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Manganese in PDB 3wu2: Crystal Structure Analysis of Photosystem II Complex

Protein crystallography data

The structure of Crystal Structure Analysis of Photosystem II Complex, PDB code: 3wu2 was solved by Y.Umena, K.Kawakami, J.R.Shen, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.190, 228.510, 286.400, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.4

Other elements in 3wu2:

The structure of Crystal Structure Analysis of Photosystem II Complex also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 4 atoms
Calcium (Ca) 9 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure Analysis of Photosystem II Complex (pdb code 3wu2). 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 Analysis of Photosystem II Complex, PDB code: 3wu2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3wu2

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Manganese binding site 1 out of 8 in the Crystal Structure Analysis of 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 Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:22.3
occ:1.00
 MN1 A:OEX401 0.0 22.3 1.0
O3 A:OEX401 1.8 23.1 1.0
O1 A:OEX401 1.9 21.8 1.0
OE2 A:GLU189 1.9 25.3 1.0
NE2 A:HIS332 2.1 19.5 1.0
OD2 A:ASP342 2.2 24.2 1.0
O5 A:OEX401 2.6 23.5 1.0
MN2 A:OEX401 2.9 23.1 1.0
CD A:GLU189 2.9 24.6 1.0
CD2 A:HIS332 3.0 18.9 1.0
CE1 A:HIS332 3.1 24.7 1.0
CG A:ASP342 3.1 22.8 1.0
MN3 A:OEX401 3.3 23.4 1.0
OD1 A:ASP342 3.4 20.5 1.0
OE1 A:GLU189 3.4 27.3 1.0
CA1 A:OEX401 3.5 25.2 1.0
O2 A:OEX401 3.8 25.9 1.0
NE2 A:HIS337 3.9 22.3 1.0
O A:HOH597 4.0 38.0 1.0
OE1 A:GLU333 4.0 24.0 1.0
O A:HOH658 4.1 39.8 1.0
CG A:GLU189 4.1 25.5 1.0
ND1 A:HIS332 4.2 18.6 1.0
CG A:HIS332 4.2 19.1 1.0
CG1 A:VAL185 4.5 21.6 1.0
OXT A:ALA344 4.5 25.2 1.0
CB A:ASP342 4.5 21.1 1.0
OE1 C:GLU354 4.5 23.3 1.0
CE1 A:HIS337 4.6 20.5 1.0
O A:HOH569 4.7 26.4 1.0
OE2 C:GLU354 4.7 23.3 1.0
CD A:GLU333 4.8 20.7 1.0
O A:HOH544 4.9 27.3 1.0
O A:ALA344 4.9 29.0 1.0
CD2 A:HIS337 5.0 20.1 1.0
MN4 A:OEX401 5.0 27.0 1.0

Manganese binding site 2 out of 8 in 3wu2

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Manganese binding site 2 out of 8 in the Crystal Structure Analysis of 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 Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:23.1
occ:1.00
 MN2 A:OEX401 0.0 23.1 1.0
OXT A:ALA344 2.0 25.2 1.0
O1 A:OEX401 2.1 21.8 1.0
OE1 C:GLU354 2.1 23.3 1.0
O3 A:OEX401 2.1 23.1 1.0
OD1 A:ASP342 2.2 20.5 1.0
O2 A:OEX401 2.2 25.9 1.0
MN1 A:OEX401 2.9 22.3 1.0
MN3 A:OEX401 2.9 23.4 1.0
C A:ALA344 3.0 26.3 1.0
CD C:GLU354 3.0 23.2 1.0
CG A:ASP342 3.1 22.8 1.0
OD2 A:ASP342 3.2 24.2 1.0
OE2 C:GLU354 3.2 23.3 1.0
O A:ALA344 3.3 29.0 1.0
CA1 A:OEX401 3.4 25.2 1.0
O5 A:OEX401 3.8 23.5 1.0
NE2 A:HIS337 3.8 22.3 1.0
O C:HOH701 3.9 25.7 1.0
O A:HOH597 4.1 38.0 1.0
CA A:ALA344 4.3 25.4 1.0
N A:ALA344 4.3 27.7 1.0
CD2 A:HIS337 4.3 20.1 1.0
CG C:GLU354 4.4 21.1 1.0
OE2 A:GLU189 4.4 25.3 1.0
CB A:ASP342 4.5 21.1 1.0
O4 A:OEX401 4.5 28.5 1.0
OE1 A:GLU333 4.5 24.0 1.0
NE2 A:HIS332 4.6 19.5 1.0
NH2 C:ARG357 4.7 24.0 1.0
CB C:GLU354 4.8 24.0 1.0
CA A:ASP342 4.8 23.1 1.0
NH1 C:ARG357 4.9 27.6 1.0
O A:HOH544 4.9 27.3 1.0
C A:ASP342 4.9 22.8 1.0

Manganese binding site 3 out of 8 in 3wu2

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Manganese binding site 3 out of 8 in the Crystal Structure Analysis of 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 Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:23.4
occ:1.00
 MN3 A:OEX401 0.0 23.4 1.0
O2 A:OEX401 1.9 25.9 1.0
OE1 A:GLU333 2.0 24.0 1.0
O4 A:OEX401 2.1 28.5 1.0
OE2 C:GLU354 2.2 23.3 1.0
O3 A:OEX401 2.2 23.1 1.0
O5 A:OEX401 2.3 23.5 1.0
MN2 A:OEX401 2.9 23.1 1.0
MN4 A:OEX401 3.0 27.0 1.0
CD A:GLU333 3.0 20.7 1.0
CD C:GLU354 3.1 23.2 1.0
MN1 A:OEX401 3.3 22.3 1.0
OE2 A:GLU333 3.3 22.2 1.0
OE1 C:GLU354 3.4 23.3 1.0
CA1 A:OEX401 3.4 25.2 1.0
O1 A:OEX401 3.5 21.8 1.0
O C:HOH633 4.0 24.1 1.0
NH2 C:ARG357 4.0 24.0 1.0
NE2 A:HIS337 4.1 22.3 1.0
OD1 A:ASP170 4.1 25.6 1.0
NE2 A:HIS332 4.2 19.5 1.0
CG A:GLU333 4.4 21.7 1.0
O A:HOH511 4.4 23.5 1.0
CD2 A:HIS332 4.4 18.9 1.0
OD2 A:ASP170 4.4 25.3 1.0
OXT A:ALA344 4.4 25.2 1.0
CG C:GLU354 4.6 21.1 1.0
O A:HOH624 4.7 27.6 1.0
CE1 A:HIS337 4.7 20.5 1.0
OD1 A:ASP342 4.7 20.5 1.0
CG A:ASP170 4.7 24.5 1.0
O A:HOH595 4.7 22.9 1.0
CB A:GLU333 4.8 21.6 1.0
O A:ALA344 4.8 29.0 1.0
OD2 A:ASP342 4.8 24.2 1.0
O A:HOH569 4.9 26.4 1.0
OE2 A:GLU189 4.9 25.3 1.0

Manganese binding site 4 out of 8 in 3wu2

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Manganese binding site 4 out of 8 in the Crystal Structure Analysis of 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 Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:27.0
occ:1.00
 MN4 A:OEX401 0.0 27.0 1.0
OD1 A:ASP170 2.1 25.6 1.0
O4 A:OEX401 2.1 28.5 1.0
O A:HOH624 2.1 27.6 1.0
OE2 A:GLU333 2.2 22.2 1.0
O A:HOH595 2.3 22.9 1.0
O5 A:OEX401 2.4 23.5 1.0
MN3 A:OEX401 3.0 23.4 1.0
CD A:GLU333 3.1 20.7 1.0
CG A:ASP170 3.2 24.5 1.0
OE1 A:GLU333 3.3 24.0 1.0
O A:HOH569 3.8 26.4 1.0
OD2 A:ASP170 3.8 25.3 1.0
CA1 A:OEX401 3.8 25.2 1.0
O2 A:OEX401 3.8 25.9 1.0
O A:HOH609 3.9 28.4 1.0
O A:HOH511 4.0 23.5 1.0
O A:HOH509 4.1 30.6 1.0
OD1 A:ASP61 4.2 22.9 1.0
O A:SER169 4.4 21.1 1.0
CB A:ASP170 4.4 23.4 1.0
CG A:GLU333 4.4 21.7 1.0
CA A:ASP170 4.6 23.5 1.0
NH2 C:ARG357 4.7 24.0 1.0
O A:HOH621 4.7 25.3 1.0
O3 A:OEX401 4.8 23.1 1.0
OE2 C:GLU354 4.8 23.3 1.0
C A:SER169 4.9 20.2 1.0
N A:ASP170 5.0 21.8 1.0
MN1 A:OEX401 5.0 22.3 1.0

