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Manganese in PDB 4pj0: Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing

Enzymatic activity of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing

All present enzymatic activity of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing:
1.10.3.9;

Protein crystallography data

The structure of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing, PDB code: 4pj0 was solved by J.Hellmich, M.Bommer, A.Burkhardt, M.Ibrahim, J.Kern, A.Meents, F.Mueh, H.Dobbek, A.Zouni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.12 / 2.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.447, 218.889, 302.202, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 25.6

Other elements in 4pj0:

The structure of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 4 atoms
Calcium (Ca) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing (pdb code 4pj0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing, PDB code: 4pj0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4pj0

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Manganese binding site 1 out of 8 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:50.1
occ:1.00
MN1 A:OEX601 0.0 50.1 1.0
O3 A:OEX601 1.8 38.4 1.0
O1 A:OEX601 1.9 49.1 1.0
OE2 A:GLU189 1.9 49.9 1.0
NE2 A:HIS332 2.2 35.6 1.0
OD2 A:ASP342 2.3 34.9 1.0
O5 A:OEX601 2.6 42.2 1.0
MN2 A:OEX601 2.8 34.9 1.0
CD A:GLU189 3.0 40.5 1.0
CD2 A:HIS332 3.1 33.5 1.0
CE1 A:HIS332 3.2 33.6 1.0
CG A:ASP342 3.2 41.4 1.0
MN3 A:OEX601 3.3 40.2 1.0
OD1 A:ASP342 3.4 32.9 1.0
CA1 A:OEX601 3.5 57.2 1.0
OE1 A:GLU189 3.6 53.9 1.0
O2 A:OEX601 3.7 37.8 1.0
CG A:GLU189 4.1 29.0 1.0
NE2 A:HIS337 4.1 36.4 1.0
OE1 A:GLU333 4.2 40.2 1.0
CG A:HIS332 4.3 41.0 1.0
ND1 A:HIS332 4.3 41.3 1.0
CG1 A:VAL185 4.4 33.0 1.0
CB A:ASP342 4.6 42.3 1.0
CE1 A:HIS337 4.6 34.0 1.0
OE1 C:GLU354 4.7 36.1 1.0
O A:HOH727 4.7 38.0 1.0
OE2 C:GLU354 4.7 40.4 1.0
MN4 A:OEX601 5.0 52.2 1.0

Manganese binding site 2 out of 8 in 4pj0

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Manganese binding site 2 out of 8 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:34.9
occ:1.00
MN2 A:OEX601 0.0 34.9 1.0
O1 A:OEX601 2.1 49.1 1.0
OD1 A:ASP342 2.1 32.9 1.0
O3 A:OEX601 2.1 38.4 1.0
OE1 C:GLU354 2.1 36.1 1.0
O2 A:OEX601 2.1 37.8 1.0
C A:ALA344 2.8 48.2 1.0
MN1 A:OEX601 2.8 50.1 1.0
MN3 A:OEX601 2.9 40.2 1.0
CG A:ASP342 3.0 41.4 1.0
CD C:GLU354 3.0 40.0 1.0
O A:ALA344 3.2 55.5 1.0
OD2 A:ASP342 3.2 34.9 1.0
OE2 C:GLU354 3.2 40.4 1.0
CA1 A:OEX601 3.4 57.2 1.0
NE2 A:HIS337 3.7 36.4 1.0
O5 A:OEX601 3.8 42.2 1.0
CA A:ALA344 4.0 50.6 1.0
N A:ALA344 4.2 52.6 1.0
CB A:ASP342 4.4 42.3 1.0
CD2 A:HIS337 4.4 34.4 1.0
CG C:GLU354 4.4 36.0 1.0
OE2 A:GLU189 4.5 49.9 1.0
O4 A:OEX601 4.5 37.4 1.0
CB A:ALA344 4.5 43.8 1.0
NE2 A:HIS332 4.5 35.6 1.0
N A:LEU343 4.7 41.1 1.0
C A:LEU343 4.7 56.0 1.0
C A:ASP342 4.7 46.2 1.0
OE1 A:GLU333 4.7 40.2 1.0
CA A:ASP342 4.7 41.5 1.0
CE1 A:HIS337 4.8 34.0 1.0
CB C:GLU354 4.9 29.2 1.0

