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Manganese in PDB 5h2f: Crystal Structure of the Psbm-Deletion Mutant of Photosystem II

Enzymatic activity of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II

All present enzymatic activity of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II:
1.10.3.9;

Protein crystallography data

The structure of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f was solved by S.Uto, K.Kawakami, Y.Umena, M.Iwai, M.Ikeuchi, J.R.Shen, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.954, 226.993, 285.886, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 22.6

Other elements in 5h2f:

The structure of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II also contains other interesting chemical elements:

Magnesium (Mg) 74 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 7 atoms
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II (pdb code 5h2f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5h2f

Go back to Manganese Binding Sites List in 5h2f
Manganese binding site 1 out of 8 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:25.5
occ:1.00
 MN1 A:OEX401 0.0 25.5 1.0
OE2 A:GLU189 1.9 27.1 1.0
O1 A:OEX401 1.9 25.9 1.0
O3 A:OEX401 1.9 26.4 1.0
NE2 A:HIS332 2.0 24.1 1.0
OD2 A:ASP342 2.2 25.2 1.0
O5 A:OEX401 2.8 31.9 1.0
MN2 A:OEX401 2.8 26.8 1.0
CD A:GLU189 2.9 28.2 1.0
CD2 A:HIS332 3.0 26.6 1.0
CE1 A:HIS332 3.0 24.9 1.0
CG A:ASP342 3.1 28.1 1.0
OE1 A:GLU189 3.3 30.4 1.0
OD1 A:ASP342 3.4 28.9 1.0
MN3 A:OEX401 3.4 27.7 1.0
O2 A:OEX401 3.6 30.0 1.0
CA1 A:OEX401 3.7 28.6 1.0
O A:HOH519 3.9 33.1 1.0
NE2 A:HIS337 3.9 25.5 1.0
OE1 A:GLU333 4.0 21.5 1.0
CG A:GLU189 4.1 27.3 1.0
O A:HOH618 4.1 50.1 1.0
ND1 A:HIS332 4.1 26.6 1.0
CG A:HIS332 4.2 26.0 1.0
CG1 A:VAL185 4.4 24.1 1.0
OE1 C:GLU354 4.5 30.5 1.0
OXT A:ALA344 4.5 24.5 1.0
CE1 A:HIS337 4.5 23.7 1.0
CB A:ASP342 4.5 25.3 1.0
O A:ALA344 4.7 28.9 1.0
CD A:GLU333 4.7 25.1 1.0
OE2 C:GLU354 4.7 30.7 1.0
O A:HOH604 4.9 30.4 1.0
C A:ALA344 4.9 25.9 1.0
MN4 A:OEX401 5.0 29.9 1.0

Manganese binding site 2 out of 8 in 5h2f

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Manganese binding site 2 out of 8 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:26.8
occ:1.00
 MN2 A:OEX401 0.0 26.8 1.0
O2 A:OEX401 1.9 30.0 1.0
OXT A:ALA344 2.0 24.5 1.0
OD1 A:ASP342 2.0 28.9 1.0
O1 A:OEX401 2.1 25.9 1.0
OE1 C:GLU354 2.1 30.5 1.0
O3 A:OEX401 2.3 26.4 1.0
MN1 A:OEX401 2.8 25.5 1.0
C A:ALA344 2.8 25.9 1.0
MN3 A:OEX401 2.9 27.7 1.0
CG A:ASP342 2.9 28.1 1.0
CD C:GLU354 3.0 30.9 1.0
O A:ALA344 3.1 28.9 1.0
OD2 A:ASP342 3.1 25.2 1.0
OE2 C:GLU354 3.2 30.7 1.0
CA1 A:OEX401 3.4 28.6 1.0
NE2 A:HIS337 3.7 25.5 1.0
O5 A:OEX401 3.8 31.9 1.0
O A:HOH519 3.9 33.1 1.0
O A:HOH611 4.1 28.2 1.0
CA A:ALA344 4.2 27.8 1.0
N A:ALA344 4.2 28.3 1.0
CD2 A:HIS337 4.3 25.0 1.0
OE2 A:GLU189 4.3 27.1 1.0
OE1 A:GLU333 4.3 21.5 1.0
CG C:GLU354 4.4 29.5 1.0
CB A:ASP342 4.4 25.3 1.0
O4 A:OEX401 4.4 32.0 1.0
NE2 A:HIS332 4.4 24.1 1.0
NH2 C:ARG357 4.5 29.8 1.0
OE1 A:GLU189 4.7 30.4 1.0
CD A:GLU189 4.8 28.2 1.0
CA A:ASP342 4.8 26.0 1.0
CE1 A:HIS337 4.9 23.7 1.0
CB C:GLU354 4.9 28.6 1.0
O A:HOH521 4.9 25.8 1.0
C A:ASP342 4.9 25.9 1.0

