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Manganese in PDB 3jcu: Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution

Other elements in 3jcu:

The structure of Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 206 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution (pdb code 3jcu). 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution, PDB code: 3jcu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3jcu

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Manganese binding site 1 out of 8 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:22.3
occ:1.00
 MN1 A:OEX401 0.0 22.3 1.0
O3 A:OEX401 1.8 23.1 1.0
O1 A:OEX401 1.8 21.8 1.0
OE2 A:GLU189 1.8 0.6 1.0
NE2 A:HIS332 2.1 0.2 1.0
OD2 A:ASP342 2.2 0.6 1.0
OE1 A:GLU333 2.3 0.1 1.0
CD2 A:HIS332 2.6 95.6 1.0
O5 A:OEX401 2.7 23.5 1.0
MN2 A:OEX401 2.7 23.1 1.0
CD A:GLU189 3.0 0.8 1.0
CG A:ASP342 3.3 0.5 1.0
CE1 A:HIS332 3.3 0.8 1.0
MN3 A:OEX401 3.4 23.4 1.0
CA1 A:OEX401 3.4 25.2 1.0
CD A:GLU333 3.5 0.9 1.0
OD1 A:ASP342 3.6 0.0 1.0
O2 A:OEX401 3.7 25.9 1.0
OE1 A:GLU189 3.7 0.8 1.0
CG A:HIS332 3.9 92.2 1.0
OE2 C:GLU354 3.9 0.8 1.0
CG A:GLU189 4.0 0.1 1.0
NE2 A:HIS337 4.1 0.3 1.0
CE1 A:HIS337 4.1 0.2 1.0
OE2 A:GLU333 4.1 0.3 1.0
ND1 A:HIS332 4.2 0.1 1.0
OXT A:ALA344 4.4 0.4 1.0
CB A:GLU333 4.4 0.2 1.0
CG A:GLU333 4.4 0.7 1.0
CG1 A:VAL185 4.5 85.2 1.0
CB A:ASP342 4.6 0.3 1.0
CD C:GLU354 4.8 0.3 1.0
OE1 C:GLU354 4.8 0.9 1.0
O A:ALA344 4.8 0.4 1.0

Manganese binding site 2 out of 8 in 3jcu

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Manganese binding site 2 out of 8 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:23.1
occ:1.00
 MN2 A:OEX401 0.0 23.1 1.0
OXT A:ALA344 2.0 0.4 1.0
OE2 C:GLU354 2.0 0.8 1.0
O1 A:OEX401 2.0 21.8 1.0
OE1 C:GLU354 2.1 0.9 1.0
OD1 A:ASP342 2.1 0.0 1.0
O3 A:OEX401 2.1 23.1 1.0
O2 A:OEX401 2.1 25.9 1.0
CD C:GLU354 2.3 0.3 1.0
CG A:ASP342 2.6 0.5 1.0
OD2 A:ASP342 2.7 0.6 1.0
MN1 A:OEX401 2.7 22.3 1.0
MN3 A:OEX401 2.9 23.4 1.0
C A:ALA344 3.0 0.4 1.0
O A:ALA344 3.3 0.4 1.0
CA1 A:OEX401 3.3 25.2 1.0
NE2 A:HIS337 3.4 0.3 1.0
OE2 A:GLU189 3.6 0.6 1.0
OE1 A:GLU333 3.6 0.1 1.0
CG C:GLU354 3.8 0.0 1.0
O5 A:OEX401 3.8 23.5 1.0
CE1 A:HIS337 3.9 0.2 1.0
CB A:ASP342 4.0 0.3 1.0
CD2 A:HIS337 4.1 0.0 1.0
NE2 A:HIS332 4.2 0.2 1.0
CA A:ALA344 4.3 0.8 1.0
CA A:ASP342 4.5 0.7 1.0
O4 A:OEX401 4.5 28.5 1.0
CB C:GLU354 4.6 0.6 1.0
NH2 C:ARG357 4.7 0.8 1.0
CD A:GLU189 4.7 0.8 1.0
CD A:GLU333 4.7 0.9 1.0
N A:ALA344 4.7 0.8 1.0
CB A:ALA344 4.8 0.4 1.0
C A:ASP342 4.9 0.8 1.0
ND1 A:HIS337 4.9 0.9 1.0
O A:ASP342 4.9 0.4 1.0
CD2 A:HIS332 4.9 95.6 1.0