Manganese binding site 3 out of 8 in 4pj0

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Manganese binding site 3 out of 8 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:40.2
occ:1.00
MN3 A:OEX601 0.0 40.2 1.0
O2 A:OEX601 1.9 37.8 1.0
O4 A:OEX601 2.1 37.4 1.0
OE1 A:GLU333 2.1 40.2 1.0
O3 A:OEX601 2.1 38.4 1.0
OE2 C:GLU354 2.2 40.4 1.0
O5 A:OEX601 2.4 42.2 1.0
MN2 A:OEX601 2.9 34.9 1.0
MN4 A:OEX601 3.0 52.2 1.0
CD A:GLU333 3.1 38.4 1.0
CD C:GLU354 3.1 40.0 1.0
MN1 A:OEX601 3.3 50.1 1.0
OE1 C:GLU354 3.4 36.1 1.0
CA1 A:OEX601 3.4 57.2 1.0
OE2 A:GLU333 3.4 41.6 1.0
O1 A:OEX601 3.5 49.1 1.0
O A:HOH730 4.1 38.7 1.0
NE2 A:HIS337 4.1 36.4 1.0
NE2 A:HIS332 4.2 35.6 1.0
OD1 A:ASP170 4.3 39.0 1.0
O A:ALA344 4.3 55.5 1.0
CE1 A:HIS337 4.4 34.0 1.0
CG A:GLU333 4.4 39.7 1.0
CD2 A:HIS332 4.5 33.5 1.0
CG C:GLU354 4.5 36.0 1.0
O A:HOH726 4.6 37.5 1.0
NH2 C:ARG357 4.6 35.3 1.0
OD2 A:ASP170 4.6 41.7 1.0
OD1 A:ASP342 4.6 32.9 1.0
C A:ALA344 4.7 48.2 1.0
CB A:GLU333 4.7 38.4 1.0
O A:HOH729 4.8 38.2 1.0
O A:HOH728 4.9 34.4 1.0
OE2 A:GLU189 4.9 49.9 1.0
OD2 A:ASP342 4.9 34.9 1.0
CG A:ASP170 4.9 36.4 1.0

Manganese binding site 4 out of 8 in 4pj0

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Manganese binding site 4 out of 8 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:52.2
occ:1.00
MN4 A:OEX601 0.0 52.2 1.0
O A:HOH728 2.1 34.4 1.0
O4 A:OEX601 2.1 37.4 1.0
OE2 A:GLU333 2.1 41.6 1.0
OD1 A:ASP170 2.2 39.0 1.0
O A:HOH729 2.2 38.2 1.0
O5 A:OEX601 2.5 42.2 1.0
MN3 A:OEX601 3.0 40.2 1.0
CD A:GLU333 3.0 38.4 1.0
OE1 A:GLU333 3.2 40.2 1.0
CG A:ASP170 3.3 36.4 1.0
O A:HOH725 3.7 33.0 1.0
O A:HOH726 3.8 37.5 1.0
O2 A:OEX601 3.8 37.8 1.0
CA1 A:OEX601 3.8 57.2 1.0
OD2 A:ASP170 3.8 41.7 1.0
OD1 A:ASP61 4.3 32.8 1.0
CG A:GLU333 4.4 39.7 1.0
O A:HOH723 4.5 29.6 1.0
CB A:ASP170 4.5 27.9 1.0
O A:HOH724 4.5 35.7 1.0
CA A:ASP170 4.6 23.6 1.0
O A:SER169 4.6 37.2 1.0
NH2 C:ARG357 4.7 35.3 1.0
O3 A:OEX601 4.7 38.4 1.0
OE2 C:GLU354 4.8 40.4 1.0
O A:HOH730 4.9 38.7 1.0
MN1 A:OEX601 5.0 50.1 1.0

