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Iodine in PDB 3a0h: Crystal Structure of I-Substituted Photosystem II Complex

Protein crystallography data

The structure of Crystal Structure of I-Substituted Photosystem II Complex, PDB code: 3a0h was solved by K.Kawakami, Y.Umena, N.Kamiya, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 4.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 128.499, 224.702, 304.919, 90.00, 90.00, 90.00
R / Rfree (%) 29 / 32.6

Other elements in 3a0h:

The structure of Crystal Structure of I-Substituted Photosystem II Complex also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of I-Substituted Photosystem II Complex (pdb code 3a0h). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of I-Substituted Photosystem II Complex, PDB code: 3a0h:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 3a0h

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Iodine binding site 1 out of 10 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I1064

b:0.4
occ:1.00
 NZ D:LYS317 2.9 0.3 1.0
N A:GLU333 3.4 0.1 1.0
CG D:LYS317 3.4 0.5 1.0
O D:LYS317 3.5 0.1 1.0
CE D:LYS317 3.6 0.2 1.0
CA A:HIS332 3.7 0.4 1.0
C A:HIS332 4.1 0.8 1.0
CD D:LYS317 4.1 0.6 1.0
CB A:HIS332 4.2 0.7 1.0
ND2 A:ASN181 4.2 0.2 1.0
C D:LYS317 4.3 0.7 1.0
CA A:GLU333 4.4 0.5 1.0
CD2 D:LEU321 4.4 0.3 1.0
CG D:LEU321 4.5 0.5 1.0
OD1 A:ASN181 4.6 0.7 1.0
CB D:LYS317 4.7 0.2 1.0
N A:HIS332 4.7 0.5 1.0
CD1 D:LEU321 4.8 0.5 1.0
CG A:GLU333 4.8 0.4 1.0
CG A:ASN181 4.9 0.4 1.0
CA D:LYS317 4.9 0.6 1.0

Iodine binding site 2 out of 10 in 3a0h

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Iodine binding site 2 out of 10 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1065

b:0.5
occ:1.00
 N A:ASN338 3.6 0.0 1.0
CD2 A:PHE339 3.6 0.3 1.0
CB A:PHE339 3.7 0.1 1.0
N A:PHE339 3.9 0.9 1.0
N C:GLU354 3.9 0.8 1.0
NE2 C:GLN313 3.9 0.3 1.0
CG2 C:THR355 4.0 0.3 1.0
C A:ASN338 4.0 0.6 1.0
CG A:PHE339 4.1 0.9 1.0
CA A:HIS337 4.2 0.7 1.0
C A:HIS337 4.3 0.1 1.0
CA A:PHE339 4.3 0.0 1.0
CA A:ASN338 4.3 0.9 1.0
CA C:GLY353 4.4 0.3 1.0
CB C:GLU354 4.4 0.4 1.0
O A:ASN338 4.5 0.7 1.0
C C:GLY353 4.5 0.8 1.0
CE2 A:PHE339 4.7 0.4 1.0
O A:LEU341 4.7 0.1 1.0
O A:PHE339 4.7 0.6 1.0
N C:THR355 4.8 0.9 1.0
CA C:GLU354 4.8 0.6 1.0
CD C:GLN313 4.8 0.5 1.0
C A:PHE339 4.9 0.1 1.0
OE1 C:GLN313 4.9 0.2 1.0
CD2 A:HIS337 4.9 0.5 1.0
OG C:SER310 5.0 0.9 1.0
CB A:HIS337 5.0 0.1 1.0
CB A:ASN338 5.0 0.0 1.0

Iodine binding site 3 out of 10 in 3a0h

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Iodine binding site 3 out of 10 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1067

b:1.0
occ:1.00
 CA B:CYS112 2.1 0.0 1.0
SG B:CYS112 2.5 0.3 1.0
C B:CYS112 2.6 0.3 1.0
CB B:CYS112 2.7 0.7 1.0
O B:CYS112 2.8 0.7 1.0
N B:CYS112 3.3 0.9 1.0
CB B:TRP115 3.3 0.3 1.0
O B:ALA111 3.7 0.8 1.0
N B:TRP113 3.7 0.6 1.0
C B:ALA111 3.9 0.8 1.0
CG B:TRP115 4.2 0.3 1.0
N B:TRP115 4.5 0.4 1.0
CA B:TRP115 4.5 0.2 1.0
CZ t:PHE5023 4.6 0.1 1.0
C29 B:BCR1045 4.7 0.2 1.0
CA B:TRP113 4.8 0.6 1.0
CD1 B:TRP115 4.9 0.1 1.0
C B:TRP113 4.9 0.4 1.0

