Atomistry » Manganese » PDB 5gjc-5hwu » 5h2f
Atomistry »
  Manganese »
    PDB 5gjc-5hwu »
      5h2f »

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

Go back to Manganese Binding Sites List in 5h2f
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

Go back to Manganese Binding Sites List in 5h2f
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

Go back to Manganese Binding Sites List in 5h2f
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

Go back to Manganese Binding Sites List in 5h2f
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

Go back to Manganese Binding Sites List in 5h2f
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

Go back to Manganese Binding Sites List in 5h2f
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy