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Manganese in PDB 5xnm: Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum

Enzymatic activity of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum

All present enzymatic activity of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum:
1.10.3.9;

Other elements in 5xnm:

The structure of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum also contains other interesting chemical elements:

Magnesium (Mg) 314 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum (pdb code 5xnm). 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 Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum, PDB code: 5xnm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5xnm

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Manganese binding site 1 out of 8 in the Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum 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
OE2 A:GLU189 2.0 42.4 1.0
O1 A:OEX401 2.0 21.8 1.0
NE2 A:HIS332 2.1 54.0 1.0
OD2 A:ASP342 2.2 79.2 1.0
O5 A:OEX401 2.6 23.5 1.0
CD A:GLU189 2.8 41.8 1.0
MN2 A:OEX401 2.8 23.1 1.0
CE1 A:HIS332 3.0 59.2 1.0
CG A:ASP342 3.1 77.7 1.0
CD2 A:HIS332 3.2 53.5 1.0
OD1 A:ASP342 3.3 75.4 1.0
MN3 A:OEX401 3.4 23.4 1.0
CA1 A:OEX401 3.5 25.2 1.0
CG A:GLU189 3.5 42.6 1.0
OE1 A:GLU189 3.6 44.4 1.0
O2 A:OEX401 3.7 25.9 1.0
OXT A:ALA344 3.8 70.4 1.0
NE2 A:HIS337 3.9 83.1 1.0
OE1 C:GLU354 4.1 82.6 1.0
ND1 A:HIS332 4.2 53.2 1.0
CG A:HIS332 4.3 53.6 1.0
CB A:ASP342 4.4 76.0 1.0
OE2 C:GLU354 4.5 82.6 1.0
CE1 A:HIS337 4.7 81.3 1.0
CD C:GLU354 4.7 82.5 1.0
CB A:GLU189 4.8 38.0 1.0
CD2 A:HIS337 5.0 80.9 1.0
MN4 A:OEX401 5.0 27.0 1.0

Manganese binding site 2 out of 8 in 5xnm

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Manganese binding site 2 out of 8 in the Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum 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
OE1 C:GLU354 1.9 82.6 1.0
OXT A:ALA344 2.0 70.4 1.0
O1 A:OEX401 2.0 21.8 1.0
OD1 A:ASP342 2.1 75.4 1.0
O2 A:OEX401 2.1 25.9 1.0
O3 A:OEX401 2.2 23.1 1.0
MN1 A:OEX401 2.8 22.3 1.0
C A:ALA344 2.9 69.5 1.0
CD C:GLU354 2.9 82.5 1.0
MN3 A:OEX401 3.0 23.4 1.0
CG A:ASP342 3.0 77.7 1.0
OD2 A:ASP342 3.3 79.2 1.0
CA1 A:OEX401 3.3 25.2 1.0
OE2 C:GLU354 3.4 82.6 1.0
N A:ALA344 3.5 70.9 1.0
CA A:ALA344 3.5 68.6 1.0
O A:ALA344 3.7 72.1 1.0
O5 A:OEX401 3.9 23.5 1.0
CB A:ALA344 3.9 68.3 1.0
NE2 A:HIS337 4.1 83.1 1.0
CG C:GLU354 4.2 80.4 1.0
CB C:GLU354 4.4 83.3 1.0
CB A:ASP342 4.4 76.0 1.0
OE2 A:GLU189 4.5 42.4 1.0
CD2 A:HIS337 4.5 80.9 1.0
O4 A:OEX401 4.6 28.5 1.0
NE2 A:HIS332 4.6 54.0 1.0
N A:LEU343 4.6 67.6 1.0
C A:ASP342 4.7 86.9 1.0
C A:LEU343 4.7 72.2 1.0
CA A:ASP342 4.8 87.2 1.0
OE1 A:GLU333 4.8 84.4 1.0

Manganese binding site 3 out of 8 in 5xnm

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Manganese binding site 3 out of 8 in the Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum 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
OE2 C:GLU354 1.8 82.6 1.0
O2 A:OEX401 1.9 25.9 1.0
OE1 A:GLU333 2.0 84.4 1.0
O4 A:OEX401 2.1 28.5 1.0
O3 A:OEX401 2.2 23.1 1.0
O5 A:OEX401 2.4 23.5 1.0
CD C:GLU354 2.6 82.5 1.0
OE1 C:GLU354 2.8 82.6 1.0
MN4 A:OEX401 2.9 27.0 1.0
CD A:GLU333 2.9 81.1 1.0
MN2 A:OEX401 3.0 23.1 1.0
MN1 A:OEX401 3.4 22.3 1.0
CA1 A:OEX401 3.4 25.2 1.0
OE2 A:GLU333 3.5 82.6 1.0
O1 A:OEX401 3.7 21.8 1.0
CG A:GLU333 3.9 82.0 1.0
NE2 A:HIS332 4.0 54.0 1.0
CG C:GLU354 4.0 80.4 1.0
OXT A:ALA344 4.1 70.4 1.0
CB A:GLU333 4.1 81.9 1.0
NH2 C:ARG357 4.1 71.8 1.0
CD2 A:HIS332 4.1 53.5 1.0
OE2 A:GLU189 4.2 42.4 1.0
OD1 A:ASP170 4.3 54.1 1.0
NE2 A:HIS337 4.3 83.1 1.0
OD1 A:ASP342 4.6 75.4 1.0
OD2 A:ASP342 4.7 79.2 1.0
CE1 A:HIS337 4.7 81.3 1.0
OD2 A:ASP170 4.7 53.9 1.0
C A:ALA344 4.8 69.5 1.0
CZ C:ARG357 4.8 58.3 1.0
CB C:GLU354 4.9 83.3 1.0
NH1 C:ARG357 4.9 58.2 1.0
O A:ALA344 4.9 72.1 1.0
CG A:ASP170 5.0 53.0 1.0