Manganese binding site 3 out of 8 in 3jcu

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Manganese binding site 3 out of 8 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:23.4
occ:1.00
 MN3 A:OEX401 0.0 23.4 1.0
O2 A:OEX401 1.9 25.9 1.0
OE1 A:GLU333 2.0 0.1 1.0
O4 A:OEX401 2.0 28.5 1.0
O3 A:OEX401 2.1 23.1 1.0
OE2 C:GLU354 2.2 0.8 1.0
O5 A:OEX401 2.3 23.5 1.0
CD A:GLU333 2.5 0.9 1.0
MN4 A:OEX401 2.8 27.0 1.0
OE2 A:GLU333 2.9 0.3 1.0
MN2 A:OEX401 2.9 23.1 1.0
CD C:GLU354 3.2 0.3 1.0
MN1 A:OEX401 3.4 22.3 1.0
CA1 A:OEX401 3.4 25.2 1.0
CG A:GLU333 3.5 0.7 1.0
NH2 C:ARG357 3.5 0.8 1.0
CB A:GLU333 3.7 0.2 1.0
O1 A:OEX401 3.7 21.8 1.0
OE1 C:GLU354 4.0 0.9 1.0
OD1 A:ASP170 4.0 0.4 1.0
CG C:GLU354 4.1 0.0 1.0
OXT A:ALA344 4.4 0.4 1.0
CE1 A:HIS337 4.7 0.2 1.0
CZ C:ARG357 4.7 0.2 1.0
CB A:ALA336 4.7 0.0 1.0
CD2 A:HIS332 4.8 95.6 1.0
O A:ALA344 4.8 0.4 1.0
OD2 A:ASP170 4.9 0.6 1.0
OE2 A:GLU189 4.9 0.6 1.0
CG A:ASP170 4.9 0.2 1.0
NE2 A:HIS332 4.9 0.2 1.0
OD2 A:ASP342 4.9 0.6 1.0
NE2 A:HIS337 5.0 0.3 1.0
OD1 A:ASP342 5.0 0.0 1.0

Manganese binding site 4 out of 8 in 3jcu

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Manganese binding site 4 out of 8 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:27.0
occ:1.00
 MN4 A:OEX401 0.0 27.0 1.0
OD1 A:ASP170 2.0 0.4 1.0
O4 A:OEX401 2.1 28.5 1.0
OE2 A:GLU333 2.2 0.3 1.0
O5 A:OEX401 2.5 23.5 1.0
MN3 A:OEX401 2.8 23.4 1.0
CD A:GLU333 3.1 0.9 1.0
CG A:ASP170 3.1 0.2 1.0
NH2 C:ARG357 3.5 0.8 1.0
OE1 A:GLU333 3.5 0.1 1.0
OG A:SER169 3.5 75.8 1.0
O2 A:OEX401 3.6 25.9 1.0
CA1 A:OEX401 3.7 25.2 1.0
OD2 A:ASP170 3.7 0.6 1.0
O A:SER169 3.9 78.7 1.0
C A:SER169 4.0 73.6 1.0
N A:ASP170 4.0 76.2 1.0
CA A:ASP170 4.0 86.0 1.0
CB A:ASP170 4.1 94.0 1.0
CG A:GLU333 4.2 0.7 1.0
CB A:SER169 4.3 77.7 1.0
CZ C:ARG357 4.4 0.2 1.0
NH1 C:ARG357 4.5 0.1 1.0
O3 A:OEX401 4.6 23.1 1.0
CA A:SER169 4.8 74.1 1.0
OE2 C:GLU354 5.0 0.8 1.0

