Manganese in PDB 7eda: Structure of Monomeric Photosystem II

Enzymatic activity of Structure of Monomeric Photosystem II

All present enzymatic activity of Structure of Monomeric Photosystem II:
1.10.3.9;

Other elements in 7eda:

The structure of Structure of Monomeric Photosystem II also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Iron (Fe) 3 atoms
Magnesium (Mg) 35 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Monomeric Photosystem II (pdb code 7eda). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Monomeric Photosystem II, PDB code: 7eda:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7eda

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Manganese binding site 1 out of 4 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Monomeric Photosystem II 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
OE2 A:GLU189 1.5 13.5 1.0
O3 A:OEX401 1.8 23.1 1.0
O1 A:OEX401 1.9 21.8 1.0
OD2 A:ASP342 2.4 25.1 1.0
NE2 A:HIS332 2.4 16.5 1.0
O5 A:OEX401 2.6 23.5 1.0
CD A:GLU189 2.8 13.5 1.0
MN2 A:OEX401 2.9 23.1 1.0
CD2 A:HIS332 3.0 16.5 1.0
CG A:ASP342 3.2 25.1 1.0
MN3 A:OEX401 3.3 23.4 1.0
OD1 A:ASP342 3.3 25.1 1.0
CA1 A:OEX401 3.5 25.2 1.0
CG A:GLU189 3.6 13.5 1.0
CE1 A:HIS332 3.6 16.5 1.0
OE1 A:GLU189 3.7 13.5 1.0
O2 A:OEX401 3.8 25.9 1.0
NE2 A:HIS337 4.0 21.5 1.0
CG A:HIS332 4.3 16.5 1.0
OE1 A:GLU333 4.3 23.0 1.0
OXT A:ALA344 4.5 25.2 1.0
ND1 A:HIS332 4.5 16.5 1.0
CE1 A:HIS337 4.5 21.5 1.0
CG1 A:VAL185 4.6 9.8 1.0
CB A:ASP342 4.6 25.1 1.0
OE2 A:GLU333 4.8 23.0 1.0
CB A:GLU189 4.8 13.5 1.0
CD A:GLU333 4.9 23.0 1.0
OE1 C:GLU354 4.9 23.8 1.0
OE2 C:GLU354 5.0 23.8 1.0
MN4 A:OEX401 5.0 27.0 1.0

Manganese binding site 2 out of 4 in 7eda

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Manganese binding site 2 out of 4 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Monomeric Photosystem II 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 25.2 1.0
O1 A:OEX401 2.1 21.8 1.0
O3 A:OEX401 2.1 23.1 1.0
O2 A:OEX401 2.2 25.9 1.0
OD1 A:ASP342 2.3 25.1 1.0
OE1 C:GLU354 2.5 23.8 1.0
MN1 A:OEX401 2.9 22.3 1.0
MN3 A:OEX401 2.9 23.4 1.0
C A:ALA344 3.0 26.3 1.0
CG A:ASP342 3.3 25.1 1.0
O A:ALA344 3.3 29.0 1.0
CA1 A:OEX401 3.4 25.2 1.0
CD C:GLU354 3.4 23.8 1.0
OD2 A:ASP342 3.5 25.1 1.0
OE2 C:GLU354 3.6 23.8 1.0
NE2 A:HIS337 3.7 21.5 1.0
O5 A:OEX401 3.8 23.5 1.0
OE2 A:GLU189 4.0 13.5 1.0
CA A:ALA344 4.3 25.4 1.0
CD2 A:HIS337 4.3 21.5 1.0
N A:ALA344 4.4 27.7 1.0
O4 A:OEX401 4.5 28.5 1.0
OE1 A:GLU333 4.5 23.0 1.0
CB A:ASP342 4.6 25.1 1.0
CG C:GLU354 4.7 23.8 1.0
CE1 A:HIS337 4.8 21.5 1.0
NE2 A:HIS332 4.9 16.5 1.0
CA A:ASP342 4.9 25.1 1.0
CB C:GLU354 4.9 23.8 1.0
C A:ASP342 5.0 25.1 1.0

Manganese binding site 3 out of 4 in 7eda

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Manganese binding site 3 out of 4 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Monomeric Photosystem II 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
O4 A:OEX401 2.1 28.5 1.0
OE1 A:GLU333 2.1 23.0 1.0
O3 A:OEX401 2.2 23.1 1.0
O5 A:OEX401 2.3 23.5 1.0
CD A:GLU333 2.8 23.0 1.0
MN2 A:OEX401 2.9 23.1 1.0
MN4 A:OEX401 3.0 27.0 1.0
OE2 A:GLU333 3.0 23.0 1.0
OE2 C:GLU354 3.1 23.8 1.0
OE1 C:GLU354 3.1 23.8 1.0
MN1 A:OEX401 3.3 22.3 1.0
CA1 A:OEX401 3.4 25.2 1.0
CD C:GLU354 3.4 23.8 1.0
O1 A:OEX401 3.5 21.8 1.0
NE2 A:HIS337 4.2 21.5 1.0
NH2 C:ARG357 4.3 14.2 1.0
OE2 A:GLU189 4.3 13.5 1.0
CG A:GLU333 4.3 23.0 1.0
OD1 A:ASP170 4.4 12.8 1.0
OXT A:ALA344 4.5 25.2 1.0
CE1 A:HIS337 4.5 21.5 1.0
CD2 A:HIS332 4.6 16.5 1.0
NE2 A:HIS332 4.7 16.5 1.0
OD1 A:ASP61 4.7 25.4 1.0
CB A:GLU333 4.8 23.0 1.0
O A:ALA344 4.8 29.0 1.0
OD1 A:ASP342 4.8 25.1 1.0
CG C:GLU354 4.8 23.8 1.0
O A:HOH595 5.0 28.4 1.0

Manganese binding site 4 out of 4 in 7eda

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Manganese binding site 4 out of 4 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Monomeric Photosystem II 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
O4 A:OEX401 2.1 28.5 1.0
OE2 A:GLU333 2.3 23.0 1.0
O A:HOH595 2.3 28.4 1.0
O5 A:OEX401 2.4 23.5 1.0
MN3 A:OEX401 3.0 23.4 1.0
OD1 A:ASP170 3.1 12.8 1.0
CD A:GLU333 3.2 23.0 1.0
OE1 A:GLU333 3.6 23.0 1.0
CA1 A:OEX401 3.8 25.2 1.0
O2 A:OEX401 3.8 25.9 1.0
CG A:ASP170 4.2 12.8 1.0
O A:SER169 4.4 12.2 1.0
CG A:GLU333 4.5 23.0 1.0
CA A:ASP170 4.6 12.8 1.0
NH2 C:ARG357 4.6 14.2 1.0
CB A:ASP170 4.7 12.8 1.0
CG1 A:VAL185 4.7 9.8 1.0
O3 A:OEX401 4.8 23.1 1.0
C A:SER169 4.9 12.2 1.0
N A:ASP170 5.0 12.8 1.0
MN1 A:OEX401 5.0 22.3 1.0

Reference:

H.Yu, T.Hamaguchi, Y.Nakajima, K.Kato, K.Kawakami, F.Akita, K.Yonekura, J.R.Shen. Structure of Monomeric Photosystem II To Be Published.
Page generated: Mon Jul 12 15:23:57 2021

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