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Manganese in PDB 7d1u: Cryo-Em Structure of Psii at 2.08 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution:
1.10.3.9;

Other elements in 7d1u:

The structure of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Magnesium (Mg) 72 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 2.08 Angstrom Resolution (pdb code 7d1u). 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 2.08 Angstrom Resolution, PDB code: 7d1u:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 7d1u

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Manganese binding site 1 out of 8 in the Cryo-Em Structure of Psii at 2.08 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 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:13.1
occ:1.00
 MN1 A:OEX401 0.0 13.1 1.0
O1 A:OEX401 1.8 13.1 1.0
O3 A:OEX401 1.9 13.1 1.0
OE2 A:GLU189 2.1 9.9 1.0
OD2 A:ASP342 2.1 15.2 1.0
NE2 A:HIS332 2.2 12.5 1.0
O5 A:OEX401 2.7 13.1 1.0
MN2 A:OEX401 2.9 13.1 1.0
CD A:GLU189 3.0 9.8 1.0
CG A:ASP342 3.0 15.2 1.0
CD2 A:HIS332 3.2 12.5 1.0
MN3 A:OEX401 3.2 13.1 1.0
CE1 A:HIS332 3.2 12.5 1.0
OD1 A:ASP342 3.3 15.2 1.0
O2 A:OEX401 3.5 13.1 1.0
OE1 A:GLU189 3.5 9.8 1.0
CA1 A:OEX401 3.6 13.1 1.0
NE2 A:HIS337 3.9 14.4 1.0
O A:HOH565 4.0 17.1 1.0
CG A:GLU189 4.0 9.7 1.0
CG A:HIS332 4.3 12.6 1.0
ND1 A:HIS332 4.3 12.6 1.0
OXT A:ALA344 4.3 15.5 1.0
OE1 A:GLU333 4.4 13.1 1.0
O A:HOH597 4.4 15.8 1.0
CB A:ASP342 4.4 15.3 1.0
OE1 C:GLU354 4.4 13.9 1.0
OE2 C:GLU354 4.6 13.9 1.0
CE1 A:HIS337 4.7 14.4 1.0
CG1 A:VAL185 4.7 8.4 1.0
CD A:GLU333 4.7 13.0 1.0
O A:ALA344 4.8 15.4 1.0
OE2 A:GLU333 4.8 13.1 1.0
O A:HOH537 4.8 11.9 1.0
CD2 A:HIS337 4.9 14.4 1.0
O A:HOH625 4.9 12.4 1.0
C A:ALA344 4.9 15.5 1.0
CD C:GLU354 4.9 13.9 1.0

Manganese binding site 2 out of 8 in 7d1u

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Manganese binding site 2 out of 8 in the Cryo-Em Structure of Psii at 2.08 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 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:13.1
occ:1.00
 MN2 A:OEX401 0.0 13.1 1.0
OXT A:ALA344 1.8 15.5 1.0
O2 A:OEX401 1.8 13.1 1.0
O1 A:OEX401 2.0 13.1 1.0
O3 A:OEX401 2.0 13.1 1.0
OE1 C:GLU354 2.2 13.9 1.0
OD1 A:ASP342 2.2 15.2 1.0
C A:ALA344 2.8 15.5 1.0
MN1 A:OEX401 2.9 13.1 1.0
MN3 A:OEX401 2.9 13.1 1.0
CD C:GLU354 3.0 13.9 1.0
OE2 C:GLU354 3.1 13.9 1.0
CG A:ASP342 3.1 15.2 1.0
O A:ALA344 3.2 15.4 1.0
OD2 A:ASP342 3.3 15.2 1.0
CA1 A:OEX401 3.4 13.1 1.0
O C:HOH696 3.7 15.8 1.0
O5 A:OEX401 4.0 13.1 1.0
O A:HOH565 4.0 17.1 1.0
NE2 A:HIS337 4.1 14.4 1.0
CA A:ALA344 4.1 15.5 1.0
N A:ALA344 4.2 15.6 1.0
CG C:GLU354 4.4 13.9 1.0
CD2 A:HIS337 4.5 14.4 1.0
O4 A:OEX401 4.5 13.1 1.0
CB A:ASP342 4.5 15.3 1.0
OE2 A:GLU189 4.7 9.9 1.0
OE1 A:GLU333 4.7 13.1 1.0
NE2 A:HIS332 4.8 12.5 1.0
CB C:GLU354 4.8 13.8 1.0
CA A:ASP342 4.8 15.4 1.0
C A:ASP342 4.9 15.5 1.0
NH2 C:ARG357 5.0 13.5 1.0