Manganese binding site 5 out of 8 in 3jcu

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Manganese binding site 5 out of 8 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:22.3
occ:1.00
 MN1 a:OEX401 0.0 22.3 1.0
O3 a:OEX401 1.8 23.1 1.0
O1 a:OEX401 1.8 21.8 1.0
OE2 a:GLU189 1.8 0.6 1.0
NE2 a:HIS332 2.1 0.2 1.0
OD2 a:ASP342 2.2 0.6 1.0
OE1 a:GLU333 2.3 0.1 1.0
CD2 a:HIS332 2.6 95.6 1.0
O5 a:OEX401 2.7 23.5 1.0
MN2 a:OEX401 2.7 23.1 1.0
CD a:GLU189 3.0 0.8 1.0
CG a:ASP342 3.3 0.5 1.0
CE1 a:HIS332 3.3 0.8 1.0
MN3 a:OEX401 3.4 23.4 1.0
CA1 a:OEX401 3.4 25.2 1.0
CD a:GLU333 3.5 0.9 1.0
OD1 a:ASP342 3.6 0.0 1.0
O2 a:OEX401 3.7 25.9 1.0
OE1 a:GLU189 3.7 0.8 1.0
CG a:HIS332 3.9 92.2 1.0
OE2 c:GLU354 3.9 0.8 1.0
CG a:GLU189 4.0 0.1 1.0
NE2 a:HIS337 4.1 0.3 1.0
CE1 a:HIS337 4.1 0.2 1.0
OE2 a:GLU333 4.1 0.3 1.0
ND1 a:HIS332 4.2 0.1 1.0
OXT a:ALA344 4.4 0.4 1.0
CB a:GLU333 4.4 0.2 1.0
CG a:GLU333 4.4 0.7 1.0
CG1 a:VAL185 4.5 85.2 1.0
CB a:ASP342 4.6 0.3 1.0
CD c:GLU354 4.8 0.3 1.0
OE1 c:GLU354 4.8 0.9 1.0
O a:ALA344 4.8 0.4 1.0

Manganese binding site 6 out of 8 in 3jcu

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Manganese binding site 6 out of 8 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:23.1
occ:1.00
 MN2 a:OEX401 0.0 23.1 1.0
OXT a:ALA344 2.0 0.4 1.0
OE2 c:GLU354 2.0 0.8 1.0
O1 a:OEX401 2.0 21.8 1.0
OE1 c:GLU354 2.1 0.9 1.0
OD1 a:ASP342 2.1 0.0 1.0
O3 a:OEX401 2.1 23.1 1.0
O2 a:OEX401 2.1 25.9 1.0
CD c:GLU354 2.3 0.3 1.0
CG a:ASP342 2.6 0.5 1.0
OD2 a:ASP342 2.7 0.6 1.0
MN1 a:OEX401 2.7 22.3 1.0
MN3 a:OEX401 2.9 23.4 1.0
C a:ALA344 3.0 0.4 1.0
O a:ALA344 3.3 0.4 1.0
CA1 a:OEX401 3.3 25.2 1.0
NE2 a:HIS337 3.4 0.3 1.0
OE2 a:GLU189 3.6 0.6 1.0
OE1 a:GLU333 3.6 0.1 1.0
CG c:GLU354 3.8 0.0 1.0
O5 a:OEX401 3.8 23.5 1.0
CE1 a:HIS337 3.9 0.2 1.0
CB a:ASP342 4.0 0.3 1.0
CD2 a:HIS337 4.1 0.0 1.0
NE2 a:HIS332 4.2 0.2 1.0
CA a:ALA344 4.3 0.8 1.0
CA a:ASP342 4.5 0.7 1.0
O4 a:OEX401 4.5 28.5 1.0
CB c:GLU354 4.6 0.6 1.0
NH2 c:ARG357 4.7 0.8 1.0
CD a:GLU189 4.7 0.8 1.0
CD a:GLU333 4.7 0.9 1.0
N a:ALA344 4.7 0.8 1.0
CB a:ALA344 4.8 0.4 1.0
C a:ASP342 4.9 0.8 1.0
ND1 a:HIS337 4.9 0.9 1.0
O a:ASP342 4.9 0.4 1.0
CD2 a:HIS332 4.9 95.6 1.0

