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Manganese in PDB 4ub8: Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser

Enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser

All present enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser:
1.10.3.9;

Protein crystallography data

The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8 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) 61.90 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.807, 230.001, 288.502, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.5

Other elements in 4ub8:

The structure of Native Structure of Photosystem II (Dataset-2) 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-2) By A Femtosecond X-Ray Laser (pdb code 4ub8). 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-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4ub8

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Manganese binding site 1 out of 8 in the Native Structure of Photosystem II (Dataset-2) 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-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:21.4
occ:1.00
 MN1 A:OEX418 0.0 21.4 1.0
O3 A:OEX418 1.8 21.0 1.0
OE2 A:GLU189 1.8 23.3 1.0
O1 A:OEX418 1.8 28.1 1.0
NE2 A:HIS332 2.1 16.8 1.0
OD2 A:ASP342 2.3 17.5 1.0
O5 A:OEX418 2.7 16.7 1.0
MN2 A:OEX418 2.7 23.2 1.0
CD A:GLU189 2.8 16.9 1.0
CE1 A:HIS332 3.1 22.1 1.0
CD2 A:HIS332 3.1 17.6 1.0
CG A:ASP342 3.1 17.8 1.0
OD1 A:ASP342 3.3 20.7 1.0
MN3 A:OEX418 3.3 22.1 1.0
OE1 A:GLU189 3.3 30.5 1.0
CA1 A:OEX418 3.5 32.5 1.0
O2 A:OEX418 3.7 23.6 1.0
O A:HOH602 3.9 48.0 1.0
NE2 A:HIS337 4.0 24.1 1.0
OE1 A:GLU333 4.0 22.1 1.0
CG A:GLU189 4.1 16.9 1.0
ND1 A:HIS332 4.2 20.5 1.0
CG A:HIS332 4.2 17.5 1.0
O A:HOH572 4.3 33.3 1.0
OXT A:ALA344 4.4 21.9 1.0
OE1 C:GLU354 4.4 22.6 1.0
O A:ALA344 4.5 31.4 1.0
CB A:ASP342 4.5 18.0 1.0
CG1 A:VAL185 4.5 24.4 1.0
CE1 A:HIS337 4.6 18.1 1.0
OE2 C:GLU354 4.7 21.4 1.0
CD A:GLU333 4.8 30.2 1.0
C A:ALA344 4.8 30.3 1.0
O A:HOH570 4.9 25.3 1.0
O A:HOH569 4.9 41.7 1.0
O4 A:OEX418 4.9 23.8 1.0
CD C:GLU354 5.0 37.4 1.0
MN4 A:OEX418 5.0 24.2 1.0

Manganese binding site 2 out of 8 in 4ub8

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Manganese binding site 2 out of 8 in the Native Structure of Photosystem II (Dataset-2) 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-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:23.2
occ:1.00
 MN2 A:OEX418 0.0 23.2 1.0
O2 A:OEX418 1.8 23.6 1.0
O1 A:OEX418 1.9 28.1 1.0
OXT A:ALA344 2.0 21.9 1.0
O3 A:OEX418 2.0 21.0 1.0
OE1 C:GLU354 2.1 22.6 1.0
OD1 A:ASP342 2.2 20.7 1.0
MN3 A:OEX418 2.7 22.1 1.0
MN1 A:OEX418 2.7 21.4 1.0
C A:ALA344 2.8 30.3 1.0
CD C:GLU354 3.0 37.4 1.0
O A:ALA344 3.0 31.4 1.0
CG A:ASP342 3.1 17.8 1.0
OE2 C:GLU354 3.2 21.4 1.0
CA1 A:OEX418 3.3 32.5 1.0
OD2 A:ASP342 3.3 17.5 1.0
O5 A:OEX418 3.7 16.7 1.0
NE2 A:HIS337 3.8 24.1 1.0
O A:HOH602 4.1 48.0 1.0
O A:HOH632 4.1 22.3 1.0
O4 A:OEX418 4.1 23.8 1.0
CA A:ALA344 4.2 27.7 1.0
N A:ALA344 4.3 44.2 1.0
OE2 A:GLU189 4.3 23.3 1.0
OE1 A:GLU333 4.3 22.1 1.0
CG C:GLU354 4.4 27.4 1.0
CD2 A:HIS337 4.4 17.9 1.0
NE2 A:HIS332 4.4 16.8 1.0
CB A:ASP342 4.5 18.0 1.0
NH2 C:ARG357 4.7 21.2 1.0
O A:HOH569 4.8 41.7 1.0
CB C:GLU354 4.8 28.6 1.0
NH1 C:ARG357 4.8 26.1 1.0
OE1 A:GLU189 4.9 30.5 1.0
OD1 A:ASP170 4.9 34.4 1.0
CA A:ASP342 4.9 26.6 1.0
CD A:GLU189 4.9 16.9 1.0
CE1 A:HIS337 4.9 18.1 1.0
C A:ASP342 5.0 22.9 1.0

