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Manganese in PDB 6jlm: Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2):
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2), PDB code: 6jlm was solved by M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.040, 228.840, 286.980, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 20.9

Other elements in 6jlm:

The structure of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 11 atoms
Chlorine (Cl) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) (pdb code 6jlm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2), PDB code: 6jlm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6jlm

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Manganese binding site 1 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn416

b:42.8
occ:1.00
 MN1 A:OEX416 0.0 42.8 1.0
OE2 A:GLU189 1.8 58.8 1.0
O1 A:OEX416 1.8 56.5 1.0
O3 A:OEX416 1.9 77.6 1.0
NE2 A:HIS332 2.1 38.7 1.0
OD2 A:ASP342 2.2 59.5 1.0
MN2 A:OEX416 2.6 43.0 1.0
O5 A:OEX416 2.7 61.3 1.0
CD A:GLU189 2.9 41.5 1.0
CE1 A:HIS332 2.9 33.5 1.0
CG A:ASP342 3.0 35.2 1.0
OD1 A:ASP342 3.2 40.8 1.0
CD2 A:HIS332 3.2 43.0 1.0
MN3 A:OEX416 3.2 42.9 1.0
OE1 A:GLU189 3.4 54.4 1.0
O2 A:OEX416 3.5 45.1 1.0
CA1 A:OEX416 3.6 51.2 1.0
O A:HOH526 3.8 53.9 1.0
NE2 A:HIS337 4.0 37.7 1.0
ND1 A:HIS332 4.0 31.7 1.0
CG A:GLU189 4.1 38.2 1.0
OXT A:ALA344 4.1 45.8 1.0
OE1 A:GLU333 4.1 47.1 1.0
CG A:HIS332 4.2 29.1 1.0
O A:HOH652 4.3 62.1 1.0
OE1 C:GLU354 4.4 44.8 1.0
CB A:ASP342 4.4 41.0 1.0
O A:ALA344 4.6 55.3 1.0
CE1 A:HIS337 4.6 45.4 1.0
CG1 A:VAL185 4.7 32.0 1.0
C A:ALA344 4.7 56.3 1.0
OE2 C:GLU354 4.7 47.0 1.0
CD A:GLU333 4.8 48.9 1.0
CD C:GLU354 4.9 43.0 1.0
O4 A:OEX416 4.9 40.0 1.0
O A:HOH639 5.0 50.3 1.0
MN4 A:OEX416 5.0 50.9 1.0

Manganese binding site 2 out of 8 in 6jlm

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Manganese binding site 2 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn416

b:43.0
occ:1.00
 MN2 A:OEX416 0.0 43.0 1.0
O1 A:OEX416 1.8 56.5 1.0
O2 A:OEX416 1.8 45.1 1.0
OXT A:ALA344 1.9 45.8 1.0
O3 A:OEX416 1.9 77.6 1.0
OE1 C:GLU354 2.1 44.8 1.0
OD1 A:ASP342 2.2 40.8 1.0
MN1 A:OEX416 2.6 42.8 1.0
MN3 A:OEX416 2.7 42.9 1.0
C A:ALA344 2.9 56.3 1.0
CD C:GLU354 3.0 43.0 1.0
CG A:ASP342 3.1 35.2 1.0
OE2 C:GLU354 3.2 47.0 1.0
O A:ALA344 3.2 55.3 1.0
OD2 A:ASP342 3.3 59.5 1.0
CA1 A:OEX416 3.5 51.2 1.0
O5 A:OEX416 3.5 61.3 1.0
NE2 A:HIS337 3.8 37.7 1.0
O A:HOH526 3.9 53.9 1.0
O C:HOH767 4.0 35.5 1.0
OE2 A:GLU189 4.0 58.8 1.0
O4 A:OEX416 4.2 40.0 1.0
CA A:ALA344 4.2 57.3 1.0
N A:ALA344 4.3 66.5 1.0
NE2 A:HIS332 4.3 38.7 1.0
CD2 A:HIS337 4.4 47.0 1.0
CG C:GLU354 4.4 45.7 1.0
OE1 A:GLU333 4.4 47.1 1.0
CB A:ASP342 4.5 41.0 1.0
NH2 C:ARG357 4.7 36.0 1.0
OE1 A:GLU189 4.7 54.4 1.0
CD A:GLU189 4.7 41.5 1.0
CA A:ASP342 4.9 36.4 1.0
CB C:GLU354 4.9 31.7 1.0
C A:ASP342 5.0 38.3 1.0
OD1 A:ASP170 5.0 50.2 1.0

