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

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

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

Other elements in 5xnl:

The structure of Structure of Stacked 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
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 8 in 5xnl

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Manganese binding site 1 out of 8 in the Structure of Stacked 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 Stacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:13.7
occ:1.00
 MN1 A:OEX401 0.0 13.7 1.0
O3 A:OEX401 1.9 14.4 1.0
OE2 A:GLU189 2.0 35.6 1.0
O1 A:OEX401 2.0 13.1 1.0
NE2 A:HIS332 2.0 27.1 1.0
OD2 A:ASP342 2.2 28.7 1.0
O5 A:OEX401 2.6 14.8 1.0
CD2 A:HIS332 2.9 26.6 1.0
MN2 A:OEX401 3.0 14.4 1.0
MN3 A:OEX401 3.0 14.7 1.0
CE1 A:HIS332 3.1 32.3 1.0
CD A:GLU189 3.1 34.9 1.0
CG A:ASP342 3.2 27.2 1.0
OD1 A:ASP342 3.4 24.9 1.0
OE1 A:GLU333 3.6 38.3 1.0
O2 A:OEX401 3.7 17.2 1.0
OE2 C:GLU354 3.8 35.9 1.0
NE2 A:HIS337 3.8 39.3 1.0
OE1 A:GLU189 3.8 37.6 1.0
CA1 A:OEX401 3.9 16.5 1.0
CG A:GLU189 4.0 35.8 1.0
CG A:HIS332 4.1 26.7 1.0
ND1 A:HIS332 4.1 26.3 1.0
CD A:GLU333 4.3 35.0 1.0
CE1 A:HIS337 4.3 37.5 1.0
OE1 C:GLU354 4.5 35.9 1.0
CD C:GLU354 4.5 35.8 1.0
O A:HOH1005 4.5 48.9 1.0
CB A:ASP342 4.6 25.5 1.0
OXT A:ALA344 4.6 39.8 1.0
CG1 A:VAL185 4.7 30.4 1.0
OE2 A:GLU333 4.7 36.5 1.0
O4 A:OEX401 4.9 19.8 1.0
CD2 A:HIS337 5.0 37.1 1.0

Manganese binding site 2 out of 8 in 5xnl

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Manganese binding site 2 out of 8 in the Structure of Stacked 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 Stacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:14.4
occ:1.00
 MN2 A:OEX401 0.0 14.4 1.0
OD1 A:ASP342 1.9 24.9 1.0
OE1 C:GLU354 1.9 35.9 1.0
OXT A:ALA344 2.0 39.8 1.0
O3 A:OEX401 2.1 14.4 1.0
O1 A:OEX401 2.1 13.1 1.0
O2 A:OEX401 2.2 17.2 1.0
CD C:GLU354 2.6 35.8 1.0
OE2 C:GLU354 2.8 35.9 1.0
CG A:ASP342 2.8 27.2 1.0
MN1 A:OEX401 3.0 13.7 1.0
MN3 A:OEX401 3.1 14.7 1.0
OD2 A:ASP342 3.1 28.7 1.0
C A:ALA344 3.2 45.6 1.0
NE2 A:HIS337 3.8 39.3 1.0
O A:HOH1005 3.8 48.9 1.0
N A:ALA344 3.9 47.0 1.0
O5 A:OEX401 3.9 14.8 1.0
CA1 A:OEX401 3.9 16.5 1.0
CA A:ALA344 4.0 44.7 1.0
CG C:GLU354 4.1 33.6 1.0
O A:ALA344 4.1 48.3 1.0
CB A:ASP342 4.1 25.5 1.0
CD2 A:HIS337 4.3 37.1 1.0
O A:HOH1080 4.4 40.1 1.0
C A:ASP342 4.4 29.8 1.0
CA A:ASP342 4.4 30.1 1.0
CB A:ALA344 4.4 37.8 1.0
CB C:GLU354 4.4 36.6 1.0
OE1 A:GLU333 4.5 38.3 1.0
OE2 A:GLU189 4.6 35.6 1.0
O A:ASP342 4.6 29.4 1.0
N A:LEU343 4.7 40.4 1.0
O4 A:OEX401 4.7 19.8 1.0
NE2 A:HIS332 4.8 27.1 1.0
C A:LEU343 4.9 45.0 1.0
CE1 A:HIS337 4.9 37.5 1.0

