Manganese in PDB 7d1t: Cryo-Em Structure of Psii at 1.95 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution:
1.10.3.9;

Other elements in 7d1t:

The structure of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Chlorine (Cl) 4 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution (pdb code 7d1t). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution, PDB code: 7d1t:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 7d1t

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Manganese binding site 1 out of 8 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:11.4
occ:0.87
MN1 A:OEX401 0.0 11.4 0.9
OE2 A:GLU189 2.1 8.6 1.0
O1 A:OEX401 2.1 11.5 0.9
O3 A:OEX401 2.1 11.5 0.9
OD2 A:ASP342 2.2 15.3 1.0
NE2 A:HIS332 2.3 11.9 1.0
O5 A:OEX401 2.7 11.4 0.9
MN2 A:OEX401 2.8 11.7 0.9
CD A:GLU189 2.9 8.5 1.0
CG A:ASP342 3.2 15.4 1.0
CE1 A:HIS332 3.2 11.9 1.0
CD2 A:HIS332 3.3 11.9 1.0
OE1 A:GLU189 3.3 8.5 1.0
MN3 A:OEX401 3.4 11.5 0.9
OD1 A:ASP342 3.4 15.4 1.0
CA1 A:OEX401 3.5 11.3 0.9
O2 A:OEX401 3.8 11.5 0.9
CG A:GLU189 4.0 8.4 1.0
NE2 A:HIS337 4.1 14.2 1.0
OE1 A:GLU333 4.1 12.7 1.0
O A:HOH581 4.2 15.9 1.0
ND1 A:HIS332 4.3 11.9 1.0
O A:HOH509 4.4 11.8 1.0
OE1 C:GLU354 4.4 13.3 1.0
CG A:HIS332 4.4 11.9 1.0
OXT A:ALA344 4.4 16.0 0.5
CB A:ASP342 4.5 15.5 1.0
OE2 C:GLU354 4.7 13.3 1.0
CG1 A:VAL185 4.7 6.9 1.0
CE1 A:HIS337 4.7 14.2 1.0
CD A:GLU333 4.9 12.7 1.0
CD C:GLU354 5.0 13.3 1.0

Manganese binding site 2 out of 8 in 7d1t

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Manganese binding site 2 out of 8 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:11.7
occ:0.87
MN2 A:OEX401 0.0 11.7 0.9
OXT A:ALA344 1.9 16.0 0.5
OD1 A:ASP342 2.1 15.4 1.0
O1 A:OEX401 2.2 11.5 0.9
OE1 C:GLU354 2.2 13.3 1.0
O2 A:OEX401 2.2 11.5 0.9
O3 A:OEX401 2.3 11.5 0.9
MN1 A:OEX401 2.8 11.4 0.9
C A:ALA344 2.9 16.1 0.5
CG A:ASP342 2.9 15.4 1.0
OD2 A:ASP342 3.1 15.3 1.0
MN3 A:OEX401 3.1 11.5 0.9
CD C:GLU354 3.1 13.3 1.0
O A:ALA344 3.4 16.0 0.5
OE2 C:GLU354 3.4 13.3 1.0
CA1 A:OEX401 3.5 11.3 0.9
CA A:ALA344 4.0 16.1 0.5
O A:ALA344 4.1 16.0 0.5
NE2 A:HIS337 4.1 14.2 1.0
N A:ALA344 4.1 16.1 0.5
CA A:ALA344 4.2 16.1 0.5
O A:HOH581 4.2 15.9 1.0
O5 A:OEX401 4.2 11.4 0.9
C A:ALA344 4.3 16.1 0.5
CB A:ASP342 4.3 15.5 1.0
O C:HOH766 4.4 16.7 1.0
CG C:GLU354 4.5 13.3 1.0
N A:ALA344 4.5 16.1 0.5
CD2 A:HIS337 4.6 14.2 1.0
OE2 A:GLU189 4.6 8.6 1.0
C A:ASP342 4.7 15.7 1.0
CA A:ASP342 4.7 15.6 1.0
N A:LEU343 4.8 15.8 0.5
OE1 A:GLU333 4.8 12.7 1.0
NE2 A:HIS332 4.8 11.9 1.0
N A:LEU343 4.9 15.8 0.5
CB C:GLU354 4.9 13.2 1.0
C A:LEU343 4.9 16.0 0.5