Manganese binding site 3 out of 8 in 5h2f

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Manganese binding site 3 out of 8 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:27.7
occ:1.00
 MN3 A:OEX401 0.0 27.7 1.0
O4 A:OEX401 1.8 32.0 1.0
OE1 A:GLU333 2.0 21.5 1.0
O2 A:OEX401 2.0 30.0 1.0
OE2 C:GLU354 2.1 30.7 1.0
O5 A:OEX401 2.2 31.9 1.0
O3 A:OEX401 2.2 26.4 1.0
MN4 A:OEX401 2.8 29.9 1.0
MN2 A:OEX401 2.9 26.8 1.0
CD A:GLU333 2.9 25.1 1.0
CD C:GLU354 3.1 30.9 1.0
OE2 A:GLU333 3.2 25.1 1.0
OE1 C:GLU354 3.3 30.5 1.0
MN1 A:OEX401 3.4 25.5 1.0
CA1 A:OEX401 3.5 28.6 1.0
O1 A:OEX401 3.5 25.9 1.0
NH2 C:ARG357 3.7 29.8 1.0
O C:HOH639 4.0 32.0 1.0
OD1 A:ASP170 4.0 23.7 1.0
NE2 A:HIS337 4.1 25.5 1.0
O A:HOH515 4.2 33.2 1.0
OD2 A:ASP170 4.3 26.8 1.0
NE2 A:HIS332 4.3 24.1 1.0
CG A:GLU333 4.3 23.0 1.0
OXT A:ALA344 4.3 24.5 1.0
CG C:GLU354 4.5 29.5 1.0
CD2 A:HIS332 4.5 26.6 1.0
O A:ALA344 4.5 28.9 1.0
O A:HOH522 4.5 26.1 1.0
O A:HOH591 4.6 27.3 1.0
CG A:ASP170 4.6 26.1 1.0
OD1 A:ASP342 4.7 28.9 1.0
CE1 A:HIS337 4.8 23.7 1.0
CB A:GLU333 4.8 22.4 1.0
OD2 A:ASP342 4.9 25.2 1.0
CZ C:ARG357 4.9 28.9 1.0
O A:HOH604 4.9 30.4 1.0
C A:ALA344 4.9 25.9 1.0
OE2 A:GLU189 5.0 27.1 1.0

Manganese binding site 4 out of 8 in 5h2f

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Manganese binding site 4 out of 8 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:29.9
occ:1.00
 MN4 A:OEX401 0.0 29.9 1.0
O4 A:OEX401 2.0 32.0 1.0
OD1 A:ASP170 2.0 23.7 1.0
OE2 A:GLU333 2.1 25.1 1.0
O A:HOH591 2.2 27.3 1.0
O A:HOH522 2.2 26.1 1.0
O5 A:OEX401 2.3 31.9 1.0
MN3 A:OEX401 2.8 27.7 1.0
CD A:GLU333 3.0 25.1 1.0
CG A:ASP170 3.2 26.1 1.0
OE1 A:GLU333 3.3 21.5 1.0
OD2 A:ASP170 3.7 26.8 1.0
O A:HOH604 3.7 30.4 1.0
O A:HOH565 3.8 32.0 1.0
CA1 A:OEX401 3.8 28.6 1.0
O2 A:OEX401 3.9 30.0 1.0
O A:HOH515 4.0 33.2 1.0
O A:HOH621 4.0 27.9 1.0
OD1 A:ASP61 4.2 24.4 1.0
O A:SER169 4.3 25.3 1.0
CG A:GLU333 4.4 23.0 1.0
CB A:ASP170 4.4 25.2 1.0
NH2 C:ARG357 4.6 29.8 1.0
CA A:ASP170 4.6 27.2 1.0
O3 A:OEX401 4.6 26.4 1.0
OE2 C:GLU354 4.7 30.7 1.0
O D:HOH531 4.9 20.9 1.0
C A:SER169 4.9 26.7 1.0
MN1 A:OEX401 5.0 25.5 1.0

