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Manganese in PDB 4ub6: Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser

Enzymatic activity of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser

All present enzymatic activity of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser:
1.10.3.9;

Protein crystallography data

The structure of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser, PDB code: 4ub6 was solved by M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimizu, K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.29 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.744, 229.989, 288.337, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.8

Other elements in 4ub6:

The structure of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser also contains other interesting chemical elements:

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

Manganese Binding Sites:

The binding sites of Manganese atom in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser (pdb code 4ub6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser, PDB code: 4ub6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4ub6

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Manganese binding site 1 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:20.2
occ:1.00
 MN1 A:OEX418 0.0 20.2 1.0
OE2 A:GLU189 1.8 16.0 1.0
O1 A:OEX418 1.9 20.9 1.0
O3 A:OEX418 1.9 24.6 1.0
NE2 A:HIS332 2.1 20.1 1.0
OD2 A:ASP342 2.2 18.3 1.0
MN2 A:OEX418 2.7 22.1 1.0
O5 A:OEX418 2.7 15.1 1.0
CD A:GLU189 2.8 15.2 1.0
CD2 A:HIS332 3.0 14.8 1.0
CG A:ASP342 3.0 19.7 1.0
CE1 A:HIS332 3.0 21.2 1.0
OD1 A:ASP342 3.2 16.8 1.0
MN3 A:OEX418 3.2 19.6 1.0
OE1 A:GLU189 3.3 30.1 1.0
CA1 A:OEX418 3.5 28.3 1.0
O2 A:OEX418 3.6 24.2 1.0
O A:HOH601 3.8 40.4 1.0
OE1 A:GLU333 4.0 19.4 1.0
NE2 A:HIS337 4.0 19.0 1.0
CG A:GLU189 4.1 17.3 1.0
ND1 A:HIS332 4.1 15.0 1.0
CG A:HIS332 4.2 14.7 1.0
OXT A:ALA344 4.2 27.9 1.0
O A:HOH571 4.3 31.6 1.0
OE1 C:GLU354 4.4 24.4 1.0
O A:ALA344 4.4 29.2 1.0
CB A:ASP342 4.4 16.4 1.0
OE2 C:GLU354 4.6 20.6 1.0
CG1 A:VAL185 4.7 17.5 1.0
CE1 A:HIS337 4.7 15.7 1.0
C A:ALA344 4.7 29.2 1.0
CD A:GLU333 4.7 30.2 1.0
CD C:GLU354 4.9 19.5 1.0
O4 A:OEX418 4.9 20.0 1.0
O A:HOH569 4.9 18.4 1.0
MN4 A:OEX418 5.0 21.5 1.0

Manganese binding site 2 out of 8 in 4ub6

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Manganese binding site 2 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:22.1
occ:1.00
 MN2 A:OEX418 0.0 22.1 1.0
O1 A:OEX418 1.8 20.9 1.0
O2 A:OEX418 1.9 24.2 1.0
OXT A:ALA344 1.9 27.9 1.0
O3 A:OEX418 1.9 24.6 1.0
OE1 C:GLU354 2.1 24.4 1.0
OD1 A:ASP342 2.1 16.8 1.0
MN1 A:OEX418 2.7 20.2 1.0
MN3 A:OEX418 2.7 19.6 1.0
C A:ALA344 2.8 29.2 1.0
CD C:GLU354 3.0 19.5 1.0
CG A:ASP342 3.0 19.7 1.0
O A:ALA344 3.0 29.2 1.0
OE2 C:GLU354 3.1 20.6 1.0
OD2 A:ASP342 3.2 18.3 1.0
CA1 A:OEX418 3.4 28.3 1.0
O5 A:OEX418 3.6 15.1 1.0
NE2 A:HIS337 3.9 19.0 1.0
O A:HOH601 4.0 40.4 1.0
O A:HOH630 4.0 18.4 1.0
O4 A:OEX418 4.2 20.0 1.0
OE2 A:GLU189 4.2 16.0 1.0
CA A:ALA344 4.2 28.3 1.0
OE1 A:GLU333 4.3 19.4 1.0
NE2 A:HIS332 4.4 20.1 1.0
N A:ALA344 4.4 32.9 1.0
CG C:GLU354 4.4 22.0 1.0
CD2 A:HIS337 4.4 19.9 1.0
CB A:ASP342 4.5 16.4 1.0
NH2 C:ARG357 4.7 20.2 1.0
OE1 A:GLU189 4.7 30.1 1.0
CD A:GLU189 4.8 15.2 1.0
CB C:GLU354 4.9 18.1 1.0
OD1 A:ASP170 4.9 28.3 1.0
CA A:ASP342 4.9 27.0 1.0
NH1 C:ARG357 5.0 27.0 1.0