Manganese binding site 3 out of 8 in 7d1t

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Manganese binding site 3 out of 8 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:11.5
occ:0.87
MN3 A:OEX401 0.0 11.5 0.9
OE1 A:GLU333 2.1 12.7 1.0
OE2 C:GLU354 2.2 13.3 1.0
O2 A:OEX401 2.2 11.5 0.9
O4 A:OEX401 2.3 11.5 0.9
O3 A:OEX401 2.5 11.5 0.9
O5 A:OEX401 2.6 11.4 0.9
MN4 A:OEX401 3.0 11.3 0.9
CD A:GLU333 3.0 12.7 1.0
MN2 A:OEX401 3.1 11.7 0.9
CD C:GLU354 3.1 13.3 1.0
OE2 A:GLU333 3.3 12.8 1.0
CA1 A:OEX401 3.3 11.3 0.9
MN1 A:OEX401 3.4 11.4 0.9
OE1 C:GLU354 3.4 13.3 1.0
O C:HOH657 3.7 14.2 1.0
O1 A:OEX401 4.0 11.5 0.9
NH2 C:ARG357 4.0 12.8 1.0
OD2 A:ASP170 4.1 8.4 1.0
O A:HOH514 4.3 11.8 1.0
OD1 A:ASP170 4.3 8.4 1.0
OXT A:ALA344 4.4 16.0 0.5
CG A:GLU333 4.4 12.7 1.0
NE2 A:HIS332 4.4 11.9 1.0
NE2 A:HIS337 4.5 14.2 1.0
CG C:GLU354 4.5 13.3 1.0
O A:HOH563 4.5 13.1 1.0
CG A:ASP170 4.7 8.4 1.0
CD2 A:HIS332 4.7 11.9 1.0
CB A:GLU333 4.8 12.6 1.0
OD1 A:ASP342 4.8 15.4 1.0
O A:HOH590 4.8 12.6 1.0
O A:ALA344 4.8 16.0 0.5
OD2 A:ASP342 5.0 15.3 1.0
CZ C:ARG357 5.0 12.8 1.0

Manganese binding site 4 out of 8 in 7d1t

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Manganese binding site 4 out of 8 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:11.3
occ:0.87
MN4 A:OEX401 0.0 11.3 0.9
O4 A:OEX401 1.8 11.5 0.9
O A:HOH563 2.0 13.1 1.0
OE2 A:GLU333 2.1 12.8 1.0
OD2 A:ASP170 2.2 8.4 1.0
O A:HOH590 2.4 12.6 1.0
O5 A:OEX401 2.5 11.4 0.9
MN3 A:OEX401 3.0 11.5 0.9
CD A:GLU333 3.1 12.7 1.0
CG A:ASP170 3.2 8.4 1.0
OE1 A:GLU333 3.3 12.7 1.0
CA1 A:OEX401 3.7 11.3 0.9
OD1 A:ASP170 3.7 8.4 1.0
O A:HOH620 3.8 14.7 1.0
O A:HOH514 3.9 11.8 1.0
O A:HOH628 4.0 11.0 1.0
O A:HOH629 4.0 11.8 1.0
O2 A:OEX401 4.1 11.5 0.9
O A:SER169 4.3 8.3 1.0
CB A:ASP170 4.4 8.3 1.0
CG A:GLU333 4.4 12.7 1.0
O A:HOH529 4.4 12.9 1.0
OD2 A:ASP61 4.5 12.6 1.0
CA A:ASP170 4.5 8.2 1.0
NH2 C:ARG357 4.6 12.8 1.0
OE2 C:GLU354 4.8 13.3 1.0
C A:SER169 4.8 8.3 1.0
N A:ASP170 4.9 8.2 1.0
O A:HOH517 4.9 10.3 1.0