Manganese binding site 3 out of 8 in 6jlm

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Manganese binding site 3 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn416

b:42.9
occ:1.00
 MN3 A:OEX416 0.0 42.9 1.0
O2 A:OEX416 1.8 45.1 1.0
O4 A:OEX416 1.9 40.0 1.0
O5 A:OEX416 2.0 61.3 1.0
OE1 A:GLU333 2.1 47.1 1.0
O3 A:OEX416 2.1 77.6 1.0
OE2 C:GLU354 2.1 47.0 1.0
MN2 A:OEX416 2.7 43.0 1.0
MN4 A:OEX416 2.9 50.9 1.0
CD A:GLU333 3.0 48.9 1.0
CD C:GLU354 3.0 43.0 1.0
OE2 A:GLU333 3.2 46.9 1.0
MN1 A:OEX416 3.2 42.8 1.0
OE1 C:GLU354 3.3 44.8 1.0
O1 A:OEX416 3.4 56.5 1.0
CA1 A:OEX416 3.5 51.2 1.0
NE2 A:HIS332 3.9 38.7 1.0
O C:HOH625 4.0 49.1 1.0
NH2 C:ARG357 4.0 36.0 1.0
NE2 A:HIS337 4.2 37.7 1.0
OXT A:ALA344 4.2 45.8 1.0
OD2 A:ASP170 4.2 49.6 1.0
O A:HOH520 4.3 40.9 1.0
CD2 A:HIS332 4.3 43.0 1.0
CG A:GLU333 4.4 46.5 1.0
OD1 A:ASP170 4.4 50.2 1.0
CG C:GLU354 4.4 45.7 1.0
O A:HOH536 4.5 33.5 1.0
OD1 A:ASP342 4.6 40.8 1.0
O A:ALA344 4.6 55.3 1.0
OE2 A:GLU189 4.7 58.8 1.0
O A:HOH560 4.7 34.0 1.0
CB A:GLU333 4.7 36.9 1.0
CG A:ASP170 4.7 51.3 1.0
OD2 A:ASP342 4.8 59.5 1.0
CE1 A:HIS337 4.8 45.4 1.0
C A:ALA344 4.9 56.3 1.0

Manganese binding site 4 out of 8 in 6jlm

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Manganese binding site 4 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn416

b:50.9
occ:1.00
 MN4 A:OEX416 0.0 50.9 1.0
O4 A:OEX416 2.0 40.0 1.0
OD2 A:ASP170 2.0 49.6 1.0
OE2 A:GLU333 2.1 46.9 1.0
O A:HOH536 2.1 33.5 1.0
O A:HOH560 2.2 34.0 1.0
O5 A:OEX416 2.3 61.3 1.0
MN3 A:OEX416 2.9 42.9 1.0
CD A:GLU333 3.0 48.9 1.0
CG A:ASP170 3.2 51.3 1.0
OE1 A:GLU333 3.3 47.1 1.0
OD1 A:ASP170 3.6 50.2 1.0
CA1 A:OEX416 3.7 51.2 1.0
O A:HOH520 3.7 40.9 1.0
O2 A:OEX416 3.8 45.1 1.0
O A:HOH639 3.8 50.3 1.0
O A:HOH649 4.0 43.1 1.0
OD1 A:ASP61 4.1 38.4 1.0
O A:HOH554 4.1 38.4 1.0
O A:SER169 4.4 39.5 1.0
CG A:GLU333 4.4 46.5 1.0
CB A:ASP170 4.4 46.7 1.0
NH2 C:ARG357 4.5 36.0 1.0
OE2 C:GLU354 4.5 47.0 1.0
CA A:ASP170 4.6 38.7 1.0
O3 A:OEX416 4.7 77.6 1.0
O D:HOH523 4.9 38.7 1.0
C A:SER169 4.9 31.1 1.0
MN1 A:OEX416 5.0 42.8 1.0