Manganese binding site 3 out of 8 in 4ub8

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Manganese binding site 3 out of 8 in the Native Structure of Photosystem II (Dataset-2) 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-2) 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
 MN3 A:OEX418 0.0 22.1 1.0
O4 A:OEX418 1.9 23.8 1.0
O2 A:OEX418 2.0 23.6 1.0
OE1 A:GLU333 2.0 22.1 1.0
O3 A:OEX418 2.1 21.0 1.0
OE2 C:GLU354 2.2 21.4 1.0
O5 A:OEX418 2.3 16.7 1.0
MN2 A:OEX418 2.7 23.2 1.0
MN4 A:OEX418 2.9 24.2 1.0
CD A:GLU333 2.9 30.2 1.0
CD C:GLU354 3.1 37.4 1.0
OE2 A:GLU333 3.1 24.0 1.0
MN1 A:OEX418 3.3 21.4 1.0
OE1 C:GLU354 3.3 22.6 1.0
CA1 A:OEX418 3.4 32.5 1.0
O1 A:OEX418 3.6 28.1 1.0
NH2 C:ARG357 4.1 21.2 1.0
NE2 A:HIS332 4.1 16.8 1.0
NE2 A:HIS337 4.1 24.1 1.0
O C:HOH660 4.1 33.9 1.0
OD2 A:ASP170 4.2 24.8 1.0
O A:HOH568 4.2 19.9 1.0
OD1 A:ASP170 4.3 34.4 1.0
OXT A:ALA344 4.3 21.9 1.0
CG A:GLU333 4.3 17.7 1.0
CD2 A:HIS332 4.4 17.6 1.0
CG C:GLU354 4.5 27.4 1.0
O A:ALA344 4.6 31.4 1.0
OD1 A:ASP342 4.6 20.7 1.0
O A:HOH608 4.6 30.3 1.0
O A:HOH609 4.6 20.1 1.0
CE1 A:HIS337 4.7 18.1 1.0
CG A:ASP170 4.7 22.8 1.0
CB A:GLU333 4.7 18.1 1.0
OE2 A:GLU189 4.8 23.3 1.0
OD2 A:ASP342 4.9 17.5 1.0
C A:ALA344 4.9 30.3 1.0
O A:HOH570 4.9 25.3 1.0

Manganese binding site 4 out of 8 in 4ub8

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Manganese binding site 4 out of 8 in the Native Structure of Photosystem II (Dataset-2) 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-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:24.2
occ:1.00
 MN4 A:OEX418 0.0 24.2 1.0
OD2 A:ASP170 2.0 24.8 1.0
O4 A:OEX418 2.0 23.8 1.0
OE2 A:GLU333 2.1 24.0 1.0
O A:HOH608 2.1 30.3 1.0
O A:HOH609 2.3 20.1 1.0
O5 A:OEX418 2.4 16.7 1.0
MN3 A:OEX418 2.9 22.1 1.0
CD A:GLU333 3.0 30.2 1.0
CG A:ASP170 3.1 22.8 1.0
OE1 A:GLU333 3.4 22.1 1.0
OD1 A:ASP170 3.5 34.4 1.0
O A:HOH570 3.6 25.3 1.0
CA1 A:OEX418 3.7 32.5 1.0
O A:HOH568 3.8 19.9 1.0
O2 A:OEX418 4.0 23.6 1.0
O A:HOH561 4.2 23.0 1.0
OD1 A:ASP61 4.2 18.4 1.0
O A:HOH558 4.2 26.8 1.0
CG A:GLU333 4.4 17.7 1.0
CB A:ASP170 4.4 18.8 1.0
O A:SER169 4.5 23.5 1.0
NH2 C:ARG357 4.6 21.2 1.0
CA A:ASP170 4.6 19.7 1.0
OE2 C:GLU354 4.6 21.4 1.0
O3 A:OEX418 4.7 21.0 1.0
O A:HOH560 4.8 21.0 1.0
MN1 A:OEX418 5.0 21.4 1.0