Manganese binding site 5 out of 8 in 7d1t

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Manganese binding site 5 out of 8 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:11.4
occ:0.87
MN1 a:OEX401 0.0 11.4 0.9
OE2 a:GLU189 2.1 8.6 1.0
O1 a:OEX401 2.1 11.5 0.9
O3 a:OEX401 2.1 11.5 0.9
OD2 a:ASP342 2.2 15.3 1.0
NE2 a:HIS332 2.3 11.9 1.0
O5 a:OEX401 2.7 11.4 0.9
MN2 a:OEX401 2.8 11.7 0.9
CD a:GLU189 2.9 8.5 1.0
CG a:ASP342 3.2 15.4 1.0
CE1 a:HIS332 3.2 11.9 1.0
CD2 a:HIS332 3.3 11.9 1.0
OE1 a:GLU189 3.3 8.5 1.0
MN3 a:OEX401 3.4 11.5 0.9
OD1 a:ASP342 3.4 15.4 1.0
CA1 a:OEX401 3.5 11.3 0.9
O2 a:OEX401 3.8 11.5 0.9
CG a:GLU189 4.0 8.4 1.0
NE2 a:HIS337 4.1 14.2 1.0
OE1 a:GLU333 4.1 12.7 1.0
O a:HOH581 4.2 15.9 1.0
ND1 a:HIS332 4.3 11.9 1.0
O a:HOH509 4.4 11.8 1.0
OE1 c:GLU354 4.4 13.3 1.0
CG a:HIS332 4.4 11.9 1.0
OXT a:ALA344 4.4 16.0 0.5
CB a:ASP342 4.5 15.5 1.0
OE2 c:GLU354 4.7 13.3 1.0
CG1 a:VAL185 4.7 6.9 1.0
CE1 a:HIS337 4.7 14.2 1.0
CD a:GLU333 4.9 12.7 1.0
CD c:GLU354 5.0 13.3 1.0

Manganese binding site 6 out of 8 in 7d1t

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Manganese binding site 6 out of 8 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:11.7
occ:0.87
MN2 a:OEX401 0.0 11.7 0.9
OXT a:ALA344 1.9 16.0 0.5
OD1 a:ASP342 2.1 15.4 1.0
O1 a:OEX401 2.2 11.5 0.9
OE1 c:GLU354 2.2 13.3 1.0
O2 a:OEX401 2.2 11.5 0.9
O3 a:OEX401 2.3 11.5 0.9
MN1 a:OEX401 2.8 11.4 0.9
C a:ALA344 2.9 16.1 0.5
CG a:ASP342 2.9 15.4 1.0
OD2 a:ASP342 3.1 15.3 1.0
MN3 a:OEX401 3.1 11.5 0.9
CD c:GLU354 3.1 13.3 1.0
O a:ALA344 3.4 16.0 0.5
OE2 c:GLU354 3.4 13.3 1.0
CA1 a:OEX401 3.5 11.3 0.9
CA a:ALA344 4.0 16.1 0.5
O a:ALA344 4.1 16.0 0.5
NE2 a:HIS337 4.1 14.2 1.0
N a:ALA344 4.1 16.1 0.5
CA a:ALA344 4.2 16.1 0.5
O a:HOH581 4.2 15.9 1.0
O5 a:OEX401 4.2 11.4 0.9
C a:ALA344 4.3 16.1 0.5
CB a:ASP342 4.3 15.5 1.0
O c:HOH766 4.4 16.7 1.0
CG c:GLU354 4.5 13.3 1.0
N a:ALA344 4.5 16.1 0.5
CD2 a:HIS337 4.6 14.2 1.0
OE2 a:GLU189 4.6 8.6 1.0
C a:ASP342 4.7 15.7 1.0
CA a:ASP342 4.7 15.6 1.0
N a:LEU343 4.8 15.8 0.5
OE1 a:GLU333 4.8 12.7 1.0
NE2 a:HIS332 4.8 11.9 1.0
N a:LEU343 4.9 15.8 0.5
C a:LEU343 4.9 16.0 0.5
CB c:GLU354 4.9 13.2 1.0

