Atomistry » Manganese » PDB 4u87-4wiu » 4ub6
Atomistry »
  Manganese »
    PDB 4u87-4wiu »
      4ub6 »

Manganese in PDB 4ub6: Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser

Enzymatic activity of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser

All present enzymatic activity of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser:
1.10.3.9;

Protein crystallography data

The structure of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser, PDB code: 4ub6 was solved by M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimizu, K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.29 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.744, 229.989, 288.337, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.8

Other elements in 4ub6:

The structure of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 6 atoms
Calcium (Ca) 9 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser (pdb code 4ub6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser, PDB code: 4ub6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4ub6

Go back to Manganese Binding Sites List in 4ub6
Manganese binding site 1 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:20.2
occ:1.00
 MN1 A:OEX418 0.0 20.2 1.0
OE2 A:GLU189 1.8 16.0 1.0
O1 A:OEX418 1.9 20.9 1.0
O3 A:OEX418 1.9 24.6 1.0
NE2 A:HIS332 2.1 20.1 1.0
OD2 A:ASP342 2.2 18.3 1.0
MN2 A:OEX418 2.7 22.1 1.0
O5 A:OEX418 2.7 15.1 1.0
CD A:GLU189 2.8 15.2 1.0
CD2 A:HIS332 3.0 14.8 1.0
CG A:ASP342 3.0 19.7 1.0
CE1 A:HIS332 3.0 21.2 1.0
OD1 A:ASP342 3.2 16.8 1.0
MN3 A:OEX418 3.2 19.6 1.0
OE1 A:GLU189 3.3 30.1 1.0
CA1 A:OEX418 3.5 28.3 1.0
O2 A:OEX418 3.6 24.2 1.0
O A:HOH601 3.8 40.4 1.0
OE1 A:GLU333 4.0 19.4 1.0
NE2 A:HIS337 4.0 19.0 1.0
CG A:GLU189 4.1 17.3 1.0
ND1 A:HIS332 4.1 15.0 1.0
CG A:HIS332 4.2 14.7 1.0
OXT A:ALA344 4.2 27.9 1.0
O A:HOH571 4.3 31.6 1.0
OE1 C:GLU354 4.4 24.4 1.0
O A:ALA344 4.4 29.2 1.0
CB A:ASP342 4.4 16.4 1.0
OE2 C:GLU354 4.6 20.6 1.0
CG1 A:VAL185 4.7 17.5 1.0
CE1 A:HIS337 4.7 15.7 1.0
C A:ALA344 4.7 29.2 1.0
CD A:GLU333 4.7 30.2 1.0
CD C:GLU354 4.9 19.5 1.0
O4 A:OEX418 4.9 20.0 1.0
O A:HOH569 4.9 18.4 1.0
MN4 A:OEX418 5.0 21.5 1.0

Manganese binding site 2 out of 8 in 4ub6

Go back to Manganese Binding Sites List in 4ub6
Manganese binding site 2 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:22.1
occ:1.00
 MN2 A:OEX418 0.0 22.1 1.0
O1 A:OEX418 1.8 20.9 1.0
O2 A:OEX418 1.9 24.2 1.0
OXT A:ALA344 1.9 27.9 1.0
O3 A:OEX418 1.9 24.6 1.0
OE1 C:GLU354 2.1 24.4 1.0
OD1 A:ASP342 2.1 16.8 1.0
MN1 A:OEX418 2.7 20.2 1.0
MN3 A:OEX418 2.7 19.6 1.0
C A:ALA344 2.8 29.2 1.0
CD C:GLU354 3.0 19.5 1.0
CG A:ASP342 3.0 19.7 1.0
O A:ALA344 3.0 29.2 1.0
OE2 C:GLU354 3.1 20.6 1.0
OD2 A:ASP342 3.2 18.3 1.0
CA1 A:OEX418 3.4 28.3 1.0
O5 A:OEX418 3.6 15.1 1.0
NE2 A:HIS337 3.9 19.0 1.0
O A:HOH601 4.0 40.4 1.0
O A:HOH630 4.0 18.4 1.0
O4 A:OEX418 4.2 20.0 1.0
OE2 A:GLU189 4.2 16.0 1.0
CA A:ALA344 4.2 28.3 1.0
OE1 A:GLU333 4.3 19.4 1.0
NE2 A:HIS332 4.4 20.1 1.0
N A:ALA344 4.4 32.9 1.0
CG C:GLU354 4.4 22.0 1.0
CD2 A:HIS337 4.4 19.9 1.0
CB A:ASP342 4.5 16.4 1.0
NH2 C:ARG357 4.7 20.2 1.0
OE1 A:GLU189 4.7 30.1 1.0
CD A:GLU189 4.8 15.2 1.0
CB C:GLU354 4.9 18.1 1.0
OD1 A:ASP170 4.9 28.3 1.0
CA A:ASP342 4.9 27.0 1.0
NH1 C:ARG357 5.0 27.0 1.0

