Manganese in PDB 8xr6: Cryo-Em Structure of Cryptophyte Photosystem II

Enzymatic activity of Cryo-Em Structure of Cryptophyte Photosystem II

All present enzymatic activity of Cryo-Em Structure of Cryptophyte Photosystem II:
1.10.3.9;

Other elements in 8xr6:

The structure of Cryo-Em Structure of Cryptophyte Photosystem II also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms
Iron (Fe) 6 atoms
Magnesium (Mg) 224 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Cryo-Em Structure of Cryptophyte Photosystem II (pdb code 8xr6). 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 Cryptophyte Photosystem II, PDB code: 8xr6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8xr6

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Manganese binding site 1 out of 8 in the Cryo-Em Structure of Cryptophyte Photosystem II


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 Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:45.9
occ:1.00
 MN1 a:OEX401 0.0 45.9 1.0
O1 a:OEX401 1.9 45.9 1.0
O3 a:OEX401 1.9 45.9 1.0
OE2 a:GLU189 1.9 24.6 1.0
NE2 a:HIS332 2.5 29.5 1.0
OD2 a:ASP342 2.5 34.5 1.0
CD a:GLU189 2.8 24.6 1.0
MN2 a:OEX401 3.0 45.9 1.0
O5 a:OEX401 3.2 45.9 1.0
CG a:ASP342 3.2 34.5 1.0
MN3 a:OEX401 3.3 45.9 1.0
OD1 a:ASP342 3.3 34.5 1.0
CD2 a:HIS332 3.3 29.5 1.0
OE1 a:GLU189 3.4 24.6 1.0
CE1 a:HIS332 3.4 29.5 1.0
CA1 a:OEX401 3.5 45.9 1.0
O2 a:OEX401 3.8 45.9 1.0
CG a:GLU189 3.8 24.6 1.0
NE2 a:HIS337 3.9 36.9 1.0
OE1 a:GLU333 4.3 33.9 1.0
CE1 a:HIS337 4.3 36.9 1.0
OE2 a:GLU333 4.3 33.9 1.0
CG a:HIS332 4.5 29.5 1.0
ND1 a:HIS332 4.5 29.5 1.0
O a:HOH512 4.5 30.0 1.0
CD a:GLU333 4.5 33.9 1.0
CG1 a:VAL185 4.6 22.7 1.0
CB a:ASP342 4.7 34.5 1.0
OE1 c:GLU354 4.8 35.5 1.0

Manganese binding site 2 out of 8 in 8xr6

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Manganese binding site 2 out of 8 in the Cryo-Em Structure of Cryptophyte Photosystem II


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 Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:45.9
occ:1.00
 MN2 a:OEX401 0.0 45.9 1.0
O1 a:OEX401 1.9 45.9 1.0
O3 a:OEX401 1.9 45.9 1.0
O2 a:OEX401 2.0 45.9 1.0
OD1 a:ASP342 2.3 34.5 1.0
OE1 c:GLU354 2.5 35.5 1.0
MN1 a:OEX401 3.0 45.9 1.0
MN3 a:OEX401 3.0 45.9 1.0
CG a:ASP342 3.3 34.5 1.0
CD c:GLU354 3.4 35.5 1.0
C a:ALA344 3.5 34.5 1.0
CA1 a:OEX401 3.5 45.9 1.0
NE2 a:HIS337 3.6 36.9 1.0
OE2 c:GLU354 3.6 35.5 1.0
O a:ALA344 3.7 34.5 1.0
OD2 a:ASP342 3.7 34.5 1.0
O5 a:OEX401 3.7 45.9 1.0
CB a:ALA344 3.9 34.5 1.0
CA a:ALA344 4.1 34.5 1.0
O c:HOH608 4.3 30.0 1.0
CD2 a:HIS337 4.3 36.9 1.0
N a:ALA344 4.3 34.5 1.0
O a:HOH512 4.5 30.0 1.0
OE2 a:GLU189 4.6 24.6 1.0
CB a:ASP342 4.6 34.5 1.0
O4 a:OEX401 4.7 45.9 1.0
OE1 a:GLU333 4.7 33.9 1.0
O a:ASP342 4.7 34.5 1.0
CE1 a:HIS337 4.7 36.9 1.0
C a:ASP342 4.8 34.5 1.0
CG c:GLU354 4.8 35.5 1.0
CA a:ASP342 4.8 34.5 1.0
NH2 c:ARG357 4.8 29.9 1.0
OE1 a:GLU189 4.9 24.6 1.0
NE2 a:HIS332 5.0 29.5 1.0