Iodine binding site 4 out of 10 in 3a0h

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Iodine binding site 4 out of 10 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I1068

b:0.9
occ:1.00
 OH D:TYR160 2.2 0.5 1.0
CG D:GLN164 2.2 0.4 1.0
CD D:GLN164 2.7 0.5 1.0
CZ D:TYR160 2.8 0.6 1.0
CE1 B:PHE362 2.8 0.7 1.0
CE1 D:TYR160 3.0 0.1 1.0
CZ B:PHE362 3.0 0.2 1.0
NE2 D:GLN164 3.2 0.1 1.0
CB D:GLN164 3.3 0.8 1.0
OE1 D:GLN164 3.3 0.1 1.0
CB D:PHE169 3.7 0.9 1.0
CE2 D:TYR160 3.8 0.1 1.0
CD1 B:PHE362 4.0 0.2 1.0
CG D:PHE169 4.2 0.4 1.0
CD1 D:TYR160 4.2 0.1 1.0
NE2 D:HIS189 4.2 0.4 1.0
CZ D:PHE184 4.4 0.5 1.0
CE2 B:PHE362 4.4 0.6 1.0
CD2 D:PHE169 4.5 0.7 1.0
CE1 D:HIS189 4.6 0.1 1.0
CA D:GLN164 4.6 1.0 1.0
CE1 D:PHE184 4.7 0.4 1.0
O D:PHE169 4.7 0.3 1.0
CD2 D:TYR160 4.8 0.3 1.0
CD1 D:PHE169 4.9 0.9 1.0
CG D:TYR160 5.0 0.7 1.0

Iodine binding site 5 out of 10 in 3a0h

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Iodine binding site 5 out of 10 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:I1066

b:0.4
occ:1.00
 SG T:CYS12 1.9 0.5 1.0
CE1 T:PHE8 3.2 0.1 1.0
CB T:CYS12 3.3 0.3 1.0
CZ T:PHE8 3.8 1.0 1.0
C17 T:BCR6046 3.8 0.3 1.0
C19 T:BCR6046 3.9 0.3 1.0
CA T:CYS12 4.0 0.9 1.0
CD1 T:PHE8 4.1 0.2 1.0
C18 T:BCR6046 4.1 0.3 1.0
C16 T:BCR6046 4.5 0.7 1.0
C20 T:BCR6046 4.5 0.4 1.0
N T:CYS12 4.6 1.0 1.0
CE2 T:PHE8 5.0 1.0 1.0

Iodine binding site 6 out of 10 in 3a0h

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Iodine binding site 6 out of 10 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
d:I6064

b:0.4
occ:1.00
 NZ d:LYS5317 2.9 0.3 1.0
N a:GLU5333 3.4 0.1 1.0
CG d:LYS5317 3.4 0.5 1.0
O d:LYS5317 3.5 0.1 1.0
CE d:LYS5317 3.6 0.2 1.0
CA a:HIS5332 3.7 0.4 1.0
C a:HIS5332 4.1 0.8 1.0
CD d:LYS5317 4.1 0.6 1.0
CB a:HIS5332 4.2 0.7 1.0
ND2 a:ASN5181 4.2 0.2 1.0
C d:LYS5317 4.3 0.7 1.0
CA a:GLU5333 4.4 0.5 1.0
CD2 d:LEU5321 4.4 0.3 1.0
CG d:LEU5321 4.5 0.5 1.0
OD1 a:ASN5181 4.6 0.7 1.0
CB d:LYS5317 4.7 0.2 1.0
N a:HIS5332 4.7 0.5 1.0
CD1 d:LEU5321 4.8 0.5 1.0
CG a:GLU5333 4.8 0.4 1.0
CG a:ASN5181 4.9 0.4 1.0
CA d:LYS5317 4.9 0.6 1.0

Iodine binding site 7 out of 10 in 3a0h

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Iodine binding site 7 out of 10 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:I6065