Manganese binding site 5 out of 8 in 3wu2

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Manganese binding site 5 out of 8 in the Crystal Structure Analysis of 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 Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn404

b:25.9
occ:1.00
 MN1 a:OEX404 0.0 25.9 1.0
OE2 a:GLU189 1.7 24.2 1.0
O1 a:OEX404 1.8 22.8 1.0
O3 a:OEX404 1.9 26.8 1.0
NE2 a:HIS332 2.2 26.0 1.0
OD2 a:ASP342 2.3 25.1 1.0
O5 a:OEX404 2.7 28.2 1.0
MN2 a:OEX404 2.8 26.4 1.0
CD a:GLU189 2.8 27.7 1.0
CE1 a:HIS332 3.1 24.8 1.0
CG a:ASP342 3.1 21.9 1.0
CD2 a:HIS332 3.2 22.9 1.0
MN3 a:OEX404 3.3 25.1 1.0
OE1 a:GLU189 3.3 30.1 1.0
OD1 a:ASP342 3.3 24.6 1.0
CA1 a:OEX404 3.5 27.7 1.0
O2 a:OEX404 3.6 27.6 1.0
NE2 a:HIS337 3.9 28.7 1.0
OE1 a:GLU333 4.0 28.5 1.0
O a:HOH609 4.1 33.4 1.0
CG a:GLU189 4.1 28.5 1.0
ND1 a:HIS332 4.2 23.8 1.0
OXT a:ALA344 4.3 33.3 1.0
O a:HOH639 4.3 39.6 1.0
CG a:HIS332 4.3 23.7 1.0
OE1 c:GLU354 4.5 25.9 1.0
CB a:ASP342 4.5 23.4 1.0
CG1 a:VAL185 4.5 22.7 1.0
CE1 a:HIS337 4.6 28.6 1.0
OE2 c:GLU354 4.6 25.1 1.0
O a:HOH585 4.7 28.8 1.0
O a:ALA344 4.7 30.3 1.0
CD a:GLU333 4.7 27.9 1.0
C a:ALA344 4.9 33.8 1.0
O a:HOH515 4.9 28.9 1.0
CD2 a:HIS337 4.9 24.6 1.0
MN4 a:OEX404 4.9 29.5 1.0
CD c:GLU354 5.0 26.9 1.0

Manganese binding site 6 out of 8 in 3wu2

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Manganese binding site 6 out of 8 in the Crystal Structure Analysis of 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 6 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn404

b:26.4
occ:1.00
 MN2 a:OEX404 0.0 26.4 1.0
OXT a:ALA344 1.8 33.3 1.0
O2 a:OEX404 2.0 27.6 1.0
O3 a:OEX404 2.0 26.8 1.0
OD1 a:ASP342 2.0 24.6 1.0
O1 a:OEX404 2.1 22.8 1.0
OE1 c:GLU354 2.2 25.9 1.0
MN1 a:OEX404 2.8 25.9 1.0
C a:ALA344 2.8 33.8 1.0
MN3 a:OEX404 2.9 25.1 1.0
CG a:ASP342 3.0 21.9 1.0
CD c:GLU354 3.0 26.9 1.0
O a:ALA344 3.2 30.3 1.0
OD2 a:ASP342 3.2 25.1 1.0
OE2 c:GLU354 3.2 25.1 1.0
CA1 a:OEX404 3.3 27.7 1.0
O5 a:OEX404 3.8 28.2 1.0
O c:HOH1084 3.8 29.0 1.0
NE2 a:HIS337 3.9 28.7 1.0
CA a:ALA344 4.2 32.8 1.0
OE2 a:GLU189 4.2 24.2 1.0
O a:HOH609 4.3 33.4 1.0
CD2 a:HIS337 4.3 24.6 1.0
N a:ALA344 4.3 31.7 1.0
CB a:ASP342 4.4 23.4 1.0
CG c:GLU354 4.4 26.3 1.0
OE1 a:GLU333 4.5 28.5 1.0
NE2 a:HIS332 4.6 26.0 1.0
O4 a:OEX404 4.6 27.2 1.0
NH2 c:ARG357 4.7 33.2 1.0
CB c:GLU354 4.8 26.3 1.0
CA a:ASP342 4.8 23.0 1.0
O a:HOH515 4.8 28.9 1.0
CD a:GLU189 4.9 27.7 1.0
OE1 a:GLU189 4.9 30.1 1.0
OD2 a:ASP170 4.9 27.4 1.0
NH1 c:ARG357 5.0 33.2 1.0
C a:ASP342 5.0 25.6 1.0