Manganese binding site 3 out of 8 in 4ub6

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Manganese binding site 3 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:19.6
occ:1.00
 MN3 A:OEX418 0.0 19.6 1.0
O2 A:OEX418 1.8 24.2 1.0
O4 A:OEX418 1.9 20.0 1.0
OE1 A:GLU333 2.0 19.4 1.0
O3 A:OEX418 2.1 24.6 1.0
OE2 C:GLU354 2.1 20.6 1.0
O5 A:OEX418 2.2 15.1 1.0
MN2 A:OEX418 2.7 22.1 1.0
MN4 A:OEX418 2.9 21.5 1.0
CD A:GLU333 2.9 30.2 1.0
CD C:GLU354 3.1 19.5 1.0
OE2 A:GLU333 3.1 22.1 1.0
MN1 A:OEX418 3.2 20.2 1.0
OE1 C:GLU354 3.3 24.4 1.0
CA1 A:OEX418 3.5 28.3 1.0
O1 A:OEX418 3.5 20.9 1.0
O C:HOH665 4.0 24.6 1.0
NH2 C:ARG357 4.1 20.2 1.0
NE2 A:HIS332 4.1 20.1 1.0
OD2 A:ASP170 4.2 21.1 1.0
NE2 A:HIS337 4.2 19.0 1.0
O A:HOH567 4.2 15.6 1.0
OXT A:ALA344 4.3 27.9 1.0
OD1 A:ASP170 4.3 28.3 1.0
CD2 A:HIS332 4.3 14.8 1.0
CG A:GLU333 4.3 14.8 1.0
CG C:GLU354 4.5 22.0 1.0
O A:HOH607 4.6 15.8 1.0
OD1 A:ASP342 4.6 16.8 1.0
O A:ALA344 4.6 29.2 1.0
CG A:ASP170 4.7 19.9 1.0
O A:HOH608 4.7 18.8 1.0
CB A:GLU333 4.8 15.0 1.0
OE2 A:GLU189 4.8 16.0 1.0
CE1 A:HIS337 4.8 15.7 1.0
OD2 A:ASP342 4.8 18.3 1.0
C A:ALA344 4.9 29.2 1.0

Manganese binding site 4 out of 8 in 4ub6

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Manganese binding site 4 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:21.5
occ:1.00
 MN4 A:OEX418 0.0 21.5 1.0
O4 A:OEX418 1.9 20.0 1.0
OD2 A:ASP170 2.1 21.1 1.0
OE2 A:GLU333 2.1 22.1 1.0
O A:HOH607 2.1 15.8 1.0
O5 A:OEX418 2.3 15.1 1.0
O A:HOH608 2.3 18.8 1.0
MN3 A:OEX418 2.9 19.6 1.0
CD A:GLU333 3.0 30.2 1.0
CG A:ASP170 3.1 19.9 1.0
OE1 A:GLU333 3.4 19.4 1.0
OD1 A:ASP170 3.6 28.3 1.0
O2 A:OEX418 3.7 24.2 1.0
O A:HOH569 3.7 18.4 1.0
CA1 A:OEX418 3.8 28.3 1.0
O A:HOH567 3.8 15.6 1.0
O A:HOH560 3.9 18.5 1.0
O A:HOH557 4.1 24.1 1.0
OD1 A:ASP61 4.2 21.1 1.0
CG A:GLU333 4.4 14.8 1.0
CB A:ASP170 4.4 15.2 1.0
O A:SER169 4.5 20.7 1.0
NH2 C:ARG357 4.6 20.2 1.0
OE2 C:GLU354 4.6 20.6 1.0
CA A:ASP170 4.6 18.4 1.0
O3 A:OEX418 4.7 24.6 1.0
O A:HOH559 4.8 18.9 1.0
MN1 A:OEX418 5.0 20.2 1.0