Manganese binding site 3 out of 8 in 4ub6

Go back to Manganese Binding Sites List in 4ub6
Manganese binding site 3 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:19.6
occ:1.00
 MN3 A:OEX418 0.0 19.6 1.0
O2 A:OEX418 1.8 24.2 1.0
O4 A:OEX418 1.9 20.0 1.0
OE1 A:GLU333 2.0 19.4 1.0
O3 A:OEX418 2.1 24.6 1.0
OE2 C:GLU354 2.1 20.6 1.0
O5 A:OEX418 2.2 15.1 1.0
MN2 A:OEX418 2.7 22.1 1.0
MN4 A:OEX418 2.9 21.5 1.0
CD A:GLU333 2.9 30.2 1.0
CD C:GLU354 3.1 19.5 1.0
OE2 A:GLU333 3.1 22.1 1.0
MN1 A:OEX418 3.2 20.2 1.0
OE1 C:GLU354 3.3 24.4 1.0
CA1 A:OEX418 3.5 28.3 1.0
O1 A:OEX418 3.5 20.9 1.0
O C:HOH665 4.0 24.6 1.0
NH2 C:ARG357 4.1 20.2 1.0
NE2 A:HIS332 4.1 20.1 1.0
OD2 A:ASP170 4.2 21.1 1.0
NE2 A:HIS337 4.2 19.0 1.0
O A:HOH567 4.2 15.6 1.0
OXT A:ALA344 4.3 27.9 1.0
OD1 A:ASP170 4.3 28.3 1.0
CD2 A:HIS332 4.3 14.8 1.0
CG A:GLU333 4.3 14.8 1.0
CG C:GLU354 4.5 22.0 1.0
O A:HOH607 4.6 15.8 1.0
OD1 A:ASP342 4.6 16.8 1.0
O A:ALA344 4.6 29.2 1.0
CG A:ASP170 4.7 19.9 1.0
O A:HOH608 4.7 18.8 1.0
CB A:GLU333 4.8 15.0 1.0
OE2 A:GLU189 4.8 16.0 1.0
CE1 A:HIS337 4.8 15.7 1.0
OD2 A:ASP342 4.8 18.3 1.0
C A:ALA344 4.9 29.2 1.0

Manganese binding site 4 out of 8 in 4ub6

Go back to Manganese Binding Sites List in 4ub6
Manganese binding site 4 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:21.5
occ:1.00
 MN4 A:OEX418 0.0 21.5 1.0
O4 A:OEX418 1.9 20.0 1.0
OD2 A:ASP170 2.1 21.1 1.0
OE2 A:GLU333 2.1 22.1 1.0
O A:HOH607 2.1 15.8 1.0
O5 A:OEX418 2.3 15.1 1.0
O A:HOH608 2.3 18.8 1.0
MN3 A:OEX418 2.9 19.6 1.0
CD A:GLU333 3.0 30.2 1.0
CG A:ASP170 3.1 19.9 1.0
OE1 A:GLU333 3.4 19.4 1.0
OD1 A:ASP170 3.6 28.3 1.0
O2 A:OEX418 3.7 24.2 1.0
O A:HOH569 3.7 18.4 1.0
CA1 A:OEX418 3.8 28.3 1.0
O A:HOH567 3.8 15.6 1.0
O A:HOH560 3.9 18.5 1.0
O A:HOH557 4.1 24.1 1.0
OD1 A:ASP61 4.2 21.1 1.0
CG A:GLU333 4.4 14.8 1.0
CB A:ASP170 4.4 15.2 1.0
O A:SER169 4.5 20.7 1.0
NH2 C:ARG357 4.6 20.2 1.0
OE2 C:GLU354 4.6 20.6 1.0
CA A:ASP170 4.6 18.4 1.0
O3 A:OEX418 4.7 24.6 1.0
O A:HOH559 4.8 18.9 1.0
MN1 A:OEX418 5.0 20.2 1.0

Manganese binding site 5 out of 8 in 4ub6

Go back to Manganese Binding Sites List in 4ub6
Manganese binding site 5 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:24.7
occ:1.00
 MN1 a:OEX416 0.0 24.7 1.0
OE2 a:GLU189 1.8 26.3 1.0
O1 a:OEX416 1.8 20.3 1.0
O3 a:OEX416 1.9 24.0 1.0
NE2 a:HIS332 2.1 22.2 1.0
OD2 a:ASP342 2.2 22.2 1.0
MN2 a:OEX416 2.6 22.9 1.0
O5 a:OEX416 2.7 18.8 1.0
CD a:GLU189 2.9 29.0 1.0
CE1 a:HIS332 3.0 19.3 1.0
CG a:ASP342 3.1 23.9 1.0
CD2 a:HIS332 3.1 18.7 1.0
MN3 a:OEX416 3.2 21.5 1.0
OD1 a:ASP342 3.2 20.4 1.0
OE1 a:GLU189 3.4 28.2 1.0
O2 a:OEX416 3.4 19.6 1.0
CA1 a:OEX416 3.5 34.0 1.0
O a:HOH561 3.8 47.5 1.0
NE2 a:HIS337 4.0 19.9 1.0
O a:HOH529 4.1 35.1 1.0
CG a:GLU189 4.1 30.6 1.0
OXT a:ALA344 4.1 20.4 1.0
ND1 a:HIS332 4.1 19.0 1.0
OE1 a:GLU333 4.2 20.9 1.0
CG a:HIS332 4.2 18.8 1.0
OE1 c:GLU354 4.3 28.0 1.0
CB a:ASP342 4.5 24.2 1.0
OE2 c:GLU354 4.5 23.0 1.0
O a:ALA344 4.5 21.8 1.0
CE1 a:HIS337 4.6 19.6 1.0
CG1 a:VAL185 4.7 19.4 1.0
C a:ALA344 4.7 37.0 1.0
CD c:GLU354 4.8 31.0 1.0
CD a:GLU333 4.9 21.1 1.0
O4 a:OEX416 5.0 18.9 1.0
MN4 a:OEX416 5.0 22.7 1.0

Manganese binding site 6 out of 8 in 4ub6

Go back to Manganese Binding Sites List in 4ub6
Manganese binding site 6 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:22.9
occ:1.00
 MN2 a:OEX416 0.0 22.9 1.0
O1 a:OEX416 1.7 20.3 1.0
O2 a:OEX416 1.7 19.6 1.0
OXT a:ALA344 1.8 20.4 1.0
O3 a:OEX416 2.1 24.0 1.0
OE1 c:GLU354 2.1 28.0 1.0
OD1 a:ASP342 2.2 20.4 1.0
MN1 a:OEX416 2.6 24.7 1.0
MN3 a:OEX416 2.7 21.5 1.0
C a:ALA344 2.8 37.0 1.0
CD c:GLU354 2.9 31.0 1.0
OE2 c:GLU354 3.0 23.0 1.0
CG a:ASP342 3.1 23.9 1.0
O a:ALA344 3.1 21.8 1.0
OD2 a:ASP342 3.3 22.2 1.0
CA1 a:OEX416 3.3 34.0 1.0
O5 a:OEX416 3.6 18.8 1.0
NE2 a:HIS337 3.8 19.9 1.0
O a:HOH561 3.8 47.5 1.0
O c:HOH1070 4.0 22.6 1.0
OE2 a:GLU189 4.1 26.3 1.0
O4 a:OEX416 4.2 18.9 1.0
CA a:ALA344 4.2 31.0 1.0
CG c:GLU354 4.3 21.7 1.0
NE2 a:HIS332 4.3 22.2 1.0
N a:ALA344 4.4 34.0 1.0
OE1 a:GLU333 4.4 20.9 1.0
CD2 a:HIS337 4.4 20.3 1.0
CB a:ASP342 4.5 24.2 1.0
CD a:GLU189 4.8 29.0 1.0
OE1 a:GLU189 4.8 28.2 1.0
NH2 c:ARG357 4.8 22.6 1.0
CB c:GLU354 4.9 24.2 1.0
NH1 c:ARG357 4.9 25.8 1.0
CE1 a:HIS337 4.9 19.6 1.0
CA a:ASP342 4.9 21.3 1.0