Manganese binding site 5 out of 8 in 4pj0

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Manganese binding site 5 out of 8 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:33.3
occ:1.00
MN1 a:OEX601 0.0 33.3 1.0
O1 a:OEX601 1.8 36.8 1.0
OE2 a:GLU189 1.8 48.5 1.0
O3 a:OEX601 1.8 33.8 1.0
NE2 a:HIS332 2.2 39.6 1.0
OD2 a:ASP342 2.3 42.6 1.0
O5 a:OEX601 2.6 42.2 1.0
MN2 a:OEX601 2.8 37.3 1.0
CD a:GLU189 2.9 44.1 1.0
CD2 a:HIS332 3.1 35.8 1.0
CG a:ASP342 3.2 38.8 1.0
CE1 a:HIS332 3.2 38.4 1.0
MN3 a:OEX601 3.3 42.8 1.0
OD1 a:ASP342 3.4 40.2 1.0
OE1 a:GLU189 3.4 51.8 1.0
CA1 a:OEX601 3.5 51.5 1.0
O2 a:OEX601 3.7 35.2 1.0
NE2 a:HIS337 3.9 40.5 1.0
OE1 a:GLU333 4.1 38.6 1.0
CG a:GLU189 4.1 40.1 1.0
CG a:HIS332 4.3 35.3 1.0
ND1 a:HIS332 4.3 41.0 1.0
CG1 a:VAL185 4.4 38.5 1.0
CE1 a:HIS337 4.4 39.0 1.0
OE2 c:GLU354 4.5 36.1 1.0
OE1 c:GLU354 4.6 34.2 1.0
CB a:ASP342 4.6 36.6 1.0
CD a:GLU333 4.8 38.3 1.0
O a:ALA344 4.8 51.4 1.0
C a:ALA344 4.9 44.7 1.0
MN4 a:OEX601 5.0 46.8 1.0
OE2 a:GLU333 5.0 43.0 1.0
CD c:GLU354 5.0 36.7 1.0

Manganese binding site 6 out of 8 in 4pj0

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Manganese binding site 6 out of 8 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:37.3
occ:1.00
MN2 a:OEX601 0.0 37.3 1.0
O1 a:OEX601 2.0 36.8 1.0
O2 a:OEX601 2.1 35.2 1.0
OD1 a:ASP342 2.1 40.2 1.0
O3 a:OEX601 2.1 33.8 1.0
OE1 c:GLU354 2.2 34.2 1.0
C a:ALA344 2.7 44.7 1.0
MN1 a:OEX601 2.8 33.3 1.0
CD c:GLU354 2.9 36.7 1.0
MN3 a:OEX601 2.9 42.8 1.0
O a:ALA344 3.0 51.4 1.0
CG a:ASP342 3.0 38.8 1.0
OE2 c:GLU354 3.1 36.1 1.0
OD2 a:ASP342 3.2 42.6 1.0
CA1 a:OEX601 3.3 51.5 1.0
NE2 a:HIS337 3.7 40.5 1.0
CA a:ALA344 3.9 43.7 1.0
O5 a:OEX601 3.9 42.2 1.0
N a:ALA344 4.1 45.9 1.0
CG c:GLU354 4.2 44.4 1.0
OE2 a:GLU189 4.3 48.5 1.0
CD2 a:HIS337 4.3 34.2 1.0
CB a:ASP342 4.4 36.6 1.0
CB a:ALA344 4.5 45.0 1.0
OE1 a:GLU333 4.5 38.6 1.0
O4 a:OEX601 4.5 40.3 1.0
NE2 a:HIS332 4.6 39.6 1.0
C a:ASP342 4.7 42.1 1.0
CA a:ASP342 4.8 35.5 1.0
CE1 a:HIS337 4.8 39.0 1.0
N a:LEU343 4.8 37.9 1.0
C a:LEU343 4.9 49.3 1.0
CD a:GLU189 4.9 44.1 1.0
OE1 a:GLU189 5.0 51.8 1.0

