 1.0
NE F:ARG36 4.2 2.0 1.0
CB F:ARG23 4.3 2.0 1.0
C1D F:HEM201 4.4 8.2 1.0
CG1 F:VAL26 4.5 2.0 1.0
CB F:VAL26 4.6 2.0 1.0
C F:ARG23 4.6 2.0 1.0
FE F:HEM201 4.6 5.8 1.0
ND F:HEM201 4.6 7.5 1.0
CG F:ARG23 4.6 2.1 1.0
N F:LYS27 4.7 2.2 1.0
CA F:ARG23 4.7 2.0 1.0
CD F:ARG23 4.7 3.2 1.0
CB F:LYS27 4.7 3.5 1.0
C1C F:HEM201 4.8 5.1 1.0
C3C F:HEM201 4.8 4.8 1.0
CA F:LYS27 5.0 2.9 1.0

Reference:

J.H.Jeoung, D.A.Pippig, B.M.Martins, N.Wagener, H.Dobbek. Hthp: A Novel Class of Hexameric, Tyrosine-Coordinated Heme Proteins J.Mol.Biol. V. 368 1122 2007.
ISSN: ISSN 0022-2836
PubMed: 17395199
DOI: 10.1016/J.JMB.2007.02.079
Page generated: Sun Aug 11 14:13:43 2024

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