Manganese binding site 5 out of 8 in 6jlm

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Manganese binding site 5 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:45.5
occ:1.00
 MN1 a:OEX416 0.0 45.5 1.0
OE2 a:GLU189 1.8 40.7 1.0
O1 a:OEX416 1.8 63.8 1.0
O3 a:OEX416 1.9 60.0 1.0
NE2 a:HIS332 2.1 40.5 1.0
OD2 a:ASP342 2.2 49.7 1.0
MN2 a:OEX416 2.5 43.2 1.0
O5 a:OEX416 2.7 47.6 1.0
CE1 a:HIS332 2.9 38.4 1.0
CD a:GLU189 2.9 47.5 1.0
CG a:ASP342 3.1 33.5 1.0
CD2 a:HIS332 3.2 41.2 1.0
MN3 a:OEX416 3.3 45.7 1.0
OD1 a:ASP342 3.3 54.1 1.0
O2 a:OEX416 3.5 74.3 1.0
OE1 a:GLU189 3.6 54.4 1.0
CA1 a:OEX416 3.7 53.0 1.0
NE2 a:HIS337 3.9 44.2 1.0
OE1 a:GLU333 3.9 47.1 1.0
O a:HOH579 4.0 44.6 1.0
O a:HOH645 4.0 60.0 1.0
ND1 a:HIS332 4.0 35.6 1.0
CG a:GLU189 4.1 47.0 1.0
OXT a:ALA344 4.1 45.3 1.0
CG a:HIS332 4.2 40.7 1.0
OE1 c:GLU354 4.3 46.5 1.0
CB a:ASP342 4.4 40.2 1.0
O a:ALA344 4.5 53.2 1.0
OE2 c:GLU354 4.5 53.7 1.0
CG1 a:VAL185 4.6 31.6 1.0
CE1 a:HIS337 4.6 46.4 1.0
C a:ALA344 4.7 56.5 1.0
CD a:GLU333 4.8 48.2 1.0
CD c:GLU354 4.8 54.4 1.0
MN4 a:OEX416 5.0 45.2 1.0
CD2 a:HIS337 5.0 50.2 1.0

Manganese binding site 6 out of 8 in 6jlm

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Manganese binding site 6 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:43.2
occ:1.00
 MN2 a:OEX416 0.0 43.2 1.0
O1 a:OEX416 1.8 63.8 1.0
O2 a:OEX416 1.9 74.3 1.0
OXT a:ALA344 1.9 45.3 1.0
O3 a:OEX416 1.9 60.0 1.0
OE1 c:GLU354 2.1 46.5 1.0
OD1 a:ASP342 2.2 54.1 1.0
MN1 a:OEX416 2.5 45.5 1.0
MN3 a:OEX416 2.7 45.7 1.0
C a:ALA344 2.8 56.5 1.0
CG a:ASP342 3.0 33.5 1.0
CD c:GLU354 3.0 54.4 1.0
OD2 a:ASP342 3.1 49.7 1.0
O a:ALA344 3.1 53.2 1.0
OE2 c:GLU354 3.2 53.7 1.0
O5 a:OEX416 3.4 47.6 1.0
CA1 a:OEX416 3.5 53.0 1.0
NE2 a:HIS337 3.9 44.2 1.0
OE2 a:GLU189 4.0 40.7 1.0
O a:HOH579 4.1 44.6 1.0
O a:HOH636 4.2 44.3 1.0
CA a:ALA344 4.2 57.4 1.0
NE2 a:HIS332 4.3 40.5 1.0
OE1 a:GLU333 4.3 47.1 1.0
O4 a:OEX416 4.4 35.5 1.0
N a:ALA344 4.4 65.1 1.0
CD2 a:HIS337 4.4 50.2 1.0
CG c:GLU354 4.4 43.3 1.0
CB a:ASP342 4.4 40.2 1.0
CD a:GLU189 4.7 47.5 1.0
OE1 a:GLU189 4.8 54.4 1.0
NH2 c:ARG357 4.9 49.0 1.0
CA a:ASP342 4.9 42.8 1.0
CB c:GLU354 4.9 38.6 1.0
OD1 a:ASP170 5.0 56.1 1.0