Manganese binding site 7 out of 8 in 4pj0

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Manganese binding site 7 out of 8 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:42.8
occ:1.00
MN3 a:OEX601 0.0 42.8 1.0
O2 a:OEX601 1.9 35.2 1.0
OE1 a:GLU333 2.0 38.6 1.0
O3 a:OEX601 2.0 33.8 1.0
O4 a:OEX601 2.1 40.3 1.0
OE2 c:GLU354 2.2 36.1 1.0
O5 a:OEX601 2.4 42.2 1.0
MN4 a:OEX601 2.9 46.8 1.0
MN2 a:OEX601 2.9 37.3 1.0
CD a:GLU333 2.9 38.3 1.0
CD c:GLU354 3.1 36.7 1.0
OE2 a:GLU333 3.2 43.0 1.0
MN1 a:OEX601 3.3 33.3 1.0
CA1 a:OEX601 3.4 51.5 1.0
OE1 c:GLU354 3.6 34.2 1.0
O1 a:OEX601 3.6 36.8 1.0
OD1 a:ASP170 4.1 50.1 1.0
NE2 a:HIS337 4.1 40.5 1.0
NH2 c:ARG357 4.2 42.5 1.0
O a:ALA344 4.2 51.4 1.0
CG c:GLU354 4.2 44.4 1.0
NE2 a:HIS332 4.3 39.6 1.0
CG a:GLU333 4.3 41.8 1.0
O a:HOH720 4.3 31.9 1.0
OD2 a:ASP170 4.5 40.8 1.0
O a:HOH722 4.6 38.0 1.0
CD2 a:HIS332 4.6 35.8 1.0
CE1 a:HIS337 4.6 39.0 1.0
O a:HOH721 4.6 41.6 1.0
C a:ALA344 4.7 44.7 1.0
OD1 a:ASP342 4.7 40.2 1.0
CB a:GLU333 4.7 39.8 1.0
CG a:ASP170 4.8 41.8 1.0
OE2 a:GLU189 4.9 48.5 1.0
OD2 a:ASP342 5.0 42.6 1.0

Manganese binding site 8 out of 8 in 4pj0

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Manganese binding site 8 out of 8 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:46.8
occ:1.00
MN4 a:OEX601 0.0 46.8 1.0
OD1 a:ASP170 2.0 50.1 1.0
O4 a:OEX601 2.1 40.3 1.0
O a:HOH722 2.1 38.0 1.0
OE2 a:GLU333 2.1 43.0 1.0
O a:HOH721 2.2 41.6 1.0
O5 a:OEX601 2.5 42.2 1.0
MN3 a:OEX601 2.9 42.8 1.0
CD a:GLU333 3.1 38.3 1.0
CG a:ASP170 3.2 41.8 1.0
OE1 a:GLU333 3.3 38.6 1.0
OD2 a:ASP170 3.7 40.8 1.0
O a:HOH720 3.8 31.9 1.0
CA1 a:OEX601 3.8 51.5 1.0
O2 a:OEX601 3.8 35.2 1.0
O a:HOH719 4.2 38.1 1.0
CB a:ASP170 4.4 38.7 1.0
OD1 a:ASP61 4.4 35.7 1.0
CG a:GLU333 4.5 41.8 1.0
CA a:ASP170 4.5 42.0 1.0
O3 a:OEX601 4.5 33.8 1.0
NH2 c:ARG357 4.6 42.5 1.0
O a:HOH718 4.6 29.5 1.0
O a:SER169 4.7 43.5 1.0
OE2 c:GLU354 4.9 36.1 1.0
N a:ASP170 4.9 36.7 1.0
MN1 a:OEX601 5.0 33.3 1.0
OG a:SER169 5.0 34.7 1.0

Reference:

J.Hellmich, M.Bommer, A.Burkhardt, M.Ibrahim, J.Kern, A.Meents, F.Mueh, H.Dobbek, A.Zouni. Native-Like Photosystem II Superstructure at 2.44 A Resolution Through Detergent Extraction From the Protein Crystal Structure 2014.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2014.09.007
Page generated: Tue Dec 15 04:26:19 2020

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