Manganese binding site 3 out of 8 in 7d1u

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Manganese binding site 3 out of 8 in the Cryo-Em Structure of Psii at 2.08 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 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:13.1
occ:1.00
 MN3 A:OEX401 0.0 13.1 1.0
O2 A:OEX401 1.8 13.1 1.0
O3 A:OEX401 2.1 13.1 1.0
OE1 A:GLU333 2.1 13.1 1.0
O4 A:OEX401 2.1 13.1 1.0
OE2 C:GLU354 2.2 13.9 1.0
O5 A:OEX401 2.3 13.1 1.0
MN2 A:OEX401 2.9 13.1 1.0
CD A:GLU333 2.9 13.0 1.0
MN4 A:OEX401 3.0 13.2 1.0
OE2 A:GLU333 3.1 13.1 1.0
CD C:GLU354 3.2 13.9 1.0
MN1 A:OEX401 3.2 13.1 1.0
CA1 A:OEX401 3.4 13.1 1.0
OE1 C:GLU354 3.5 13.9 1.0
O1 A:OEX401 3.5 13.1 1.0
NE2 A:HIS337 4.1 14.4 1.0
CG A:GLU333 4.2 13.0 1.0
OD2 A:ASP170 4.3 9.5 1.0
O A:HOH615 4.3 14.6 1.0
NH2 C:ARG357 4.3 13.5 1.0
O A:HOH528 4.3 12.3 1.0
NE2 A:HIS332 4.3 12.5 1.0
OXT A:ALA344 4.4 15.5 1.0
CG C:GLU354 4.5 13.9 1.0
CD2 A:HIS332 4.5 12.5 1.0
OD1 A:ASP170 4.6 9.5 1.0
OD1 A:ASP342 4.6 15.2 1.0
O A:HOH554 4.7 12.5 1.0
CB A:GLU333 4.7 13.0 1.0
CE1 A:HIS337 4.8 14.4 1.0
O A:ALA344 4.8 15.4 1.0
OD2 A:ASP61 4.8 12.5 1.0
OD2 A:ASP342 4.8 15.2 1.0
CG A:ASP170 4.9 9.5 1.0
O A:HOH519 5.0 12.5 1.0
OE2 A:GLU189 5.0 9.9 1.0

Manganese binding site 4 out of 8 in 7d1u

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Manganese binding site 4 out of 8 in the Cryo-Em Structure of Psii at 2.08 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 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:13.2
occ:1.00
 MN4 A:OEX401 0.0 13.2 1.0
O4 A:OEX401 1.9 13.1 1.0
OE2 A:GLU333 2.1 13.1 1.0
OD2 A:ASP170 2.1 9.5 1.0
O A:HOH554 2.2 12.5 1.0
O A:HOH519 2.3 12.5 1.0
O5 A:OEX401 2.5 13.1 1.0
MN3 A:OEX401 3.0 13.1 1.0
CD A:GLU333 3.1 13.0 1.0
CG A:ASP170 3.3 9.5 1.0
OE1 A:GLU333 3.4 13.1 1.0
CA1 A:OEX401 3.8 13.1 1.0
O A:HOH528 3.9 12.3 1.0
OD1 A:ASP170 3.9 9.5 1.0
O2 A:OEX401 3.9 13.1 1.0
OD2 A:ASP61 4.0 12.5 1.0
O A:HOH625 4.0 12.4 1.0
O A:HOH559 4.2 11.1 1.0
O A:SER169 4.3 9.4 1.0
O A:HOH583 4.3 12.3 1.0
CG A:GLU333 4.4 13.0 1.0
CA A:ASP170 4.5 9.3 1.0
CB A:ASP170 4.5 9.4 1.0
NH2 C:ARG357 4.5 13.5 1.0
OE2 C:GLU354 4.8 13.9 1.0
O A:HOH526 4.8 14.0 1.0
C A:SER169 4.8 9.4 1.0
OG A:SER169 4.8 9.5 1.0
O3 A:OEX401 4.8 13.1 1.0
N A:ASP170 4.9 9.3 1.0
O A:HOH533 4.9 10.6 1.0