Manganese binding site 5 out of 8 in 5h2f

Go back to Manganese Binding Sites List in 5h2f
Manganese binding site 5 out of 8 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn403

b:31.3
occ:1.00
 MN1 a:OEX403 0.0 31.3 1.0
OE2 a:GLU189 1.8 27.4 1.0
O1 a:OEX403 1.9 31.1 1.0
NE2 a:HIS332 2.0 29.5 1.0
O3 a:OEX403 2.1 30.4 1.0
OD2 a:ASP342 2.2 29.9 1.0
MN2 a:OEX403 2.7 32.4 1.0
O5 a:OEX403 2.8 29.3 1.0
CD a:GLU189 2.8 29.9 1.0
CE1 a:HIS332 2.9 28.4 1.0
CD2 a:HIS332 3.1 29.6 1.0
CG a:ASP342 3.1 28.8 1.0
OE1 a:GLU189 3.3 30.0 1.0
MN3 a:OEX403 3.3 31.0 1.0
OD1 a:ASP342 3.3 26.7 1.0
CA1 a:OEX403 3.5 33.1 1.0
O2 a:OEX403 3.8 32.4 1.0
OE1 a:GLU333 3.8 30.9 1.0
NE2 a:HIS337 3.9 34.5 1.0
ND1 a:HIS332 4.0 27.9 1.0
CG a:GLU189 4.1 27.8 1.0
O a:HOH579 4.2 58.0 1.0
CG a:HIS332 4.2 26.4 1.0
O a:HOH617 4.3 46.0 1.0
OXT a:ALA344 4.3 30.0 1.0
CG1 a:VAL185 4.4 23.9 1.0
CB a:ASP342 4.5 25.1 1.0
OE1 c:GLU354 4.5 32.6 1.0
CE1 a:HIS337 4.6 29.8 1.0
OE2 c:GLU354 4.8 34.3 1.0
CD a:GLU333 4.8 30.9 1.0
O a:HOH599 4.8 36.0 1.0
MN4 a:OEX403 4.9 31.1 1.0
O a:ALA344 4.9 30.3 1.0
C a:ALA344 5.0 29.8 1.0

Manganese binding site 6 out of 8 in 5h2f

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Manganese binding site 6 out of 8 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn403

b:32.4
occ:1.00
 MN2 a:OEX403 0.0 32.4 1.0
O1 a:OEX403 1.8 31.1 1.0
O2 a:OEX403 1.8 32.4 1.0
OXT a:ALA344 2.0 30.0 1.0
O3 a:OEX403 2.0 30.4 1.0
OD1 a:ASP342 2.0 26.7 1.0
OE1 c:GLU354 2.1 32.6 1.0
MN1 a:OEX403 2.7 31.3 1.0
MN3 a:OEX403 2.8 31.0 1.0
CG a:ASP342 2.9 28.8 1.0
C a:ALA344 2.9 29.8 1.0
CD c:GLU354 3.0 34.4 1.0
OD2 a:ASP342 3.1 29.9 1.0
OE2 c:GLU354 3.2 34.3 1.0
O a:ALA344 3.3 30.3 1.0
CA1 a:OEX403 3.4 33.1 1.0
O5 a:OEX403 3.7 29.3 1.0
NE2 a:HIS337 3.8 34.5 1.0
O c:HOH1133 3.9 28.8 1.0
O a:HOH579 4.2 58.0 1.0
OE2 a:GLU189 4.2 27.4 1.0
CA a:ALA344 4.3 31.6 1.0
OE1 a:GLU333 4.3 30.9 1.0
CD2 a:HIS337 4.3 34.3 1.0
N a:ALA344 4.3 31.5 1.0
CB a:ASP342 4.4 25.1 1.0
NE2 a:HIS332 4.4 29.5 1.0
O4 a:OEX403 4.4 29.7 1.0
CG c:GLU354 4.4 34.2 1.0
NH2 c:ARG357 4.6 28.2 1.0
OE1 a:GLU189 4.7 30.0 1.0
CD a:GLU189 4.8 29.9 1.0
CA a:ASP342 4.8 27.8 1.0
CB c:GLU354 4.9 29.5 1.0
NH1 c:ARG357 4.9 30.6 1.0
CE1 a:HIS337 4.9 29.8 1.0
C a:ASP342 4.9 30.9 1.0
OD1 a:ASP170 5.0 36.5 1.0