b:0.5
occ:1.00
 N a:ASN5338 3.7 0.0 1.0
CD2 a:PHE5339 3.8 0.3 1.0
CA a:HIS5337 3.9 0.7 1.0
N c:GLU5354 3.9 0.8 1.0
NE2 c:GLN5313 3.9 0.3 1.0
CB a:PHE5339 3.9 0.1 1.0
CG2 c:THR5355 4.0 0.3 1.0
N a:PHE5339 4.1 0.9 1.0
C a:HIS5337 4.1 0.1 1.0
CG a:PHE5339 4.4 0.9 1.0
CA c:GLY5353 4.4 0.3 1.0
CB c:GLU5354 4.4 0.4 1.0
C a:ASN5338 4.4 0.6 1.0
CB a:HIS5337 4.5 0.1 1.0
C c:GLY5353 4.5 0.8 1.0
CA a:PHE5339 4.5 0.0 1.0
CA a:ASN5338 4.7 0.9 1.0
O a:LEU5341 4.7 0.1 1.0
N c:THR5355 4.8 0.9 1.0
CA c:GLU5354 4.8 0.6 1.0
CD c:GLN5313 4.8 0.5 1.0
CE2 a:PHE5339 4.9 0.4 1.0
OE1 c:GLN5313 4.9 0.2 1.0
N a:HIS5337 4.9 0.6 1.0
OG c:SER5310 5.0 0.9 1.0

Iodine binding site 8 out of 10 in 3a0h

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Iodine binding site 8 out of 10 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
b:I6067

b:0.2
occ:1.00
 SG b:CYS5112 1.9 0.3 1.0
CB b:CYS5112 2.3 0.7 1.0
CA b:CYS5112 2.5 0.0 1.0
N b:CYS5112 3.4 0.9 1.0
C b:CYS5112 3.6 0.3 1.0
C29 b:BCR6045 3.8 0.2 1.0
O b:CYS5112 3.9 0.7 1.0
CZ T:PHE23 4.0 0.1 1.0
C b:ALA5111 4.3 0.8 1.0
CE1 T:PHE23 4.4 0.2 1.0
C28 b:BCR6045 4.4 0.4 1.0
O b:ALA5111 4.6 0.8 1.0
C27 b:BCR6045 4.8 0.4 1.0
N b:TRP5113 4.8 0.6 1.0
CB b:TRP5115 4.8 0.3 1.0
C39 b:BCR6045 4.8 0.2 1.0
C30 b:BCR6045 4.9 0.4 1.0

Iodine binding site 9 out of 10 in 3a0h

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Iodine binding site 9 out of 10 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
d:I6068

b:0.2
occ:1.00
 CE1 d:PHE5184 2.2 0.4 1.0
O d:PHE5169 2.2 0.3 1.0
OH d:TYR5160 2.5 0.5 1.0
CB d:PHE5169 2.6 0.9 1.0
CZ d:PHE5184 2.9 0.5 1.0
C d:PHE5169 3.0 0.2 1.0
CA d:PHE5169 3.1 0.3 1.0
CD1 d:PHE5184 3.3 0.6 1.0
CZ d:TYR5160 3.4 0.6 1.0
CE2 d:TYR5160 3.5 0.1 1.0
CG d:PHE5169 3.5 0.4 1.0
CD1 d:PHE5169 3.8 0.9 1.0
NH1 d:ARG5180 4.2 0.2 1.0
N d:ALA5170 4.3 0.1 1.0
CE2 d:PHE5184 4.3 0.2 1.0
CG d:PHE5184 4.6 0.4 1.0
N d:PHE5169 4.6 0.9 1.0
CE1 b:PHE5362 4.6 0.7 1.0
CE2 d:PHE5185 4.6 0.3 1.0
CE1 d:TYR5160 4.6 0.1 1.0
CD2 d:PHE5169 4.7 0.7 1.0
CE2 d:PHE5181 4.8 0.5 1.0
CD2 d:TYR5160 4.8 0.3 1.0
CD2 d:PHE5184 4.9 0.4 1.0

Iodine binding site 10 out of 10 in 3a0h

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Iodine binding site 10 out of 10 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
t:I6066

b:0.7
occ:1.00
 SG t:CYS5012 1.7 0.4 1.0
CB t:CYS5012 3.1 0.8 1.0
CA t:CYS5012 3.4 0.6 1.0
O t:CYS5012 4.4 0.7 1.0
N t:CYS5012 4.4 0.3 1.0
C t:CYS5012 4.4 0.9 1.0
CE1 t:PHE5008 4.4 0.1 1.0
CZ t:PHE5008 4.7 1.0 1.0
C17 t:BCR1046 4.7 0.3 1.0
C16 t:BCR1046 4.9 0.7 1.0

Reference:

K.Kawakami, Y.Umena, N.Kamiya, J.-R.Shen. Location of Chloride and Its Possible Functions in Oxygen-Evolving Photosystem II Revealed By X-Ray Crystallography Proc.Natl.Acad.Sci.Usa V. 106 8567 2009.
ISSN: ISSN 0027-8424
PubMed: 19433803
DOI: 10.1073/PNAS.0812797106
Page generated: Sun Aug 11 14:40:33 2024

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