Manganese binding site 7 out of 8 in 3jcu

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Manganese binding site 7 out of 8 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:23.4
occ:1.00
 MN3 a:OEX401 0.0 23.4 1.0
O2 a:OEX401 1.9 25.9 1.0
OE1 a:GLU333 2.0 0.1 1.0
O4 a:OEX401 2.0 28.5 1.0
O3 a:OEX401 2.1 23.1 1.0
OE2 c:GLU354 2.2 0.8 1.0
O5 a:OEX401 2.3 23.5 1.0
CD a:GLU333 2.5 0.9 1.0
MN4 a:OEX401 2.8 27.0 1.0
OE2 a:GLU333 2.9 0.3 1.0
MN2 a:OEX401 2.9 23.1 1.0
CD c:GLU354 3.2 0.3 1.0
MN1 a:OEX401 3.4 22.3 1.0
CA1 a:OEX401 3.4 25.2 1.0
CG a:GLU333 3.5 0.7 1.0
NH2 c:ARG357 3.5 0.8 1.0
CB a:GLU333 3.7 0.2 1.0
O1 a:OEX401 3.7 21.8 1.0
OE1 c:GLU354 4.0 0.9 1.0
OD1 a:ASP170 4.0 0.4 1.0
CG c:GLU354 4.1 0.0 1.0
OXT a:ALA344 4.4 0.4 1.0
CE1 a:HIS337 4.7 0.2 1.0
CZ c:ARG357 4.7 0.2 1.0
CB a:ALA336 4.7 0.0 1.0
CD2 a:HIS332 4.8 95.6 1.0
O a:ALA344 4.8 0.4 1.0
OD2 a:ASP170 4.9 0.6 1.0
OE2 a:GLU189 4.9 0.6 1.0
CG a:ASP170 4.9 0.2 1.0
NE2 a:HIS332 4.9 0.2 1.0
OD2 a:ASP342 4.9 0.6 1.0
NE2 a:HIS337 5.0 0.3 1.0
OD1 a:ASP342 5.0 0.0 1.0

Manganese binding site 8 out of 8 in 3jcu

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Manganese binding site 8 out of 8 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:27.0
occ:1.00
 MN4 a:OEX401 0.0 27.0 1.0
OD1 a:ASP170 2.0 0.4 1.0
O4 a:OEX401 2.1 28.5 1.0
OE2 a:GLU333 2.2 0.3 1.0
O5 a:OEX401 2.5 23.5 1.0
MN3 a:OEX401 2.8 23.4 1.0
CD a:GLU333 3.1 0.9 1.0
CG a:ASP170 3.1 0.2 1.0
NH2 c:ARG357 3.5 0.8 1.0
OE1 a:GLU333 3.5 0.1 1.0
OG a:SER169 3.5 75.8 1.0
O2 a:OEX401 3.6 25.9 1.0
CA1 a:OEX401 3.7 25.2 1.0
OD2 a:ASP170 3.7 0.6 1.0
O a:SER169 3.9 78.7 1.0
C a:SER169 4.0 73.6 1.0
N a:ASP170 4.0 76.2 1.0
CA a:ASP170 4.0 86.0 1.0
CB a:ASP170 4.1 94.0 1.0
CG a:GLU333 4.2 0.7 1.0
CB a:SER169 4.3 77.7 1.0
CZ c:ARG357 4.4 0.2 1.0
NH1 c:ARG357 4.5 0.1 1.0
O3 a:OEX401 4.6 23.1 1.0
CA a:SER169 4.8 74.1 1.0
OE2 c:GLU354 5.0 0.8 1.0

Reference:

X.P.Wei, X.D.Su, P.Cao, X.Y.Liu, W.R.Chang, M.Li, X.Z.Zhang, Z.F.Liu. Structure of Spinach Photosystem II-Lhcii Supercomplex at 3.2 A Resolution Nature V. 534 69 2016.
ISSN: ISSN 0028-0836
DOI: 10.1038/NATURE18020
Page generated: Sat Oct 5 16:42:13 2024

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