Manganese binding site 7 out of 8 in 5h2f

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Manganese binding site 7 out of 8 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn403

b:31.0
occ:1.00
 MN3 a:OEX403 0.0 31.0 1.0
O3 a:OEX403 1.7 30.4 1.0
O4 a:OEX403 1.9 29.7 1.0
O5 a:OEX403 2.0 29.3 1.0
OE1 a:GLU333 2.1 30.9 1.0
O2 a:OEX403 2.1 32.4 1.0
OE2 c:GLU354 2.3 34.3 1.0
MN2 a:OEX403 2.8 32.4 1.0
MN4 a:OEX403 2.8 31.1 1.0
CD a:GLU333 3.0 30.9 1.0
CD c:GLU354 3.2 34.4 1.0
MN1 a:OEX403 3.3 31.3 1.0
OE2 a:GLU333 3.3 27.7 1.0
OE1 c:GLU354 3.4 32.6 1.0
CA1 a:OEX403 3.4 33.1 1.0
O1 a:OEX403 3.5 31.1 1.0
NH2 c:ARG357 3.8 28.2 1.0
O c:HOH1075 4.1 37.4 1.0
NE2 a:HIS332 4.1 29.5 1.0
OD2 a:ASP170 4.1 34.0 1.0
OD1 a:ASP170 4.2 36.5 1.0
O a:HOH502 4.2 26.0 1.0
NE2 a:HIS337 4.3 34.5 1.0
OXT a:ALA344 4.3 30.0 1.0
CD2 a:HIS332 4.4 29.6 1.0
CG a:GLU333 4.5 28.1 1.0
O a:HOH544 4.5 29.5 1.0
O a:ALA344 4.6 30.3 1.0
OD1 a:ASP342 4.6 26.7 1.0
CG a:ASP170 4.6 35.8 1.0
CG c:GLU354 4.6 34.2 1.0
O a:HOH597 4.7 23.4 1.0
OE2 a:GLU189 4.8 27.4 1.0
OD2 a:ASP342 4.8 29.9 1.0
CZ c:ARG357 4.8 30.4 1.0
CB a:GLU333 4.9 26.7 1.0
CE1 a:HIS337 4.9 29.8 1.0
C a:ALA344 4.9 29.8 1.0
O a:HOH599 5.0 36.0 1.0

Manganese binding site 8 out of 8 in 5h2f

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Manganese binding site 8 out of 8 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn403

b:31.1
occ:1.00
 MN4 a:OEX403 0.0 31.1 1.0
OE2 a:GLU333 2.0 27.7 1.0
O5 a:OEX403 2.1 29.3 1.0
OD2 a:ASP170 2.1 34.0 1.0
O a:HOH544 2.2 29.5 1.0
O4 a:OEX403 2.2 29.7 1.0
O a:HOH597 2.3 23.4 1.0
MN3 a:OEX403 2.8 31.0 1.0
CD a:GLU333 2.9 30.9 1.0
OE1 a:GLU333 3.2 30.9 1.0
CG a:ASP170 3.2 35.8 1.0
OD1 a:ASP170 3.6 36.5 1.0
O a:HOH599 3.8 36.0 1.0
CA1 a:OEX403 3.8 33.1 1.0
O a:HOH502 3.9 26.0 1.0
O a:HOH536 4.1 30.5 1.0
O a:HOH605 4.1 25.7 1.0
OD1 a:ASP61 4.1 26.3 1.0
O3 a:OEX403 4.2 30.4 1.0
O2 a:OEX403 4.2 32.4 1.0
O a:SER169 4.3 28.6 1.0
CG a:GLU333 4.4 28.1 1.0
CB a:ASP170 4.5 34.9 1.0
NH2 c:ARG357 4.5 28.2 1.0
CA a:ASP170 4.7 31.3 1.0
O d:HOH544 4.7 25.7 1.0
OE2 c:GLU354 4.7 34.3 1.0
MN1 a:OEX403 4.9 31.3 1.0
C a:SER169 5.0 27.9 1.0
CG1 a:VAL185 5.0 23.9 1.0
CD2 a:HIS332 5.0 29.6 1.0

Reference:

S.Uto, K.Kawakami, Y.Umena, M.Iwai, M.Ikeuchi, J.R.Shen, N.Kamiya. Mutual Relationships Between Structural and Functional Changes in A Psbm-Deletion Mutant of Photosystem II. Faraday Discuss. V. 198 107 2017.
ISSN: ISSN 1359-6640
PubMed: 28272640
DOI: 10.1039/C6FD00213G
Page generated: Sun Oct 6 00:27:55 2024

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