Manganese binding site 5 out of 8 in 4ub6

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Manganese binding site 5 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:24.7
occ:1.00
 MN1 a:OEX416 0.0 24.7 1.0
OE2 a:GLU189 1.8 26.3 1.0
O1 a:OEX416 1.8 20.3 1.0
O3 a:OEX416 1.9 24.0 1.0
NE2 a:HIS332 2.1 22.2 1.0
OD2 a:ASP342 2.2 22.2 1.0
MN2 a:OEX416 2.6 22.9 1.0
O5 a:OEX416 2.7 18.8 1.0
CD a:GLU189 2.9 29.0 1.0
CE1 a:HIS332 3.0 19.3 1.0
CG a:ASP342 3.1 23.9 1.0
CD2 a:HIS332 3.1 18.7 1.0
MN3 a:OEX416 3.2 21.5 1.0
OD1 a:ASP342 3.2 20.4 1.0
OE1 a:GLU189 3.4 28.2 1.0
O2 a:OEX416 3.4 19.6 1.0
CA1 a:OEX416 3.5 34.0 1.0
O a:HOH561 3.8 47.5 1.0
NE2 a:HIS337 4.0 19.9 1.0
O a:HOH529 4.1 35.1 1.0
CG a:GLU189 4.1 30.6 1.0
OXT a:ALA344 4.1 20.4 1.0
ND1 a:HIS332 4.1 19.0 1.0
OE1 a:GLU333 4.2 20.9 1.0
CG a:HIS332 4.2 18.8 1.0
OE1 c:GLU354 4.3 28.0 1.0
CB a:ASP342 4.5 24.2 1.0
OE2 c:GLU354 4.5 23.0 1.0
O a:ALA344 4.5 21.8 1.0
CE1 a:HIS337 4.6 19.6 1.0
CG1 a:VAL185 4.7 19.4 1.0
C a:ALA344 4.7 37.0 1.0
CD c:GLU354 4.8 31.0 1.0
CD a:GLU333 4.9 21.1 1.0
O4 a:OEX416 5.0 18.9 1.0
MN4 a:OEX416 5.0 22.7 1.0

Manganese binding site 6 out of 8 in 4ub6

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Manganese binding site 6 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:22.9
occ:1.00
 MN2 a:OEX416 0.0 22.9 1.0
O1 a:OEX416 1.7 20.3 1.0
O2 a:OEX416 1.7 19.6 1.0
OXT a:ALA344 1.8 20.4 1.0
O3 a:OEX416 2.1 24.0 1.0
OE1 c:GLU354 2.1 28.0 1.0
OD1 a:ASP342 2.2 20.4 1.0
MN1 a:OEX416 2.6 24.7 1.0
MN3 a:OEX416 2.7 21.5 1.0
C a:ALA344 2.8 37.0 1.0
CD c:GLU354 2.9 31.0 1.0
OE2 c:GLU354 3.0 23.0 1.0
CG a:ASP342 3.1 23.9 1.0
O a:ALA344 3.1 21.8 1.0
OD2 a:ASP342 3.3 22.2 1.0
CA1 a:OEX416 3.3 34.0 1.0
O5 a:OEX416 3.6 18.8 1.0
NE2 a:HIS337 3.8 19.9 1.0
O a:HOH561 3.8 47.5 1.0
O c:HOH1070 4.0 22.6 1.0
OE2 a:GLU189 4.1 26.3 1.0
O4 a:OEX416 4.2 18.9 1.0
CA a:ALA344 4.2 31.0 1.0
CG c:GLU354 4.3 21.7 1.0
NE2 a:HIS332 4.3 22.2 1.0
N a:ALA344 4.4 34.0 1.0
OE1 a:GLU333 4.4 20.9 1.0
CD2 a:HIS337 4.4 20.3 1.0
CB a:ASP342 4.5 24.2 1.0
CD a:GLU189 4.8 29.0 1.0
OE1 a:GLU189 4.8 28.2 1.0
NH2 c:ARG357 4.8 22.6 1.0
CB c:GLU354 4.9 24.2 1.0
NH1 c:ARG357 4.9 25.8 1.0
CE1 a:HIS337 4.9 19.6 1.0
CA a:ASP342 4.9 21.3 1.0

