Atomistry » Manganese » PDB 3hw6-3ki9 » 3jcu
Atomistry »
  Manganese »
    PDB 3hw6-3ki9 »
      3jcu »

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

Go back to Manganese Binding Sites List in 3jcu
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

Go back to Manganese Binding Sites List in 3jcu
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

Go back to Manganese Binding Sites List in 3jcu
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

Go back to Manganese Binding Sites List in 3jcu
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

Go back to Manganese Binding Sites List in 3jcu
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

Go back to Manganese Binding Sites List in 3jcu
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

Go back to Manganese Binding Sites List in 3jcu
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

Go back to Manganese Binding Sites List in 3jcu
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy