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Manganese 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
Iodine (I) 10 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of I-Substituted Photosystem II Complex, PDB code: 3a0h:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3a0h

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Manganese binding site 1 out of 8 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:0.5
occ:1.00
 MN1 A:OEC1001 0.0 0.5 1.0
MN2 A:OEC1001 2.2 0.8 1.0
NE2 A:HIS332 2.5 0.1 1.0
OE1 A:GLU189 2.6 0.5 1.0
MN3 A:OEC1001 2.6 0.3 1.0
OE2 A:GLU189 2.6 1.0 1.0
OD2 A:ASP342 2.8 0.3 1.0
OD1 A:ASP342 2.9 0.3 1.0
CD A:GLU189 2.9 0.5 1.0
CA1 A:OEC1001 3.0 0.6 1.0
CG A:ASP342 3.1 0.9 1.0
O A:ALA344 3.2 0.8 1.0
CD2 A:HIS332 3.2 0.8 1.0
NE2 A:HIS337 3.3 0.0 1.0
CE1 A:HIS332 3.6 0.7 1.0
OE2 A:GLU333 3.7 0.5 1.0
CE1 A:HIS337 3.8 0.5 1.0
OXT A:ALA344 3.9 0.2 1.0
C A:ALA344 3.9 0.4 1.0
OE2 C:GLU354 4.2 0.4 1.0
CG A:GLU189 4.3 0.9 1.0
OE1 C:GLU354 4.4 0.2 1.0
CD A:GLU333 4.4 0.2 1.0
CG A:HIS332 4.5 0.2 1.0
CD2 A:HIS337 4.5 0.5 1.0
ND1 A:HIS332 4.6 0.5 1.0
CB A:ASP342 4.6 0.8 1.0
OE1 A:GLU333 4.7 0.6 1.0
CD C:GLU354 4.8 0.2 1.0

Manganese binding site 2 out of 8 in 3a0h

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Manganese binding site 2 out of 8 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1001

b:0.8
occ:1.00
 MN2 A:OEC1001 0.0 0.8 1.0
OE2 C:GLU354 2.2 0.4 1.0
MN1 A:OEC1001 2.2 0.5 1.0
OXT A:ALA344 2.3 0.2 1.0
OD1 A:ASP342 2.3 0.3 1.0
MN3 A:OEC1001 2.6 0.3 1.0
C A:ALA344 2.7 0.4 1.0
O A:ALA344 2.8 0.8 1.0
NE2 A:HIS337 2.8 0.0 1.0
CD C:GLU354 3.1 0.2 1.0
CG A:ASP342 3.3 0.9 1.0
OE1 C:GLU354 3.3 0.2 1.0
CA1 A:OEC1001 3.3 0.6 1.0
CD2 A:HIS337 3.5 0.5 1.0
OD2 A:ASP342 3.7 0.3 1.0
OE2 A:GLU189 3.9 1.0 1.0
CE1 A:HIS337 3.9 0.5 1.0
CA A:ALA344 3.9 0.7 1.0
N A:ALA344 4.1 0.2 1.0
NE2 A:HIS332 4.3 0.1 1.0
NH1 C:ARG357 4.4 0.1 1.0
CB A:ASP342 4.4 0.8 1.0
CG C:GLU354 4.5 0.5 1.0
CA A:ASP342 4.6 0.1 1.0
CD A:GLU189 4.6 0.5 1.0
CB A:ALA344 4.6 0.2 1.0
OE1 A:GLU333 4.7 0.6 1.0
OE1 A:GLU189 4.7 0.5 1.0
C A:ASP342 4.7 0.4 1.0
OE2 A:GLU333 4.7 0.5 1.0
CG A:HIS337 4.7 0.7 1.0
O A:ASP342 4.8 0.8 1.0
ND1 A:HIS337 4.9 0.9 1.0
CB C:GLU354 4.9 0.4 1.0
CD A:GLU333 5.0 0.2 1.0

Manganese binding site 3 out of 8 in 3a0h

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Manganese binding site 3 out of 8 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:0.3
occ:1.00
 MN3 A:OEC1001 0.0 0.3 1.0
OE1 C:GLU354 2.2 0.2 1.0
OE2 A:GLU333 2.5 0.5 1.0
OE1 A:GLU333 2.6 0.6 1.0
CA1 A:OEC1001 2.6 0.6 1.0
MN2 A:OEC1001 2.6 0.8 1.0
MN1 A:OEC1001 2.6 0.5 1.0
CD A:GLU333 2.8 0.2 1.0
CD C:GLU354 3.0 0.2 1.0
OE2 C:GLU354 3.2 0.4 1.0
MN4 A:OEC1001 3.2 0.3 1.0
NH1 C:ARG357 3.2 0.1 1.0
OXT A:ALA344 3.3 0.2 1.0
OD2 A:ASP170 3.6 0.7 1.0
NE2 A:HIS337 3.7 0.0 1.0
O A:ALA344 3.9 0.8 1.0
C A:ALA344 4.0 0.4 1.0
OD1 A:ASP170 4.2 0.4 1.0
CG A:ASP170 4.3 1.0 1.0
CG A:GLU333 4.3 0.4 1.0
CE1 A:HIS337 4.4 0.5 1.0
CG C:GLU354 4.4 0.5 1.0
CZ C:ARG357 4.4 0.2 1.0
NE2 A:HIS332 4.5 0.1 1.0
OE2 A:GLU189 4.5 1.0 1.0
CD2 A:HIS332 4.6 0.8 1.0
OD1 A:ASP342 4.6 0.3 1.0
CD2 A:HIS337 4.7 0.5 1.0
OE1 A:GLU189 4.8 0.5 1.0
CB A:GLU333 4.8 0.7 1.0
NH2 C:ARG357 4.9 0.9 1.0

Manganese binding site 4 out of 8 in 3a0h

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Manganese binding site 4 out of 8 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:0.3
occ:1.00
 MN4 A:OEC1001 0.0 0.3 1.0
OE2 A:GLU333 2.3 0.5 1.0
OD1 A:ASP170 2.4 0.4 1.0
CD A:GLU333 2.7 0.2 1.0
OD2 A:ASP170 2.7 0.7 1.0
OE1 A:GLU333 2.7 0.6 1.0
CG A:ASP170 2.8 1.0 1.0
MN3 A:OEC1001 3.2 0.3 1.0
OG A:SER169 3.8 0.4 1.0
CG A:GLU333 3.9 0.4 1.0
OE1 C:GLU354 4.1 0.2 1.0
CB A:ASP170 4.2 0.0 1.0
NH1 C:ARG357 4.2 0.1 1.0
CA1 A:OEC1001 4.3 0.6 1.0
CA A:ASP170 4.5 0.9 1.0
OD1 A:ASP61 4.6 0.0 1.0
O A:SER169 4.8 0.8 1.0
N A:ASP170 4.8 0.9 1.0
C A:SER169 4.9 0.4 1.0

Manganese binding site 5 out of 8 in 3a0h

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Manganese binding site 5 out of 8 in the Crystal Structure of I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn6001

b:0.5
occ:1.00
 MN1 a:OEC6001 0.0 0.5 1.0
MN2 a:OEC6001 2.2 0.8 1.0
NE2 a:HIS5332 2.5 0.1 1.0
OE1 a:GLU5189 2.6 0.5 1.0
MN3 a:OEC6001 2.6 0.3 1.0
OE2 a:GLU5189 2.6 1.0 1.0
OD2 a:ASP5342 2.8 0.3 1.0
OD1 a:ASP5342 2.9 0.3 1.0
CD a:GLU5189 2.9 0.5 1.0
CA1 a:OEC6001 3.0 0.6 1.0
CG a:ASP5342 3.1 0.9 1.0
NE2 a:HIS5337 3.2 0.0 1.0
O a:ALA5344 3.2 0.8 1.0
CD2 a:HIS5332 3.2 0.8 1.0
CE1 a:HIS5332 3.6 0.7 1.0
OE2 a:GLU5333 3.7 0.5 1.0
OXT a:ALA5344 3.9 0.2 1.0
C a:ALA5344 3.9 0.4 1.0
CD2 a:HIS5337 3.9 0.5 1.0
CE1 a:HIS5337 4.2 0.5 1.0
OE2 c:GLU5354 4.2 0.4 1.0
CG a:GLU5189 4.3 0.9 1.0
OE1 c:GLU5354 4.4 0.2 1.0
CD a:GLU5333 4.4 0.2 1.0
CG a:HIS5332 4.5 0.2 1.0
ND1 a:HIS5332 4.6 0.5 1.0
CB a:ASP5342 4.6 0.8 1.0
OE1 a:GLU5333 4.7 0.6 1.0
CD c:GLU5354 4.8 0.2 1.0

Manganese binding site 6 out of 8 in 3a0h

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Manganese binding site 6 out of 8 in the Crystal Structure of I-Substituted Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn6001

b:0.8
occ:1.00
 MN2 a:OEC6001 0.0 0.8 1.0
OE2 c:GLU5354 2.2 0.4 1.0
MN1 a:OEC6001 2.2 0.5 1.0
OXT a:ALA5344 2.3 0.2 1.0
OD1 a:ASP5342 2.3 0.3 1.0
MN3 a:OEC6001 2.6 0.3 1.0
NE2 a:HIS5337 2.6 0.0 1.0
C a:ALA5344 2.7 0.4 1.0
O a:ALA5344 2.8 0.8 1.0
CD c:GLU5354 3.1 0.2 1.0
CD2 a:HIS5337 3.1 0.5 1.0
CG a:ASP5342 3.3 0.9 1.0
OE1 c:GLU5354 3.3 0.2 1.0
CA1 a:OEC6001 3.3 0.6 1.0
CE1 a:HIS5337 3.7 0.5 1.0
OD2 a:ASP5342 3.7 0.3 1.0
OE2 a:GLU5189 3.9 1.0 1.0
CA a:ALA5344 3.9 0.7 1.0
N a:ALA5344 4.1 0.2 1.0
CG a:HIS5337 4.3 0.7 1.0
NE2 a:HIS5332 4.3 0.1 1.0
NH1 c:ARG5357 4.4 0.1 1.0
CB a:ASP5342 4.4 0.8 1.0
CG c:GLU5354 4.5 0.5 1.0
ND1 a:HIS5337 4.5 0.9 1.0
CA a:ASP5342 4.6 0.1 1.0
CD a:GLU5189 4.6 0.5 1.0
CB a:ALA5344 4.6 0.2 1.0
OE1 a:GLU5333 4.7 0.6 1.0
OE1 a:GLU5189 4.7 0.5 1.0
C a:ASP5342 4.7 0.4 1.0
OE2 a:GLU5333 4.7 0.5 1.0
O a:ASP5342 4.8 0.8 1.0
CB c:GLU5354 4.9 0.4 1.0
CD a:GLU5333 5.0 0.2 1.0

Manganese binding site 7 out of 8 in 3a0h

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Manganese binding site 7 out of 8 in the Crystal Structure of I-Substituted Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn6001

b:0.3
occ:1.00
 MN3 a:OEC6001 0.0 0.3 1.0
OE1 c:GLU5354 2.2 0.2 1.0
OE2 a:GLU5333 2.5 0.5 1.0
OE1 a:GLU5333 2.6 0.6 1.0
CA1 a:OEC6001 2.6 0.6 1.0
MN2 a:OEC6001 2.6 0.8 1.0
MN1 a:OEC6001 2.6 0.5 1.0
CD a:GLU5333 2.8 0.2 1.0
CD c:GLU5354 3.0 0.2 1.0
OE2 c:GLU5354 3.2 0.4 1.0
MN4 a:OEC6001 3.2 0.3 1.0
NE2 a:HIS5337 3.2 0.0 1.0
NH1 c:ARG5357 3.2 0.1 1.0
OXT a:ALA5344 3.3 0.2 1.0
OD2 a:ASP5170 3.6 0.7 1.0
CE1 a:HIS5337 3.6 0.5 1.0
O a:ALA5344 3.9 0.8 1.0
C a:ALA5344 4.0 0.4 1.0
OD1 a:ASP5170 4.2 0.4 1.0
CG a:ASP5170 4.3 1.0 1.0
CG a:GLU5333 4.3 0.4 1.0
CG c:GLU5354 4.4 0.5 1.0
CZ c:ARG5357 4.4 0.2 1.0
CD2 a:HIS5337 4.4 0.5 1.0
NE2 a:HIS5332 4.5 0.1 1.0
OE2 a:GLU5189 4.5 1.0 1.0
CD2 a:HIS5332 4.6 0.8 1.0
OD1 a:ASP5342 4.6 0.3 1.0
ND1 a:HIS5337 4.8 0.9 1.0
OE1 a:GLU5189 4.8 0.5 1.0
CB a:GLU5333 4.8 0.7 1.0
NH2 c:ARG5357 4.9 0.9 1.0

Manganese binding site 8 out of 8 in 3a0h

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn6001

b:0.3
occ:1.00
 MN4 a:OEC6001 0.0 0.3 1.0
OE2 a:GLU5333 2.3 0.5 1.0
OD1 a:ASP5170 2.4 0.4 1.0
CD a:GLU5333 2.7 0.2 1.0
OD2 a:ASP5170 2.7 0.7 1.0
OE1 a:GLU5333 2.7 0.6 1.0
CG a:ASP5170 2.8 1.0 1.0
MN3 a:OEC6001 3.2 0.3 1.0
OG a:SER5169 3.8 0.4 1.0
CG a:GLU5333 3.9 0.4 1.0
OE1 c:GLU5354 4.1 0.2 1.0
CB a:ASP5170 4.2 0.0 1.0
NH1 c:ARG5357 4.2 0.1 1.0
CA1 a:OEC6001 4.3 0.6 1.0
CA a:ASP5170 4.5 0.9 1.0
OD1 a:ASP5061 4.6 0.0 1.0
O a:SER5169 4.8 0.8 1.0
N a:ASP5170 4.8 0.9 1.0
C a:SER5169 4.9 0.4 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: Sat Oct 5 15:39:06 2024

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