Manganese binding site 3 out of 8 in 8xr6

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Manganese binding site 3 out of 8 in the Cryo-Em Structure of Cryptophyte Photosystem II


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 Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:45.9
occ:1.00
 MN3 a:OEX401 0.0 45.9 1.0
O5 a:OEX401 1.9 45.9 1.0
O3 a:OEX401 1.9 45.9 1.0
O2 a:OEX401 2.0 45.9 1.0
O4 a:OEX401 2.0 45.9 1.0
OE1 a:GLU333 2.2 33.9 1.0
OE2 c:GLU354 2.6 35.5 1.0
OE2 a:GLU333 2.7 33.9 1.0
CD a:GLU333 2.8 33.9 1.0
MN2 a:OEX401 3.0 45.9 1.0
MN4 a:OEX401 3.0 45.9 1.0
MN1 a:OEX401 3.3 45.9 1.0
O1 a:OEX401 3.3 45.9 1.0
CD c:GLU354 3.5 35.5 1.0
OE1 c:GLU354 3.6 35.5 1.0
CA1 a:OEX401 3.6 45.9 1.0
NE2 a:HIS337 3.9 36.9 1.0
NH2 c:ARG357 4.0 29.9 1.0
CE1 a:HIS337 4.3 36.9 1.0
CG a:GLU333 4.3 33.9 1.0
OD1 a:ASP170 4.4 24.5 1.0
NE2 a:HIS332 4.5 29.5 1.0
O a:HOH516 4.5 30.0 1.0
OE2 a:GLU189 4.6 24.6 1.0
CD2 a:HIS332 4.6 29.5 1.0
OD1 a:ASP342 4.7 34.5 1.0
CB a:GLU333 4.8 33.9 1.0
CG c:GLU354 4.9 35.5 1.0
CD2 a:HIS337 5.0 36.9 1.0
CZ c:ARG357 5.0 29.9 1.0

Manganese binding site 4 out of 8 in 8xr6

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Manganese binding site 4 out of 8 in the Cryo-Em Structure of Cryptophyte Photosystem II


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 Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:45.9
occ:1.00
 MN4 a:OEX401 0.0 45.9 1.0
O5 a:OEX401 1.9 45.9 1.0
O4 a:OEX401 2.0 45.9 1.0
O a:HOH516 2.0 30.0 1.0
OD1 a:ASP170 2.3 24.5 1.0
OE2 a:GLU333 2.7 33.9 1.0
MN3 a:OEX401 3.0 45.9 1.0
CG a:ASP170 3.6 24.5 1.0
CA1 a:OEX401 3.7 45.9 1.0
CD a:GLU333 3.7 33.9 1.0
O2 a:OEX401 3.9 45.9 1.0
OE1 a:GLU333 4.1 33.9 1.0
NH2 c:ARG357 4.2 29.9 1.0
OD2 a:ASP170 4.3 24.5 1.0
CA a:ASP170 4.3 24.5 1.0
O a:SER169 4.3 24.9 1.0
OG a:SER169 4.5 24.9 1.0
CB a:ASP170 4.5 24.5 1.0
O3 a:OEX401 4.6 45.9 1.0
O a:HOH514 4.6 30.0 1.0
C a:SER169 4.7 24.9 1.0
N a:ASP170 4.7 24.5 1.0
O a:HOH507 4.8 30.0 1.0
CG a:GLU333 4.9 33.9 1.0
O1 a:OEX401 5.0 45.9 1.0
OD1 a:ASP61 5.0 31.1 1.0