Manganese binding site 3 out of 8 in 5xnl

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Manganese binding site 3 out of 8 in the Structure of Stacked 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 Stacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:14.7
occ:1.00
 MN3 A:OEX401 0.0 14.7 1.0
OE2 C:GLU354 1.9 35.9 1.0
O5 A:OEX401 2.0 14.8 1.0
OE1 A:GLU333 2.0 38.3 1.0
O3 A:OEX401 2.0 14.4 1.0
O4 A:OEX401 2.0 19.8 1.0
O2 A:OEX401 2.0 17.2 1.0
CD A:GLU333 2.9 35.0 1.0
CD C:GLU354 3.0 35.8 1.0
MN1 A:OEX401 3.0 13.7 1.0
MN2 A:OEX401 3.1 14.4 1.0
OE2 A:GLU333 3.1 36.5 1.0
O1 A:OEX401 3.3 13.1 1.0
CA1 A:OEX401 3.5 16.5 1.0
MN4 A:OEX401 3.6 18.4 1.0
OE1 C:GLU354 3.6 35.9 1.0
OD1 A:ASP170 3.7 36.8 1.0
NH2 C:ARG357 3.8 48.6 1.0
OXT A:ALA344 4.0 39.8 1.0
CG C:GLU354 4.1 33.6 1.0
CG A:GLU333 4.3 35.9 1.0
NE2 A:HIS337 4.3 39.3 1.0
OD2 A:ASP170 4.3 36.6 1.0
NE2 A:HIS332 4.4 27.1 1.0
CG A:ASP170 4.4 35.7 1.0
OE2 A:GLU189 4.5 35.6 1.0
OD1 A:ASP342 4.5 24.9 1.0
CZ C:ARG357 4.6 35.0 1.0
CD2 A:HIS332 4.6 26.6 1.0
NH1 C:ARG357 4.7 34.9 1.0
CB A:GLU333 4.7 35.9 1.0
OD2 A:ASP342 4.7 28.7 1.0
CE1 A:HIS337 4.8 37.5 1.0

Manganese binding site 4 out of 8 in 5xnl

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Manganese binding site 4 out of 8 in the Structure of Stacked 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 Stacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:18.4
occ:1.00
 MN4 A:OEX401 0.0 18.4 1.0
OD1 A:ASP170 2.0 36.8 1.0
O4 A:OEX401 2.2 19.8 1.0
OE2 A:GLU333 2.2 36.5 1.0
CG A:ASP170 3.2 35.7 1.0
O5 A:OEX401 3.3 14.8 1.0
CD A:GLU333 3.3 35.0 1.0
MN3 A:OEX401 3.6 14.7 1.0
O A:SER169 3.6 30.3 1.0
CA A:ASP170 3.8 23.1 1.0
OE1 A:GLU333 3.8 38.3 1.0
O A:HOH1085 3.9 42.7 1.0
C A:SER169 3.9 29.3 1.0
O A:HOH1049 3.9 40.4 1.0
N A:ASP170 4.0 21.4 1.0
CB A:ASP170 4.1 34.6 1.0
OD2 A:ASP170 4.1 36.6 1.0
OD1 A:ASP61 4.1 50.3 1.0
OG A:SER169 4.2 34.7 1.0
O A:HOH1042 4.2 43.2 1.0
NH2 C:ARG357 4.5 48.6 1.0
CB A:SER169 4.5 34.0 1.0
CG A:GLU333 4.5 35.9 1.0
O A:HOH1020 4.6 36.0 1.0
CA1 A:OEX401 4.6 16.5 1.0
O2 A:OEX401 4.7 17.2 1.0
CA A:SER169 4.9 27.2 1.0

Manganese binding site 5 out of 8 in 5xnl

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Manganese binding site 5 out of 8 in the Structure of Stacked 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 Stacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:13.7
occ:1.00
 MN1 a:OEX401 0.0 13.7 1.0
O3 a:OEX401 1.9 14.4 1.0
OE2 a:GLU189 2.0 35.6 1.0
O1 a:OEX401 2.0 13.1 1.0
NE2 a:HIS332 2.0 27.1 1.0
OD2 a:ASP342 2.2 28.7 1.0
O5 a:OEX401 2.6 14.8 1.0
CD2 a:HIS332 2.9 26.6 1.0
MN2 a:OEX401 3.0 14.4 1.0
MN3 a:OEX401 3.0 14.7 1.0
CE1 a:HIS332 3.1 32.3 1.0
CD a:GLU189 3.1 34.9 1.0
CG a:ASP342 3.2 27.2 1.0
OD1 a:ASP342 3.4 24.9 1.0
OE1 a:GLU333 3.6 38.3 1.0
O2 a:OEX401 3.7 17.2 1.0
OE2 c:GLU354 3.8 35.9 1.0
NE2 a:HIS337 3.8 39.3 1.0
OE1 a:GLU189 3.8 37.6 1.0
CA1 a:OEX401 3.9 16.5 1.0
CG a:GLU189 4.0 35.8 1.0
CG a:HIS332 4.1 26.7 1.0
ND1 a:HIS332 4.1 26.3 1.0
CD a:GLU333 4.3 35.0 1.0
CE1 a:HIS337 4.3 37.5 1.0
OE1 c:GLU354 4.5 35.9 1.0
CD c:GLU354 4.5 35.8 1.0
O a:HOH1005 4.5 48.9 1.0
CB a:ASP342 4.6 25.5 1.0
OXT a:ALA344 4.6 39.8 1.0
CG1 a:VAL185 4.7 30.4 1.0
OE2 a:GLU333 4.7 36.5 1.0
O4 a:OEX401 4.9 19.8 1.0
CD2 a:HIS337 5.0 37.1 1.0

Manganese binding site 6 out of 8 in 5xnl

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Manganese binding site 6 out of 8 in the Structure of Stacked 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 Stacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:14.4
occ:1.00
 MN2 a:OEX401 0.0 14.4 1.0
OD1 a:ASP342 1.9 24.9 1.0
OE1 c:GLU354 1.9 35.9 1.0
OXT a:ALA344 2.0 39.8 1.0
O3 a:OEX401 2.1 14.4 1.0
O1 a:OEX401 2.1 13.1 1.0
O2 a:OEX401 2.2 17.2 1.0
CD c:GLU354 2.6 35.8 1.0
OE2 c:GLU354 2.8 35.9 1.0
CG a:ASP342 2.8 27.2 1.0
MN1 a:OEX401 3.0 13.7 1.0
MN3 a:OEX401 3.1 14.7 1.0
OD2 a:ASP342 3.1 28.7 1.0
C a:ALA344 3.2 45.6 1.0
NE2 a:HIS337 3.8 39.3 1.0
O a:HOH1005 3.8 48.9 1.0
N a:ALA344 3.9 47.0 1.0
O5 a:OEX401 3.9 14.8 1.0
CA1 a:OEX401 3.9 16.5 1.0
CA a:ALA344 4.0 44.7 1.0
CG c:GLU354 4.1 33.6 1.0
O a:ALA344 4.1 48.3 1.0
CB a:ASP342 4.1 25.5 1.0
CD2 a:HIS337 4.3 37.1 1.0
O a:HOH1080 4.4 40.1 1.0
C a:ASP342 4.4 29.8 1.0
CA a:ASP342 4.4 30.1 1.0
CB a:ALA344 4.4 37.8 1.0
CB c:GLU354 4.4 36.6 1.0
OE1 a:GLU333 4.5 38.3 1.0
O a:ASP342 4.6 29.4 1.0
OE2 a:GLU189 4.6 35.6 1.0
N a:LEU343 4.7 40.4 1.0
O4 a:OEX401 4.7 19.8 1.0
NE2 a:HIS332 4.8 27.1 1.0
C a:LEU343 4.9 45.0 1.0
CE1 a:HIS337 4.9 37.5 1.0

Manganese binding site 7 out of 8 in 5xnl

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Manganese binding site 7 out of 8 in the Structure of Stacked 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 Stacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:14.7
occ:1.00
 MN3 a:OEX401 0.0 14.7 1.0
OE2 c:GLU354 1.9 35.9 1.0
O5 a:OEX401 2.0 14.8 1.0
OE1 a:GLU333 2.0 38.3 1.0
O3 a:OEX401 2.0 14.4 1.0
O4 a:OEX401 2.0 19.8 1.0
O2 a:OEX401 2.0 17.2 1.0
CD a:GLU333 2.9 35.0 1.0
CD c:GLU354 3.0 35.8 1.0
MN1 a:OEX401 3.0 13.7 1.0
MN2 a:OEX401 3.1 14.4 1.0
OE2 a:GLU333 3.1 36.5 1.0
O1 a:OEX401 3.3 13.1 1.0
CA1 a:OEX401 3.5 16.5 1.0
MN4 a:OEX401 3.6 18.4 1.0
OE1 c:GLU354 3.6 35.9 1.0
OD1 a:ASP170 3.7 36.8 1.0
NH2 c:ARG357 3.8 48.6 1.0
OXT a:ALA344 4.0 39.8 1.0
CG c:GLU354 4.1 33.6 1.0
CG a:GLU333 4.3 35.9 1.0
NE2 a:HIS337 4.3 39.3 1.0
OD2 a:ASP170 4.3 36.6 1.0
NE2 a:HIS332 4.4 27.1 1.0
CG a:ASP170 4.4 35.7 1.0
OE2 a:GLU189 4.5 35.6 1.0
OD1 a:ASP342 4.5 24.9 1.0
CZ c:ARG357 4.6 35.0 1.0
CD2 a:HIS332 4.6 26.6 1.0
NH1 c:ARG357 4.7 34.9 1.0
CB a:GLU333 4.7 35.9 1.0
OD2 a:ASP342 4.7 28.7 1.0
CE1 a:HIS337 4.8 37.5 1.0

Manganese binding site 8 out of 8 in 5xnl

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Manganese binding site 8 out of 8 in the Structure of Stacked 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 Stacked C2S2M2-Type Psii-Lhcii Supercomplex From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:18.4
occ:1.00
 MN4 a:OEX401 0.0 18.4 1.0
OD1 a:ASP170 2.0 36.8 1.0
O4 a:OEX401 2.2 19.8 1.0
OE2 a:GLU333 2.2 36.5 1.0
CG a:ASP170 3.2 35.7 1.0
O5 a:OEX401 3.3 14.8 1.0
CD a:GLU333 3.3 35.0 1.0
MN3 a:OEX401 3.6 14.7 1.0
O a:SER169 3.6 30.3 1.0
CA a:ASP170 3.8 23.1 1.0
OE1 a:GLU333 3.8 38.3 1.0
O a:HOH1085 3.9 42.7 1.0
C a:SER169 3.9 29.3 1.0
O a:HOH1049 3.9 40.4 1.0
N a:ASP170 4.0 21.4 1.0
CB a:ASP170 4.1 34.6 1.0
OD2 a:ASP170 4.1 36.6 1.0
OD1 a:ASP61 4.1 50.3 1.0
OG a:SER169 4.2 34.7 1.0
O a:HOH1042 4.2 43.2 1.0
NH2 c:ARG357 4.5 48.6 1.0
CB a:SER169 4.5 34.0 1.0
CG a:GLU333 4.5 35.9 1.0
O a:HOH1020 4.6 36.0 1.0
CA1 a:OEX401 4.6 16.5 1.0
O2 a:OEX401 4.7 17.2 1.0
CA a:SER169 4.9 27.2 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: Sun Oct 6 03:26:34 2024

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