Manganese binding site 4 out of 8 in 5xnm

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Manganese binding site 4 out of 8 in the Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum 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 54.1 1.0
O4 A:OEX401 2.1 28.5 1.0
OE2 A:GLU333 2.1 82.6 1.0
O5 A:OEX401 2.4 23.5 1.0
CD A:GLU333 2.6 81.1 1.0
MN3 A:OEX401 2.9 23.4 1.0
OE1 A:GLU333 2.9 84.4 1.0
CG A:ASP170 3.2 53.0 1.0
CA1 A:OEX401 3.6 25.2 1.0
OD2 A:ASP170 3.7 53.9 1.0
CG A:GLU333 3.7 82.0 1.0
O2 A:OEX401 3.7 25.9 1.0
NH2 C:ARG357 4.1 71.8 1.0
OE2 C:GLU354 4.4 82.6 1.0
CB A:ASP170 4.4 51.9 1.0
CA A:ASP170 4.5 45.3 1.0
NH1 C:ARG357 4.6 58.2 1.0
O3 A:OEX401 4.6 23.1 1.0
OE2 A:GLU189 4.6 42.4 1.0
CD2 A:HIS332 4.7 53.5 1.0
OG A:SER169 4.8 45.4 1.0
CB A:GLU333 4.8 81.9 1.0
N A:ASP170 4.8 43.6 1.0
CZ C:ARG357 4.9 58.3 1.0
CG1 A:VAL185 4.9 34.9 1.0
O A:SER169 5.0 40.8 1.0
MN1 A:OEX401 5.0 22.3 1.0

Manganese binding site 5 out of 8 in 5xnm

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Manganese binding site 5 out of 8 in the Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum 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
OE2 a:GLU189 2.0 42.0 1.0
O1 a:OEX401 2.0 21.8 1.0
NE2 a:HIS332 2.1 55.0 1.0
OD2 a:ASP342 2.2 84.8 1.0
O5 a:OEX401 2.6 23.5 1.0
CD a:GLU189 2.8 41.4 1.0
MN2 a:OEX401 2.8 23.1 1.0
CE1 a:HIS332 3.0 60.2 1.0
CG a:ASP342 3.1 83.4 1.0
CD2 a:HIS332 3.2 54.4 1.0
OD1 a:ASP342 3.3 81.1 1.0
MN3 a:OEX401 3.4 23.4 1.0
CA1 a:OEX401 3.5 25.2 1.0
CG a:GLU189 3.5 42.2 1.0
OE1 a:GLU189 3.6 44.0 1.0
O2 a:OEX401 3.7 25.9 1.0
OXT a:ALA344 3.8 74.6 1.0
NE2 a:HIS337 3.9 86.3 1.0
OE1 c:GLU354 4.1 85.4 1.0
ND1 a:HIS332 4.2 54.1 1.0
CG a:HIS332 4.3 54.6 1.0
CB a:ASP342 4.4 81.7 1.0
OE2 c:GLU354 4.5 85.4 1.0
CE1 a:HIS337 4.7 84.5 1.0
CD c:GLU354 4.7 85.3 1.0
CB a:GLU189 4.8 37.6 1.0
CD2 a:HIS337 5.0 84.0 1.0
MN4 a:OEX401 5.0 27.0 1.0

