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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

Go back to Iodine Binding Sites List in 2oyy
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

Go back to Iodine Binding Sites List in 2oyy
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 Dec 13 19:24:51 2020

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