Manganese binding site 5 out of 8 in 8xr6

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Manganese binding site 5 out of 8 in the Cryo-Em Structure of Cryptophyte Photosystem II


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 Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:45.9
occ:1.00
 MN1 A:OEX401 0.0 45.9 1.0
O1 A:OEX401 1.9 45.9 1.0
O3 A:OEX401 1.9 45.9 1.0
OE2 A:GLU189 1.9 24.6 1.0
NE2 A:HIS332 2.5 29.5 1.0
OD2 A:ASP342 2.5 34.5 1.0
CD A:GLU189 2.8 24.6 1.0
MN2 A:OEX401 3.0 45.9 1.0
O5 A:OEX401 3.2 45.9 1.0
CG A:ASP342 3.2 34.5 1.0
MN3 A:OEX401 3.3 45.9 1.0
OD1 A:ASP342 3.3 34.5 1.0
CD2 A:HIS332 3.3 29.5 1.0
OE1 A:GLU189 3.4 24.6 1.0
CE1 A:HIS332 3.4 29.5 1.0
CA1 A:OEX401 3.5 45.9 1.0
O2 A:OEX401 3.8 45.9 1.0
CG A:GLU189 3.8 24.6 1.0
NE2 A:HIS337 3.9 36.9 1.0
OE1 A:GLU333 4.3 33.9 1.0
CE1 A:HIS337 4.3 36.9 1.0
OE2 A:GLU333 4.3 33.9 1.0
CG A:HIS332 4.5 29.5 1.0
ND1 A:HIS332 4.5 29.5 1.0
O A:HOH512 4.5 30.0 1.0
CD A:GLU333 4.5 33.9 1.0
CG1 A:VAL185 4.6 22.7 1.0
CB A:ASP342 4.7 34.5 1.0
OE1 C:GLU354 4.8 35.5 1.0

Manganese binding site 6 out of 8 in 8xr6

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Manganese binding site 6 out of 8 in the Cryo-Em Structure of Cryptophyte Photosystem II


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 Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:45.9
occ:1.00
 MN2 A:OEX401 0.0 45.9 1.0
O1 A:OEX401 1.9 45.9 1.0
O3 A:OEX401 1.9 45.9 1.0
O2 A:OEX401 2.0 45.9 1.0
OD1 A:ASP342 2.3 34.5 1.0
OE1 C:GLU354 2.5 35.5 1.0
MN1 A:OEX401 3.0 45.9 1.0
MN3 A:OEX401 3.0 45.9 1.0
CG A:ASP342 3.3 34.5 1.0
CD C:GLU354 3.4 35.5 1.0
C A:ALA344 3.5 34.5 1.0
CA1 A:OEX401 3.5 45.9 1.0
NE2 A:HIS337 3.6 36.9 1.0
OE2 C:GLU354 3.6 35.5 1.0
O A:ALA344 3.7 34.5 1.0
OD2 A:ASP342 3.7 34.5 1.0
O5 A:OEX401 3.7 45.9 1.0
CB A:ALA344 3.9 34.5 1.0
CA A:ALA344 4.1 34.5 1.0
O C:HOH608 4.3 30.0 1.0
CD2 A:HIS337 4.3 36.9 1.0
N A:ALA344 4.3 34.5 1.0
O A:HOH512 4.5 30.0 1.0
OE2 A:GLU189 4.6 24.6 1.0
CB A:ASP342 4.6 34.5 1.0
O4 A:OEX401 4.7 45.9 1.0
OE1 A:GLU333 4.7 33.9 1.0
O A:ASP342 4.7 34.5 1.0
CE1 A:HIS337 4.7 36.9 1.0
C A:ASP342 4.8 34.5 1.0
CG C:GLU354 4.8 35.5 1.0
CA A:ASP342 4.8 34.5 1.0
NH2 C:ARG357 4.8 29.9 1.0
OE1 A:GLU189 4.9 24.6 1.0
NE2 A:HIS332 5.0 29.5 1.0