Manganese binding site 7 out of 8 in 4ub6

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Manganese binding site 7 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:21.5
occ:1.00
 MN3 a:OEX416 0.0 21.5 1.0
O2 a:OEX416 1.8 19.6 1.0
O4 a:OEX416 1.9 18.9 1.0
O3 a:OEX416 2.0 24.0 1.0
O5 a:OEX416 2.0 18.8 1.0
OE1 a:GLU333 2.1 20.9 1.0
OE2 c:GLU354 2.1 23.0 1.0
MN2 a:OEX416 2.7 22.9 1.0
MN4 a:OEX416 2.8 22.7 1.0
CD a:GLU333 3.0 21.1 1.0
CD c:GLU354 3.1 31.0 1.0
MN1 a:OEX416 3.2 24.7 1.0
OE2 a:GLU333 3.3 21.1 1.0
CA1 a:OEX416 3.4 34.0 1.0
OE1 c:GLU354 3.4 28.0 1.0
O1 a:OEX416 3.4 20.3 1.0
NE2 a:HIS332 4.1 22.2 1.0
NH2 c:ARG357 4.1 22.6 1.0
OXT a:ALA344 4.2 20.4 1.0
OD2 a:ASP170 4.2 26.2 1.0
O c:HOH1060 4.2 24.4 1.0
NE2 a:HIS337 4.3 19.9 1.0
O a:HOH525 4.3 20.7 1.0
OD1 a:ASP170 4.3 37.8 1.0
O a:HOH566 4.3 17.9 1.0
CD2 a:HIS332 4.4 18.7 1.0
CG a:GLU333 4.4 18.8 1.0
CG c:GLU354 4.5 21.7 1.0
OD1 a:ASP342 4.6 20.4 1.0
O a:HOH567 4.6 20.7 1.0
O a:ALA344 4.6 21.8 1.0
OE2 a:GLU189 4.6 26.3 1.0
CG a:ASP170 4.7 27.9 1.0
CE1 a:HIS337 4.8 19.6 1.0
CB a:GLU333 4.8 18.4 1.0
O a:HOH527 4.8 39.4 1.0
C a:ALA344 4.8 37.0 1.0
OD2 a:ASP342 4.9 22.2 1.0

Manganese binding site 8 out of 8 in 4ub6

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Manganese binding site 8 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:22.7
occ:1.00
 MN4 a:OEX416 0.0 22.7 1.0
O a:HOH566 2.0 17.9 1.0
O4 a:OEX416 2.0 18.9 1.0
OD2 a:ASP170 2.1 26.2 1.0
OE2 a:GLU333 2.1 21.1 1.0
O a:HOH567 2.2 20.7 1.0
O5 a:OEX416 2.3 18.8 1.0
MN3 a:OEX416 2.8 21.5 1.0
CD a:GLU333 3.0 21.1 1.0
CG a:ASP170 3.2 27.9 1.0
OE1 a:GLU333 3.2 20.9 1.0
O a:HOH527 3.6 39.4 1.0
OD1 a:ASP170 3.6 37.8 1.0
O a:HOH525 3.8 20.7 1.0
O2 a:OEX416 3.8 19.6 1.0
CA1 a:OEX416 3.9 34.0 1.0
O a:HOH519 3.9 20.2 1.0
OD1 a:ASP61 4.1 24.6 1.0
O a:HOH516 4.2 20.7 1.0
O a:SER169 4.3 17.7 1.0
CG a:GLU333 4.4 18.8 1.0
CB a:ASP170 4.5 23.4 1.0
O3 a:OEX416 4.5 24.0 1.0
NH2 c:ARG357 4.5 22.6 1.0
OE2 c:GLU354 4.6 23.0 1.0
CA a:ASP170 4.6 18.2 1.0
O a:HOH518 4.7 20.2 1.0
C a:SER169 4.9 20.1 1.0
CG a:ASP61 4.9 21.6 1.0
MN1 a:OEX416 5.0 24.7 1.0

Reference:

M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimizu, K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen. Native Structure of Photosystem II at 1.95A Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13991
Page generated: Sat Oct 5 21:18:33 2024

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