Manganese binding site 5 out of 8 in 7d1u

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Manganese binding site 5 out of 8 in the Cryo-Em Structure of Psii at 2.08 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 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:13.1
occ:1.00
 MN1 a:OEX401 0.0 13.1 1.0
O1 a:OEX401 1.8 13.1 1.0
O3 a:OEX401 1.9 13.1 1.0
OE2 a:GLU189 2.1 9.8 1.0
OD2 a:ASP342 2.1 15.1 1.0
NE2 a:HIS332 2.2 12.6 1.0
O5 a:OEX401 2.7 13.1 1.0
MN2 a:OEX401 2.9 13.1 1.0
CD a:GLU189 3.0 9.7 1.0
CG a:ASP342 3.0 15.2 1.0
CD2 a:HIS332 3.2 12.6 1.0
MN3 a:OEX401 3.2 13.1 1.0
CE1 a:HIS332 3.2 12.6 1.0
OD1 a:ASP342 3.3 15.2 1.0
O2 a:OEX401 3.5 13.1 1.0
OE1 a:GLU189 3.5 9.8 1.0
CA1 a:OEX401 3.6 13.1 1.0
NE2 a:HIS337 3.9 14.5 1.0
O a:HOH564 4.0 17.0 1.0
CG a:GLU189 4.0 9.7 1.0
ND1 a:HIS332 4.3 12.6 1.0
CG a:HIS332 4.3 12.6 1.0
OXT a:ALA344 4.3 15.4 1.0
OE1 a:GLU333 4.4 13.1 1.0
O a:HOH596 4.4 15.8 1.0
CB a:ASP342 4.4 15.2 1.0
OE1 c:GLU354 4.4 13.9 1.0
OE2 c:GLU354 4.6 13.9 1.0
CE1 a:HIS337 4.7 14.5 1.0
CG1 a:VAL185 4.7 8.4 1.0
CD a:GLU333 4.7 13.1 1.0
O a:ALA344 4.8 15.3 1.0
OE2 a:GLU333 4.8 13.1 1.0
O a:HOH537 4.8 12.0 1.0
CD2 a:HIS337 4.9 14.5 1.0
O a:HOH624 4.9 12.2 1.0
C a:ALA344 4.9 15.4 1.0
CD c:GLU354 4.9 13.9 1.0

Manganese binding site 6 out of 8 in 7d1u

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Manganese binding site 6 out of 8 in the Cryo-Em Structure of Psii at 2.08 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 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:13.1
occ:1.00
 MN2 a:OEX401 0.0 13.1 1.0
OXT a:ALA344 1.8 15.4 1.0
O2 a:OEX401 1.8 13.1 1.0
O1 a:OEX401 2.0 13.1 1.0
O3 a:OEX401 2.0 13.1 1.0
OE1 c:GLU354 2.2 13.9 1.0
OD1 a:ASP342 2.2 15.2 1.0
C a:ALA344 2.8 15.4 1.0
MN1 a:OEX401 2.9 13.1 1.0
MN3 a:OEX401 2.9 13.1 1.0
CD c:GLU354 3.0 13.9 1.0
OE2 c:GLU354 3.1 13.9 1.0
CG a:ASP342 3.1 15.2 1.0
O a:ALA344 3.2 15.3 1.0
OD2 a:ASP342 3.3 15.1 1.0
CA1 a:OEX401 3.4 13.1 1.0
O c:HOH696 3.7 15.7 1.0
O5 a:OEX401 4.0 13.1 1.0
O a:HOH564 4.0 17.0 1.0
NE2 a:HIS337 4.1 14.5 1.0
CA a:ALA344 4.1 15.4 1.0
N a:ALA344 4.2 15.5 1.0
CG c:GLU354 4.4 13.9 1.0
CD2 a:HIS337 4.5 14.5 1.0
O4 a:OEX401 4.5 13.1 1.0
CB a:ASP342 4.5 15.2 1.0
OE2 a:GLU189 4.7 9.8 1.0
OE1 a:GLU333 4.7 13.1 1.0
NE2 a:HIS332 4.8 12.6 1.0
CB c:GLU354 4.8 13.9 1.0
CA a:ASP342 4.8 15.3 1.0
C a:ASP342 4.9 15.4 1.0
NH2 c:ARG357 5.0 13.5 1.0

