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Manganese in PDB 8eqm: Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light

Other elements in 8eqm:

The structure of Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 4 atoms
Iron (Fe) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light (pdb code 8eqm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light, PDB code: 8eqm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8eqm

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Manganese binding site 1 out of 8 in the Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:44.7
occ:1.00
 MN1 A:OEX401 0.0 44.7 1.0
OD2 A:ASP343 1.7 54.4 1.0
CE1 A:HIS333 2.4 41.7 1.0
NE2 A:HIS333 2.4 41.7 1.0
CG A:ASP343 2.4 54.4 1.0
OE2 A:GLU190 2.7 27.3 1.0
OD1 A:ASP343 2.8 54.4 1.0
NE2 A:HIS338 2.8 56.5 1.0
MN2 A:OEX401 3.2 44.7 1.0
MN3 A:OEX401 3.2 44.7 1.0
OE1 A:GLU334 3.3 51.5 1.0
CE1 A:HIS338 3.5 56.5 1.0
ND1 A:HIS333 3.7 41.7 1.0
CD2 A:HIS333 3.8 41.7 1.0
CB A:ASP343 3.8 54.4 1.0
CD A:GLU190 3.8 27.3 1.0
CD2 A:HIS338 4.0 56.5 1.0
CA1 A:OEX401 4.0 44.7 1.0
OE1 C:GLU357 4.0 44.9 1.0
O A:HOH501 4.0 44.5 1.0
O A:HOH564 4.3 39.0 1.0
CG A:HIS333 4.4 41.7 1.0
OE1 A:GLU190 4.5 27.3 1.0
CD A:GLU334 4.5 51.5 1.0
MN4 A:OEX401 4.6 44.7 1.0
OE2 C:GLU357 4.6 44.9 1.0
CG A:GLU190 4.7 27.3 1.0
CD C:GLU357 4.7 44.9 1.0
ND1 A:HIS338 4.8 56.5 1.0
O C:HOH637 4.9 56.5 1.0
CA A:ASP343 5.0 54.4 1.0
O A:LEU344 5.0 49.4 1.0
CG A:HIS338 5.0 56.5 1.0

Manganese binding site 2 out of 8 in 8eqm

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Manganese binding site 2 out of 8 in the Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:44.7
occ:1.00
 MN2 A:OEX401 0.0 44.7 1.0
OD1 A:ASP343 2.3 54.4 1.0
O A:LEU344 2.7 49.4 1.0
MN3 A:OEX401 3.0 44.7 1.0
OE1 C:GLU357 3.0 44.9 1.0
MN1 A:OEX401 3.2 44.7 1.0
CG A:ASP343 3.2 54.4 1.0
O A:ALA345 3.2 42.8 1.0
CD C:GLU357 3.3 44.9 1.0
OD2 A:ASP343 3.4 54.4 1.0
OE2 C:GLU357 3.4 44.9 1.0
O C:HOH613 3.4 52.1 1.0
CA1 A:OEX401 3.5 44.7 1.0
C A:ALA345 3.8 42.8 1.0
C A:LEU344 4.0 49.4 1.0
NH1 C:ARG360 4.4 33.3 1.0
NH2 C:ARG360 4.4 33.3 1.0
CG C:GLU357 4.4 44.9 1.0
CA A:ALA345 4.5 42.8 1.0
NE2 A:HIS338 4.5 56.5 1.0
O A:HOH517 4.5 28.2 1.0
CB A:ASP343 4.6 54.4 1.0
CZ C:ARG360 4.6 33.3 1.0
N A:ALA345 4.7 42.8 1.0
C A:ASP343 4.7 54.4 1.0
N A:LEU344 4.7 49.4 1.0
OE2 A:GLU190 4.8 27.3 1.0
CA A:ASP343 4.9 54.4 1.0
OE1 A:GLU334 4.9 51.5 1.0
CD2 A:HIS338 4.9 56.5 1.0
O A:ASP343 5.0 54.4 1.0

Manganese binding site 3 out of 8 in 8eqm

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Manganese binding site 3 out of 8 in the Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:44.7
occ:1.00
 MN3 A:OEX401 0.0 44.7 1.0
OE2 C:GLU357 2.0 44.9 1.0
OE1 A:GLU334 2.3 51.5 1.0
O A:HOH527 2.8 40.7 1.0
CD C:GLU357 2.9 44.9 1.0
CD A:GLU334 3.0 51.5 1.0
MN2 A:OEX401 3.0 44.7 1.0
MN4 A:OEX401 3.1 44.7 1.0
OE1 C:GLU357 3.2 44.9 1.0
MN1 A:OEX401 3.2 44.7 1.0
OE2 A:GLU334 3.3 51.5 1.0
CA1 A:OEX401 3.6 44.7 1.0
NH2 C:ARG360 3.7 33.3 1.0
NE2 A:HIS333 3.9 41.7 1.0
OD2 A:ASP171 4.0 31.9 1.0
CG A:GLU334 4.1 51.5 1.0
O C:HOH637 4.2 56.5 1.0
O A:HOH540 4.3 41.9 1.0
CG C:GLU357 4.3 44.9 1.0
NE2 A:HIS338 4.3 56.5 1.0
OD1 A:ASP343 4.3 54.4 1.0
CB A:GLU334 4.6 51.5 1.0
OD2 A:ASP343 4.6 54.4 1.0
CZ C:ARG360 4.7 33.3 1.0
CD2 A:HIS333 4.7 41.7 1.0
CE1 A:HIS333 4.7 41.7 1.0
OE2 A:GLU190 4.7 27.3 1.0
OD1 A:ASP171 4.8 31.9 1.0
OD2 A:ASP62 4.8 42.4 1.0
CG A:ASP171 4.8 31.9 1.0
CG A:ASP343 4.9 54.4 1.0
CE1 A:HIS338 5.0 56.5 1.0

Manganese binding site 4 out of 8 in 8eqm

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Manganese binding site 4 out of 8 in the Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:44.7
occ:1.00
 MN4 A:OEX401 0.0 44.7 1.0
OE2 A:GLU334 2.3 51.5 1.0
OE1 A:GLU334 3.0 51.5 1.0
CD A:GLU334 3.0 51.5 1.0
O A:HOH518 3.0 33.1 1.0
O A:HOH527 3.1 40.7 1.0
MN3 A:OEX401 3.1 44.7 1.0
CA1 A:OEX401 3.3 44.7 1.0
OD2 A:ASP171 3.4 31.9 1.0
O A:HOH562 3.5 32.3 1.0
NE2 A:HIS333 3.6 41.7 1.0
CD2 A:HIS333 3.6 41.7 1.0
O A:HOH573 3.8 33.0 1.0
CG1 A:VAL186 3.9 20.4 1.0
OE2 A:GLU190 4.2 27.3 1.0
CG A:ASP171 4.2 31.9 1.0
O A:HOH572 4.3 25.1 1.0
CG A:GLU334 4.4 51.5 1.0
MN1 A:OEX401 4.6 44.7 1.0
OE1 A:GLU190 4.8 27.3 1.0
OD1 A:ASP171 4.8 31.9 1.0
CE1 A:HIS333 4.9 41.7 1.0
CD A:GLU190 4.9 27.3 1.0
CG A:HIS333 4.9 41.7 1.0
OE2 C:GLU357 5.0 44.9 1.0
O A:HOH505 5.0 21.1 1.0

Manganese binding site 5 out of 8 in 8eqm

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Manganese binding site 5 out of 8 in the Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:44.7
occ:1.00
 MN1 a:OEX401 0.0 44.7 1.0
OD2 a:ASP343 1.7 54.4 1.0
CE1 a:HIS333 2.4 41.7 1.0
NE2 a:HIS333 2.4 41.7 1.0
CG a:ASP343 2.4 54.4 1.0
OE2 a:GLU190 2.7 27.3 1.0
OD1 a:ASP343 2.8 54.4 1.0
NE2 a:HIS338 2.8 56.5 1.0
MN2 a:OEX401 3.2 44.7 1.0
MN3 a:OEX401 3.2 44.7 1.0
OE1 a:GLU334 3.3 51.5 1.0
CE1 a:HIS338 3.5 56.5 1.0
ND1 a:HIS333 3.7 41.7 1.0
CD2 a:HIS333 3.8 41.7 1.0
CB a:ASP343 3.8 54.4 1.0
CD a:GLU190 3.8 27.3 1.0
CD2 a:HIS338 4.0 56.5 1.0
CA1 a:OEX401 4.0 44.7 1.0
OE1 c:GLU357 4.0 44.9 1.0
O a:HOH501 4.0 44.5 1.0
O a:HOH564 4.3 39.0 1.0
CG a:HIS333 4.4 41.7 1.0
OE1 a:GLU190 4.5 27.3 1.0
CD a:GLU334 4.5 51.5 1.0
MN4 a:OEX401 4.6 44.7 1.0
OE2 c:GLU357 4.6 44.9 1.0
CG a:GLU190 4.7 27.3 1.0
CD c:GLU357 4.7 44.9 1.0
ND1 a:HIS338 4.8 56.5 1.0
O c:HOH637 4.9 56.5 1.0
CA a:ASP343 5.0 54.4 1.0
O a:LEU344 5.0 49.4 1.0
CG a:HIS338 5.0 56.5 1.0

Manganese binding site 6 out of 8 in 8eqm

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Manganese binding site 6 out of 8 in the Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:44.7
occ:1.00
 MN2 a:OEX401 0.0 44.7 1.0
OD1 a:ASP343 2.3 54.4 1.0
O a:LEU344 2.7 49.4 1.0
MN3 a:OEX401 3.0 44.7 1.0
OE1 c:GLU357 3.0 44.9 1.0
MN1 a:OEX401 3.2 44.7 1.0
CG a:ASP343 3.2 54.4 1.0
O a:ALA345 3.2 42.8 1.0
CD c:GLU357 3.3 44.9 1.0
OD2 a:ASP343 3.4 54.4 1.0
OE2 c:GLU357 3.4 44.9 1.0
O c:HOH613 3.4 52.1 1.0
CA1 a:OEX401 3.5 44.7 1.0
C a:ALA345 3.8 42.8 1.0
C a:LEU344 4.0 49.4 1.0
NH1 c:ARG360 4.4 33.3 1.0
NH2 c:ARG360 4.4 33.3 1.0
CG c:GLU357 4.4 44.9 1.0
CA a:ALA345 4.5 42.8 1.0
NE2 a:HIS338 4.5 56.5 1.0
O a:HOH517 4.5 28.2 1.0
CB a:ASP343 4.6 54.4 1.0
CZ c:ARG360 4.6 33.3 1.0
N a:ALA345 4.7 42.8 1.0
C a:ASP343 4.7 54.4 1.0
N a:LEU344 4.7 49.4 1.0
OE2 a:GLU190 4.8 27.3 1.0
CA a:ASP343 4.9 54.4 1.0
OE1 a:GLU334 4.9 51.5 1.0
CD2 a:HIS338 4.9 56.5 1.0
O a:ASP343 5.0 54.4 1.0

Manganese binding site 7 out of 8 in 8eqm

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Manganese binding site 7 out of 8 in the Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:44.7
occ:1.00
 MN3 a:OEX401 0.0 44.7 1.0
OE2 c:GLU357 2.0 44.9 1.0
OE1 a:GLU334 2.3 51.5 1.0
O a:HOH527 2.8 40.7 1.0
CD c:GLU357 2.9 44.9 1.0
CD a:GLU334 3.0 51.5 1.0
MN2 a:OEX401 3.0 44.7 1.0
MN4 a:OEX401 3.1 44.7 1.0
OE1 c:GLU357 3.2 44.9 1.0
MN1 a:OEX401 3.2 44.7 1.0
OE2 a:GLU334 3.3 51.5 1.0
CA1 a:OEX401 3.6 44.7 1.0
NH2 c:ARG360 3.7 33.3 1.0
NE2 a:HIS333 3.9 41.7 1.0
OD2 a:ASP171 4.0 31.9 1.0
CG a:GLU334 4.1 51.5 1.0
O c:HOH637 4.2 56.5 1.0
O a:HOH540 4.3 41.9 1.0
CG c:GLU357 4.3 44.9 1.0
NE2 a:HIS338 4.3 56.5 1.0
OD1 a:ASP343 4.3 54.4 1.0
CB a:GLU334 4.6 51.5 1.0
OD2 a:ASP343 4.6 54.4 1.0
CZ c:ARG360 4.7 33.3 1.0
CD2 a:HIS333 4.7 41.7 1.0
CE1 a:HIS333 4.7 41.7 1.0
OE2 a:GLU190 4.7 27.3 1.0
OD1 a:ASP171 4.8 31.9 1.0
OD2 a:ASP62 4.8 42.4 1.0
CG a:ASP171 4.8 31.9 1.0
CG a:ASP343 4.9 54.4 1.0
CE1 a:HIS338 5.0 56.5 1.0

Manganese binding site 8 out of 8 in 8eqm

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Manganese binding site 8 out of 8 in the Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of A Dimeric Photosystem II Complex Acclimated to Far-Red Light within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:44.7
occ:1.00
 MN4 a:OEX401 0.0 44.7 1.0
OE2 a:GLU334 2.3 51.5 1.0
OE1 a:GLU334 3.0 51.5 1.0
CD a:GLU334 3.0 51.5 1.0
O a:HOH518 3.0 33.1 1.0
O a:HOH527 3.1 40.7 1.0
MN3 a:OEX401 3.1 44.7 1.0
CA1 a:OEX401 3.3 44.7 1.0
OD2 a:ASP171 3.4 31.9 1.0
O a:HOH562 3.5 32.3 1.0
NE2 a:HIS333 3.6 41.7 1.0
CD2 a:HIS333 3.6 41.7 1.0
O a:HOH573 3.8 33.0 1.0
CG1 a:VAL186 3.9 20.4 1.0
OE2 a:GLU190 4.2 27.3 1.0
CG a:ASP171 4.2 31.9 1.0
O a:HOH572 4.3 25.1 1.0
CG a:GLU334 4.4 51.5 1.0
MN1 a:OEX401 4.6 44.7 1.0
OE1 a:GLU190 4.8 27.3 1.0
OD1 a:ASP171 4.8 31.9 1.0
CE1 a:HIS333 4.9 41.7 1.0
CD a:GLU190 4.9 27.3 1.0
CG a:HIS333 4.9 41.7 1.0
OE2 c:GLU357 5.0 44.9 1.0
O a:HOH505 5.0 21.1 1.0

Reference:

C.J.Gisriel, G.Shen, D.A.Flesher, V.Kurashov, J.H.Golbeck, G.W.Brudvig, M.Amin, D.A.Bryant. Structure of A Dimeric Photosystem II Complex From A Cyanobacterium Acclimated to Far-Red Light. J.Biol.Chem. 02815 2022.
ISSN: ESSN 1083-351X
PubMed: 36549647
DOI: 10.1016/J.JBC.2022.102815
Page generated: Sun Oct 6 11:43:03 2024

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