Manganese binding site 7 out of 8 in 4ub6

Go back to Manganese Binding Sites List in 4ub6
Manganese binding site 7 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:21.5
occ:1.00
 MN3 a:OEX416 0.0 21.5 1.0
O2 a:OEX416 1.8 19.6 1.0
O4 a:OEX416 1.9 18.9 1.0
O3 a:OEX416 2.0 24.0 1.0
O5 a:OEX416 2.0 18.8 1.0
OE1 a:GLU333 2.1 20.9 1.0
OE2 c:GLU354 2.1 23.0 1.0
MN2 a:OEX416 2.7 22.9 1.0
MN4 a:OEX416 2.8 22.7 1.0
CD a:GLU333 3.0 21.1 1.0
CD c:GLU354 3.1 31.0 1.0
MN1 a:OEX416 3.2 24.7 1.0
OE2 a:GLU333 3.3 21.1 1.0
CA1 a:OEX416 3.4 34.0 1.0
OE1 c:GLU354 3.4 28.0 1.0
O1 a:OEX416 3.4 20.3 1.0
NE2 a:HIS332 4.1 22.2 1.0
NH2 c:ARG357 4.1 22.6 1.0
OXT a:ALA344 4.2 20.4 1.0
OD2 a:ASP170 4.2 26.2 1.0
O c:HOH1060 4.2 24.4 1.0
NE2 a:HIS337 4.3 19.9 1.0
O a:HOH525 4.3 20.7 1.0
OD1 a:ASP170 4.3 37.8 1.0
O a:HOH566 4.3 17.9 1.0
CD2 a:HIS332 4.4 18.7 1.0
CG a:GLU333 4.4 18.8 1.0
CG c:GLU354 4.5 21.7 1.0
OD1 a:ASP342 4.6 20.4 1.0
O a:HOH567 4.6 20.7 1.0
O a:ALA344 4.6 21.8 1.0
OE2 a:GLU189 4.6 26.3 1.0
CG a:ASP170 4.7 27.9 1.0
CE1 a:HIS337 4.8 19.6 1.0
CB a:GLU333 4.8 18.4 1.0
O a:HOH527 4.8 39.4 1.0
C a:ALA344 4.8 37.0 1.0
OD2 a:ASP342 4.9 22.2 1.0

Manganese binding site 8 out of 8 in 4ub6

Go back to Manganese Binding Sites List in 4ub6
Manganese binding site 8 out of 8 in the Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn416

b:22.7
occ:1.00
 MN4 a:OEX416 0.0 22.7 1.0
O a:HOH566 2.0 17.9 1.0
O4 a:OEX416 2.0 18.9 1.0
OD2 a:ASP170 2.1 26.2 1.0
OE2 a:GLU333 2.1 21.1 1.0
O a:HOH567 2.2 20.7 1.0
O5 a:OEX416 2.3 18.8 1.0
MN3 a:OEX416 2.8 21.5 1.0
CD a:GLU333 3.0 21.1 1.0
CG a:ASP170 3.2 27.9 1.0
OE1 a:GLU333 3.2 20.9 1.0
O a:HOH527 3.6 39.4 1.0
OD1 a:ASP170 3.6 37.8 1.0
O a:HOH525 3.8 20.7 1.0
O2 a:OEX416 3.8 19.6 1.0
CA1 a:OEX416 3.9 34.0 1.0
O a:HOH519 3.9 20.2 1.0
OD1 a:ASP61 4.1 24.6 1.0
O a:HOH516 4.2 20.7 1.0
O a:SER169 4.3 17.7 1.0
CG a:GLU333 4.4 18.8 1.0
CB a:ASP170 4.5 23.4 1.0
O3 a:OEX416 4.5 24.0 1.0
NH2 c:ARG357 4.5 22.6 1.0
OE2 c:GLU354 4.6 23.0 1.0
CA a:ASP170 4.6 18.2 1.0
O a:HOH518 4.7 20.2 1.0
C a:SER169 4.9 20.1 1.0
CG a:ASP61 4.9 21.6 1.0
MN1 a:OEX416 5.0 24.7 1.0

Reference:

M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimizu, K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen. Native Structure of Photosystem II at 1.95A Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13991
Page generated: Sat Oct 5 21:18:33 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