Manganese binding site 5 out of 8 in 4ub8

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Manganese binding site 5 out of 8 in the Native Structure of Photosystem II (Dataset-2) 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-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn415

b:27.4
occ:1.00
 MN1 a:OEX415 0.0 27.4 1.0
O1 a:OEX415 1.7 24.0 1.0
O3 a:OEX415 1.8 35.8 1.0
OE2 a:GLU189 1.8 31.2 1.0
NE2 a:HIS332 2.2 26.5 1.0
OD2 a:ASP342 2.2 22.9 1.0
MN2 a:OEX415 2.7 25.3 1.0
O5 a:OEX415 2.7 20.2 1.0
CD a:GLU189 2.9 35.4 1.0
MN3 a:OEX415 3.1 25.0 1.0
CG a:ASP342 3.1 22.7 1.0
CE1 a:HIS332 3.1 21.3 1.0
CD2 a:HIS332 3.1 20.1 1.0
OD1 a:ASP342 3.3 23.5 1.0
OE1 a:GLU189 3.4 30.9 1.0
CA1 a:OEX415 3.4 37.4 1.0
O2 a:OEX415 3.6 22.9 1.0
O a:HOH560 3.9 45.6 1.0
NE2 a:HIS337 3.9 21.3 1.0
OE1 a:GLU333 4.0 31.7 1.0
CG a:GLU189 4.2 27.2 1.0
ND1 a:HIS332 4.2 20.4 1.0
OXT a:ALA344 4.3 21.9 1.0
CG a:HIS332 4.3 20.4 1.0
O a:HOH528 4.3 39.9 1.0
OE1 c:GLU354 4.4 28.4 1.0
O a:ALA344 4.5 29.1 1.0
OE2 c:GLU354 4.5 24.0 1.0
CB a:ASP342 4.5 27.3 1.0
CE1 a:HIS337 4.6 26.3 1.0
CG1 a:VAL185 4.7 21.6 1.0
CD a:GLU333 4.7 25.0 1.0
C a:ALA344 4.7 34.1 1.0
O4 a:OEX415 4.8 20.3 1.0
CD c:GLU354 4.8 28.3 1.0
MN4 a:OEX415 4.9 25.2 1.0
O a:HOH526 4.9 36.8 1.0
CD2 a:HIS337 5.0 21.7 1.0

Manganese binding site 6 out of 8 in 4ub8

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Manganese binding site 6 out of 8 in the Native Structure of Photosystem II (Dataset-2) 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-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn415

b:25.3
occ:1.00
 MN2 a:OEX415 0.0 25.3 1.0
O1 a:OEX415 1.8 24.0 1.0
O2 a:OEX415 1.8 22.9 1.0
OXT a:ALA344 1.9 21.9 1.0
O3 a:OEX415 2.1 35.8 1.0
OE1 c:GLU354 2.1 28.4 1.0
OD1 a:ASP342 2.2 23.5 1.0
MN1 a:OEX415 2.7 27.4 1.0
MN3 a:OEX415 2.7 25.0 1.0
C a:ALA344 2.7 34.1 1.0
CD c:GLU354 2.9 28.3 1.0
O a:ALA344 3.0 29.1 1.0
CG a:ASP342 3.0 22.7 1.0
OE2 c:GLU354 3.1 24.0 1.0
OD2 a:ASP342 3.2 22.9 1.0
CA1 a:OEX415 3.3 37.4 1.0
O5 a:OEX415 3.8 20.2 1.0
O a:HOH560 3.9 45.6 1.0
NE2 a:HIS337 3.9 21.3 1.0
O c:HOH671 4.0 25.1 1.0
CA a:ALA344 4.1 33.2 1.0
OE2 a:GLU189 4.2 31.2 1.0
O4 a:OEX415 4.2 20.3 1.0
N a:ALA344 4.4 37.2 1.0
CG c:GLU354 4.4 32.3 1.0
CD2 a:HIS337 4.4 21.7 1.0
OE1 a:GLU333 4.4 31.7 1.0
CB a:ASP342 4.4 27.3 1.0
NE2 a:HIS332 4.5 26.5 1.0
NH2 c:ARG357 4.8 24.5 1.0
NH1 c:ARG357 4.8 26.6 1.0
CA a:ASP342 4.9 22.8 1.0
CB c:GLU354 4.9 27.8 1.0
CD a:GLU189 4.9 35.4 1.0
OE1 a:GLU189 4.9 30.9 1.0
O a:HOH525 4.9 46.4 1.0
C a:ASP342 5.0 32.8 1.0