Manganese binding site 7 out of 8 in 7d1t

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Manganese binding site 7 out of 8 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:11.5
occ:0.87
MN3 a:OEX401 0.0 11.5 0.9
OE1 a:GLU333 2.1 12.7 1.0
OE2 c:GLU354 2.2 13.3 1.0
O2 a:OEX401 2.2 11.5 0.9
O4 a:OEX401 2.3 11.5 0.9
O3 a:OEX401 2.5 11.5 0.9
O5 a:OEX401 2.6 11.4 0.9
MN4 a:OEX401 3.0 11.3 0.9
CD a:GLU333 3.0 12.7 1.0
MN2 a:OEX401 3.1 11.7 0.9
CD c:GLU354 3.1 13.3 1.0
OE2 a:GLU333 3.3 12.8 1.0
CA1 a:OEX401 3.3 11.3 0.9
MN1 a:OEX401 3.4 11.4 0.9
OE1 c:GLU354 3.4 13.3 1.0
O c:HOH658 3.7 14.2 1.0
O1 a:OEX401 4.0 11.5 0.9
NH2 c:ARG357 4.0 12.8 1.0
OD2 a:ASP170 4.1 8.4 1.0
O a:HOH514 4.3 11.8 1.0
OD1 a:ASP170 4.3 8.4 1.0
OXT a:ALA344 4.4 16.0 0.5
CG a:GLU333 4.4 12.7 1.0
NE2 a:HIS332 4.4 11.9 1.0
NE2 a:HIS337 4.5 14.2 1.0
CG c:GLU354 4.5 13.3 1.0
O a:HOH563 4.5 13.1 1.0
CG a:ASP170 4.7 8.4 1.0
CD2 a:HIS332 4.7 11.9 1.0
CB a:GLU333 4.8 12.6 1.0
OD1 a:ASP342 4.8 15.4 1.0
O a:HOH590 4.8 12.6 1.0
O a:ALA344 4.8 16.0 0.5
OD2 a:ASP342 5.0 15.3 1.0
CZ c:ARG357 5.0 12.8 1.0

Manganese binding site 8 out of 8 in 7d1t

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Manganese binding site 8 out of 8 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:11.3
occ:0.87
MN4 a:OEX401 0.0 11.3 0.9
O4 a:OEX401 1.8 11.5 0.9
O a:HOH563 2.0 13.1 1.0
OE2 a:GLU333 2.1 12.8 1.0
OD2 a:ASP170 2.2 8.4 1.0
O a:HOH590 2.4 12.6 1.0
O5 a:OEX401 2.5 11.4 0.9
MN3 a:OEX401 3.0 11.5 0.9
CD a:GLU333 3.1 12.7 1.0
CG a:ASP170 3.2 8.4 1.0
OE1 a:GLU333 3.3 12.7 1.0
CA1 a:OEX401 3.7 11.3 0.9
OD1 a:ASP170 3.7 8.4 1.0
O a:HOH620 3.8 14.7 1.0
O a:HOH514 3.9 11.8 1.0
O a:HOH628 4.0 11.0 1.0
O a:HOH629 4.0 11.8 1.0
O2 a:OEX401 4.1 11.5 0.9
O a:SER169 4.3 8.3 1.0
CB a:ASP170 4.4 8.3 1.0
CG a:GLU333 4.4 12.7 1.0
O a:HOH529 4.4 12.9 1.0
OD2 a:ASP61 4.5 12.6 1.0
CA a:ASP170 4.5 8.2 1.0
NH2 c:ARG357 4.6 12.8 1.0
OE2 c:GLU354 4.8 13.3 1.0
C a:SER169 4.8 8.3 1.0
N a:ASP170 4.9 8.2 1.0
O a:HOH517 4.9 10.3 1.0

Reference:

K.Kato, N.Miyazaki, T.Hamaguchi, Y.Nakajima, F.Akita, K.Yonekura, J.R.Shen. High-Resolution Cryo-Em Structure of Photosystem II Reveals Damage From High-Dose Electron Beams Commun Biol 2021.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-021-01919-3
Page generated: Sat Apr 3 17:35:53 2021

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