Manganese binding site 7 out of 8 in 8xr6

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Manganese binding site 7 out of 8 in the Cryo-Em Structure of Cryptophyte Photosystem II


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 Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:45.9
occ:1.00
 MN3 A:OEX401 0.0 45.9 1.0
O5 A:OEX401 1.9 45.9 1.0
O3 A:OEX401 1.9 45.9 1.0
O2 A:OEX401 2.0 45.9 1.0
O4 A:OEX401 2.0 45.9 1.0
OE1 A:GLU333 2.2 33.9 1.0
OE2 C:GLU354 2.6 35.5 1.0
OE2 A:GLU333 2.7 33.9 1.0
CD A:GLU333 2.8 33.9 1.0
MN2 A:OEX401 3.0 45.9 1.0
MN4 A:OEX401 3.0 45.9 1.0
MN1 A:OEX401 3.3 45.9 1.0
O1 A:OEX401 3.3 45.9 1.0
CD C:GLU354 3.5 35.5 1.0
OE1 C:GLU354 3.6 35.5 1.0
CA1 A:OEX401 3.6 45.9 1.0
NE2 A:HIS337 3.9 36.9 1.0
NH2 C:ARG357 4.0 29.9 1.0
CE1 A:HIS337 4.3 36.9 1.0
CG A:GLU333 4.3 33.9 1.0
OD1 A:ASP170 4.4 24.5 1.0
NE2 A:HIS332 4.5 29.5 1.0
O A:HOH516 4.5 30.0 1.0
OE2 A:GLU189 4.6 24.6 1.0
CD2 A:HIS332 4.6 29.5 1.0
OD1 A:ASP342 4.7 34.5 1.0
CB A:GLU333 4.8 33.9 1.0
CG C:GLU354 4.9 35.5 1.0
CD2 A:HIS337 5.0 36.9 1.0
CZ C:ARG357 5.0 29.9 1.0

Manganese binding site 8 out of 8 in 8xr6

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Manganese binding site 8 out of 8 in the Cryo-Em Structure of Cryptophyte Photosystem II


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 Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:45.9
occ:1.00
 MN4 A:OEX401 0.0 45.9 1.0
O5 A:OEX401 1.9 45.9 1.0
O4 A:OEX401 2.0 45.9 1.0
O A:HOH516 2.0 30.0 1.0
OD1 A:ASP170 2.3 24.5 1.0
OE2 A:GLU333 2.7 33.9 1.0
MN3 A:OEX401 3.0 45.9 1.0
CG A:ASP170 3.6 24.5 1.0
CA1 A:OEX401 3.7 45.9 1.0
CD A:GLU333 3.7 33.9 1.0
O2 A:OEX401 3.9 45.9 1.0
OE1 A:GLU333 4.1 33.9 1.0
NH2 C:ARG357 4.2 29.9 1.0
OD2 A:ASP170 4.3 24.5 1.0
CA A:ASP170 4.3 24.5 1.0
O A:SER169 4.3 24.9 1.0
OG A:SER169 4.5 24.9 1.0
CB A:ASP170 4.5 24.5 1.0
O3 A:OEX401 4.6 45.9 1.0
O A:HOH514 4.6 30.0 1.0
C A:SER169 4.7 24.9 1.0
N A:ASP170 4.7 24.5 1.0
O A:HOH507 4.8 30.0 1.0
CG A:GLU333 4.9 33.9 1.0
O1 A:OEX401 4.9 45.9 1.0
OD1 A:ASP61 5.0 31.1 1.0

Reference:

K.Li, L.S.Zhao, Y.Z.Zhang, L.N.Liu. Cryo-Em Structure of Cryptophyte Photosystem II To Be Published.
Page generated: Sun Oct 6 14:11:55 2024

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