Manganese binding site 7 out of 8 in 3wu2

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Manganese binding site 7 out of 8 in the Crystal Structure Analysis of 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 7 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn404

b:25.1
occ:1.00
 MN3 a:OEX404 0.0 25.1 1.0
O3 a:OEX404 1.9 26.8 1.0
O2 a:OEX404 1.9 27.6 1.0
OE1 a:GLU333 1.9 28.5 1.0
O4 a:OEX404 2.1 27.2 1.0
OE2 c:GLU354 2.2 25.1 1.0
O5 a:OEX404 2.3 28.2 1.0
MN4 a:OEX404 2.9 29.5 1.0
MN2 a:OEX404 2.9 26.4 1.0
CD a:GLU333 3.0 27.9 1.0
CD c:GLU354 3.1 26.9 1.0
MN1 a:OEX404 3.3 25.9 1.0
OE2 a:GLU333 3.3 25.1 1.0
CA1 a:OEX404 3.4 27.7 1.0
OE1 c:GLU354 3.5 25.9 1.0
O1 a:OEX404 3.6 22.8 1.0
NH2 c:ARG357 4.0 33.2 1.0
O c:HOH1086 4.0 28.7 1.0
OD1 a:ASP170 4.1 27.7 1.0
NE2 a:HIS337 4.2 28.7 1.0
NE2 a:HIS332 4.2 26.0 1.0
O a:HOH542 4.3 25.6 1.0
OD2 a:ASP170 4.3 27.4 1.0
CG a:GLU333 4.4 25.4 1.0
OXT a:ALA344 4.4 33.3 1.0
CD2 a:HIS332 4.5 22.9 1.0
CG c:GLU354 4.5 26.3 1.0
O a:HOH574 4.5 26.2 1.0
CG a:ASP170 4.7 27.3 1.0
OD1 a:ASP342 4.7 24.6 1.0
O a:ALA344 4.7 30.3 1.0
CB a:GLU333 4.7 24.9 1.0
O a:HOH543 4.7 30.5 1.0
OE2 a:GLU189 4.8 24.2 1.0
CE1 a:HIS337 4.8 28.6 1.0
O a:HOH585 4.8 28.8 1.0
OD2 a:ASP342 4.9 25.1 1.0

Manganese binding site 8 out of 8 in 3wu2

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Manganese binding site 8 out of 8 in the Crystal Structure Analysis of 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 Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn404

b:29.5
occ:1.00
 MN4 a:OEX404 0.0 29.5 1.0
O4 a:OEX404 2.1 27.2 1.0
OD1 a:ASP170 2.1 27.7 1.0
OE2 a:GLU333 2.1 25.1 1.0
O a:HOH574 2.2 26.2 1.0
O a:HOH543 2.2 30.5 1.0
O5 a:OEX404 2.3 28.2 1.0
MN3 a:OEX404 2.9 25.1 1.0
CD a:GLU333 3.0 27.9 1.0
OE1 a:GLU333 3.2 28.5 1.0
CG a:ASP170 3.2 27.3 1.0
O a:HOH585 3.7 28.8 1.0
OD2 a:ASP170 3.7 27.4 1.0
CA1 a:OEX404 3.8 27.7 1.0
O2 a:OEX404 3.9 27.6 1.0
O a:HOH542 4.0 25.6 1.0
O a:HOH513 4.0 27.5 1.0
OD1 a:ASP61 4.2 28.5 1.0
O a:HOH605 4.3 24.7 1.0
CG a:GLU333 4.4 25.4 1.0
O3 a:OEX404 4.4 26.8 1.0
O a:SER169 4.4 24.3 1.0
CB a:ASP170 4.5 25.2 1.0
CA a:ASP170 4.6 22.1 1.0
O a:HOH608 4.8 26.4 1.0
OE2 c:GLU354 4.8 25.1 1.0
NH2 c:ARG357 4.8 33.2 1.0
MN1 a:OEX404 4.9 25.9 1.0
C a:SER169 5.0 22.4 1.0

Reference:

Y.Umena, K.Kawakami, J.-R.Shen, N.Kamiya. Crystal Structure of Oxygen-Evolving Photosystem II at A Resolution of 1.9 A Nature V. 473 55 2011.
ISSN: ISSN 0028-0836
PubMed: 21499260
DOI: 10.1038/NATURE09913
Page generated: Sat Oct 5 18:28:12 2024

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