Manganese binding site 6 out of 8 in 5xnm

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Manganese binding site 6 out of 8 in the Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum 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
OE1 c:GLU354 1.9 85.4 1.0
OXT a:ALA344 2.0 74.6 1.0
O1 a:OEX401 2.0 21.8 1.0
OD1 a:ASP342 2.1 81.1 1.0
O2 a:OEX401 2.1 25.9 1.0
O3 a:OEX401 2.2 23.1 1.0
MN1 a:OEX401 2.8 22.3 1.0
C a:ALA344 2.9 72.6 1.0
CD c:GLU354 2.9 85.3 1.0
MN3 a:OEX401 3.0 23.4 1.0
CG a:ASP342 3.0 83.4 1.0
OD2 a:ASP342 3.3 84.8 1.0
CA1 a:OEX401 3.3 25.2 1.0
OE2 c:GLU354 3.4 85.4 1.0
N a:ALA344 3.5 74.0 1.0
CA a:ALA344 3.5 71.7 1.0
O a:ALA344 3.7 75.3 1.0
O5 a:OEX401 3.9 23.5 1.0
CB a:ALA344 3.9 72.6 1.0
NE2 a:HIS337 4.1 86.3 1.0
CG c:GLU354 4.2 83.2 1.0
CB c:GLU354 4.4 86.1 1.0
CB a:ASP342 4.4 81.7 1.0
OE2 a:GLU189 4.4 42.0 1.0
CD2 a:HIS337 4.5 84.0 1.0
O4 a:OEX401 4.6 28.5 1.0
NE2 a:HIS332 4.6 55.0 1.0
N a:LEU343 4.6 73.3 1.0
C a:ASP342 4.7 91.5 1.0
C a:LEU343 4.7 77.9 1.0
CA a:ASP342 4.8 91.8 1.0
OE1 a:GLU333 4.8 86.5 1.0

Manganese binding site 7 out of 8 in 5xnm

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Manganese binding site 7 out of 8 in the Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum 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
OE2 c:GLU354 1.8 85.4 1.0
O2 a:OEX401 1.9 25.9 1.0
OE1 a:GLU333 2.0 86.5 1.0
O4 a:OEX401 2.1 28.5 1.0
O3 a:OEX401 2.2 23.1 1.0
O5 a:OEX401 2.4 23.5 1.0
CD c:GLU354 2.6 85.3 1.0
OE1 c:GLU354 2.8 85.4 1.0
MN4 a:OEX401 2.9 27.0 1.0
CD a:GLU333 2.9 83.2 1.0
MN2 a:OEX401 3.0 23.1 1.0
MN1 a:OEX401 3.4 22.3 1.0
CA1 a:OEX401 3.4 25.2 1.0
OE2 a:GLU333 3.5 84.7 1.0
O1 a:OEX401 3.7 21.8 1.0
CG a:GLU333 3.9 84.2 1.0
NE2 a:HIS332 4.0 55.0 1.0
CG c:GLU354 4.0 83.2 1.0
OXT a:ALA344 4.1 74.6 1.0
CB a:GLU333 4.1 84.1 1.0
NH2 c:ARG357 4.1 72.4 1.0
CD2 a:HIS332 4.1 54.4 1.0
OE2 a:GLU189 4.2 42.0 1.0
OD1 a:ASP170 4.3 56.5 1.0
NE2 a:HIS337 4.3 86.3 1.0
OD1 a:ASP342 4.6 81.1 1.0
OD2 a:ASP342 4.7 84.8 1.0
CE1 a:HIS337 4.7 84.5 1.0
OD2 a:ASP170 4.7 56.3 1.0
C a:ALA344 4.8 72.6 1.0
CZ c:ARG357 4.8 58.9 1.0
CB c:GLU354 4.9 86.1 1.0
NH1 c:ARG357 4.9 58.8 1.0
O a:ALA344 4.9 75.3 1.0
CG a:ASP170 5.0 55.4 1.0

Manganese binding site 8 out of 8 in 5xnm

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Manganese binding site 8 out of 8 in the Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of Unstacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum 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 56.5 1.0
O4 a:OEX401 2.1 28.5 1.0
OE2 a:GLU333 2.1 84.7 1.0
O5 a:OEX401 2.4 23.5 1.0
CD a:GLU333 2.6 83.2 1.0
MN3 a:OEX401 2.9 23.4 1.0
OE1 a:GLU333 2.9 86.5 1.0
CG a:ASP170 3.2 55.4 1.0
CA1 a:OEX401 3.6 25.2 1.0
OD2 a:ASP170 3.7 56.3 1.0
CG a:GLU333 3.7 84.2 1.0
O2 a:OEX401 3.7 25.9 1.0
NH2 c:ARG357 4.1 72.4 1.0
OE2 c:GLU354 4.4 85.4 1.0
CB a:ASP170 4.4 54.3 1.0
CA a:ASP170 4.5 45.8 1.0
NH1 c:ARG357 4.6 58.8 1.0
O3 a:OEX401 4.6 23.1 1.0
OE2 a:GLU189 4.6 42.0 1.0
CD2 a:HIS332 4.7 54.4 1.0
OG a:SER169 4.8 46.7 1.0
CB a:GLU333 4.8 84.1 1.0
N a:ASP170 4.8 44.1 1.0
CZ c:ARG357 4.9 58.9 1.0
CG1 a:VAL185 4.9 36.7 1.0
O a:SER169 5.0 42.5 1.0
MN1 a:OEX401 5.0 22.3 1.0

Reference:

X.Su, J.Ma, X.Wei, P.Cao, D.Zhu, W.Chang, Z.Liu, X.Zhang, M.Li. Structure and Assembly Mechanism of Plant C2S2M2-Type Psii-Lhcii Supercomplex Science V. 357 815 2017.
ISSN: ESSN 1095-9203
PubMed: 28839073
DOI: 10.1126/SCIENCE.AAN0327
Page generated: Tue Dec 15 04:49:10 2020

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