Manganese binding site 7 out of 8 in 6jlm

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Manganese binding site 7 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:45.7
occ:1.00
 MN3 a:OEX416 0.0 45.7 1.0
O2 a:OEX416 1.8 74.3 1.0
O4 a:OEX416 1.9 35.5 1.0
O5 a:OEX416 2.0 47.6 1.0
OE1 a:GLU333 2.1 47.1 1.0
O3 a:OEX416 2.1 60.0 1.0
OE2 c:GLU354 2.1 53.7 1.0
MN2 a:OEX416 2.7 43.2 1.0
MN4 a:OEX416 2.9 45.2 1.0
CD c:GLU354 3.0 54.4 1.0
CD a:GLU333 3.0 48.2 1.0
OE1 c:GLU354 3.2 46.5 1.0
MN1 a:OEX416 3.3 45.5 1.0
OE2 a:GLU333 3.3 45.0 1.0
O1 a:OEX416 3.5 63.8 1.0
CA1 a:OEX416 3.6 53.0 1.0
O c:HOH1083 4.0 47.6 1.0
NH2 c:ARG357 4.0 49.0 1.0
NE2 a:HIS332 4.1 40.5 1.0
OD2 a:ASP170 4.1 51.3 1.0
OXT a:ALA344 4.2 45.3 1.0
OD1 a:ASP170 4.2 56.1 1.0
O a:HOH517 4.2 41.3 1.0
NE2 a:HIS337 4.3 44.2 1.0
CG c:GLU354 4.4 43.3 1.0
CG a:GLU333 4.4 45.2 1.0
CD2 a:HIS332 4.5 41.2 1.0
O a:HOH574 4.6 43.2 1.0
CG a:ASP170 4.6 42.9 1.0
O a:HOH537 4.7 41.2 1.0
OE2 a:GLU189 4.7 40.7 1.0
O a:ALA344 4.7 53.2 1.0
OD1 a:ASP342 4.7 54.1 1.0
OD2 a:ASP342 4.8 49.7 1.0
CB a:GLU333 4.8 38.6 1.0
C a:ALA344 4.9 56.5 1.0

Manganese binding site 8 out of 8 in 6jlm

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Manganese binding site 8 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:45.2
occ:1.00
 MN4 a:OEX416 0.0 45.2 1.0
O4 a:OEX416 2.0 35.5 1.0
OD2 a:ASP170 2.1 51.3 1.0
O a:HOH574 2.1 43.2 1.0
OE2 a:GLU333 2.1 45.0 1.0
O a:HOH537 2.2 41.2 1.0
O5 a:OEX416 2.3 47.6 1.0
MN3 a:OEX416 2.9 45.7 1.0
CD a:GLU333 3.0 48.2 1.0
CG a:ASP170 3.2 42.9 1.0
OE1 a:GLU333 3.2 47.1 1.0
OD1 a:ASP170 3.6 56.1 1.0
O2 a:OEX416 3.8 74.3 1.0
O a:HOH632 3.9 57.9 1.0
O a:HOH517 3.9 41.3 1.0
CA1 a:OEX416 3.9 53.0 1.0
O a:HOH530 4.1 44.6 1.0
OD1 a:ASP61 4.1 41.7 1.0
O a:HOH649 4.1 45.1 1.0
O a:SER169 4.3 41.8 1.0
CG a:GLU333 4.4 45.2 1.0
CB a:ASP170 4.4 59.8 1.0
CA a:ASP170 4.6 48.0 1.0
O3 a:OEX416 4.6 60.0 1.0
OE2 c:GLU354 4.6 53.7 1.0
O d:HOH520 4.7 34.6 1.0
NH2 c:ARG357 4.8 49.0 1.0
C a:SER169 4.9 31.0 1.0
MN1 a:OEX416 5.0 45.5 1.0
O a:HOH560 5.0 39.1 1.0

Reference:

M.Suga, F.Akita, K.Yamashita, Y.Nakajima, G.Ueno, H.Li, T.Yamane, K.Hirata, Y.Umena, S.Yonekura, L.J.Yu, H.Murakami, T.Nomura, T.Kimura, M.Kubo, S.Baba, T.Kumasaka, K.Tono, M.Yabashi, H.Isobe, K.Yamaguchi, M.Yamamoto, H.Ago, J.R.Shen. An Oxyl/Oxo Mechanism For Oxygen-Oxygen Coupling in Psii Revealed By An X-Ray Free-Electron Laser. Science V. 366 334 2019.
ISSN: ESSN 1095-9203
PubMed: 31624207
DOI: 10.1126/SCIENCE.AAX6998
Page generated: Sun Oct 6 04:59:06 2024

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