Manganese binding site 7 out of 8 in 7d1u

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Manganese binding site 7 out of 8 in the Cryo-Em Structure of Psii at 2.08 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 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:13.1
occ:1.00
 MN3 a:OEX401 0.0 13.1 1.0
O2 a:OEX401 1.8 13.1 1.0
O3 a:OEX401 2.1 13.1 1.0
OE1 a:GLU333 2.1 13.1 1.0
O4 a:OEX401 2.1 13.1 1.0
OE2 c:GLU354 2.2 13.9 1.0
O5 a:OEX401 2.3 13.1 1.0
MN2 a:OEX401 2.9 13.1 1.0
CD a:GLU333 2.9 13.1 1.0
MN4 a:OEX401 3.0 13.2 1.0
OE2 a:GLU333 3.1 13.1 1.0
CD c:GLU354 3.2 13.9 1.0
MN1 a:OEX401 3.2 13.1 1.0
CA1 a:OEX401 3.4 13.1 1.0
OE1 c:GLU354 3.5 13.9 1.0
O1 a:OEX401 3.5 13.1 1.0
NE2 a:HIS337 4.1 14.5 1.0
CG a:GLU333 4.2 13.1 1.0
OD2 a:ASP170 4.3 9.5 1.0
O a:HOH614 4.3 14.7 1.0
NH2 c:ARG357 4.3 13.5 1.0
O a:HOH528 4.3 12.4 1.0
NE2 a:HIS332 4.3 12.6 1.0
OXT a:ALA344 4.4 15.4 1.0
CG c:GLU354 4.5 13.9 1.0
CD2 a:HIS332 4.5 12.6 1.0
OD1 a:ASP170 4.6 9.5 1.0
OD1 a:ASP342 4.6 15.2 1.0
CB a:GLU333 4.7 13.1 1.0
O a:HOH554 4.7 12.4 1.0
CE1 a:HIS337 4.8 14.5 1.0
O a:ALA344 4.8 15.3 1.0
OD2 a:ASP61 4.8 12.5 1.0
OD2 a:ASP342 4.8 15.1 1.0
CG a:ASP170 4.9 9.5 1.0
O a:HOH519 5.0 12.4 1.0
OE2 a:GLU189 5.0 9.8 1.0

Manganese binding site 8 out of 8 in 7d1u

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Manganese binding site 8 out of 8 in the Cryo-Em Structure of Psii at 2.08 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 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:13.2
occ:1.00
 MN4 a:OEX401 0.0 13.2 1.0
O4 a:OEX401 1.9 13.1 1.0
OE2 a:GLU333 2.1 13.1 1.0
OD2 a:ASP170 2.1 9.5 1.0
O a:HOH554 2.2 12.4 1.0
O a:HOH519 2.3 12.4 1.0
O5 a:OEX401 2.5 13.1 1.0
MN3 a:OEX401 3.0 13.1 1.0
CD a:GLU333 3.1 13.1 1.0
CG a:ASP170 3.3 9.5 1.0
OE1 a:GLU333 3.4 13.1 1.0
CA1 a:OEX401 3.8 13.1 1.0
O a:HOH528 3.9 12.4 1.0
OD1 a:ASP170 3.9 9.5 1.0
O2 a:OEX401 3.9 13.1 1.0
OD2 a:ASP61 4.0 12.5 1.0
O a:HOH624 4.0 12.2 1.0
O a:HOH559 4.2 11.1 1.0
O a:SER169 4.3 9.4 1.0
O a:HOH582 4.3 11.3 1.0
CG a:GLU333 4.4 13.1 1.0
CA a:ASP170 4.5 9.3 1.0
CB a:ASP170 4.5 9.4 1.0
NH2 c:ARG357 4.5 13.5 1.0
OE2 c:GLU354 4.8 13.9 1.0
O a:HOH526 4.8 13.6 1.0
C a:SER169 4.8 9.4 1.0
OG a:SER169 4.8 9.5 1.0
O3 a:OEX401 4.8 13.1 1.0
N a:ASP170 4.9 9.3 1.0
O a:HOH533 4.9 10.6 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: Sun Oct 6 08:23:05 2024

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