Manganese binding site 7 out of 8 in 4ub8

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Manganese binding site 7 out of 8 in the Native Structure of Photosystem II (Dataset-2) 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-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn415

b:25.0
occ:1.00
 MN3 a:OEX415 0.0 25.0 1.0
O4 a:OEX415 1.9 20.3 1.0
O2 a:OEX415 2.0 22.9 1.0
O3 a:OEX415 2.0 35.8 1.0
OE1 a:GLU333 2.1 31.7 1.0
OE2 c:GLU354 2.1 24.0 1.0
O5 a:OEX415 2.3 20.2 1.0
MN2 a:OEX415 2.7 25.3 1.0
MN4 a:OEX415 2.9 25.2 1.0
CD a:GLU333 3.0 25.0 1.0
CD c:GLU354 3.1 28.3 1.0
MN1 a:OEX415 3.1 27.4 1.0
OE2 a:GLU333 3.2 23.4 1.0
CA1 a:OEX415 3.3 37.4 1.0
OE1 c:GLU354 3.4 28.4 1.0
O1 a:OEX415 3.4 24.0 1.0
O c:HOH661 4.0 26.8 1.0
NH2 c:ARG357 4.1 24.5 1.0
NE2 a:HIS332 4.1 26.5 1.0
OXT a:ALA344 4.2 21.9 1.0
NE2 a:HIS337 4.2 21.3 1.0
OD2 a:ASP170 4.2 25.0 1.0
O a:HOH524 4.3 20.2 1.0
OD1 a:ASP170 4.4 39.1 1.0
CD2 a:HIS332 4.4 20.1 1.0
CG a:GLU333 4.4 27.8 1.0
CG c:GLU354 4.5 32.3 1.0
O a:ALA344 4.5 29.1 1.0
OD1 a:ASP342 4.6 23.5 1.0
O a:HOH565 4.6 26.9 1.0
O a:HOH566 4.7 20.6 1.0
OE2 a:GLU189 4.7 31.2 1.0
CG a:ASP170 4.7 30.3 1.0
OD2 a:ASP342 4.8 22.9 1.0
CB a:GLU333 4.8 20.3 1.0
C a:ALA344 4.8 34.1 1.0
CE1 a:HIS337 4.8 26.3 1.0
O a:HOH526 4.9 36.8 1.0

Manganese binding site 8 out of 8 in 4ub8

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Manganese binding site 8 out of 8 in the Native Structure of Photosystem II (Dataset-2) 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-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn415

b:25.2
occ:1.00
 MN4 a:OEX415 0.0 25.2 1.0
OD2 a:ASP170 2.0 25.0 1.0
O4 a:OEX415 2.0 20.3 1.0
OE2 a:GLU333 2.1 23.4 1.0
O a:HOH565 2.1 26.9 1.0
O a:HOH566 2.2 20.6 1.0
O5 a:OEX415 2.3 20.2 1.0
MN3 a:OEX415 2.9 25.0 1.0
CD a:GLU333 3.0 25.0 1.0
CG a:ASP170 3.1 30.3 1.0
OE1 a:GLU333 3.3 31.7 1.0
OD1 a:ASP170 3.5 39.1 1.0
O a:HOH526 3.6 36.8 1.0
CA1 a:OEX415 3.8 37.4 1.0
O a:HOH524 4.0 20.2 1.0
O a:HOH515 4.0 28.1 1.0
O a:HOH518 4.1 25.4 1.0
O2 a:OEX415 4.1 22.9 1.0
OD1 a:ASP61 4.2 24.1 1.0
CB a:ASP170 4.4 26.4 1.0
CG a:GLU333 4.4 27.8 1.0
O a:SER169 4.5 20.5 1.0
CA a:ASP170 4.6 26.1 1.0
O3 a:OEX415 4.6 35.8 1.0
OE2 c:GLU354 4.6 24.0 1.0
NH2 c:ARG357 4.7 24.5 1.0
O a:HOH517 4.8 21.9 1.0
MN1 a:OEX415 4.9 27.4 1.0
C a:SER169 5.0 25.3 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 21:18:31 2024

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