Atomistry » Calcium » PDB 4tx8-4uix » 4ub8
Atomistry »
  Calcium »
    PDB 4tx8-4uix »
      4ub8 »

Calcium in PDB 4ub8: Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser

Enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser

All present enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser:
1.10.3.9;

Protein crystallography data

The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8 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) 61.90 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.807, 230.001, 288.502, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.5

Other elements in 4ub8:

The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser (pdb code 4ub8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4ub8

Go back to Calcium Binding Sites List in 4ub8
Calcium binding site 1 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca418

b:32.5
occ:1.00
 CA1 A:OEX418 0.0 32.5 1.0
OD1 A:ASP170 2.3 34.4 1.0
O A:ALA344 2.4 31.4 1.0
O5 A:OEX418 2.4 16.7 1.0
O A:HOH569 2.4 41.7 1.0
O A:HOH570 2.6 25.3 1.0
O1 A:OEX418 2.6 28.1 1.0
O2 A:OEX418 2.7 23.6 1.0
OE1 A:GLU189 3.2 30.5 1.0
CG A:ASP170 3.2 22.8 1.0
MN2 A:OEX418 3.3 23.2 1.0
MN3 A:OEX418 3.4 22.1 1.0
MN1 A:OEX418 3.5 21.4 1.0
C A:ALA344 3.5 30.3 1.0
OD2 A:ASP170 3.5 24.8 1.0
MN4 A:OEX418 3.7 24.2 1.0
O4 A:OEX418 3.7 23.8 1.0
OXT A:ALA344 3.9 21.9 1.0
CD A:GLU189 4.0 16.9 1.0
O3 A:OEX418 4.0 21.0 1.0
OE2 A:GLU189 4.0 23.3 1.0
O A:HOH602 4.1 48.0 1.0
NH1 C:ARG357 4.3 26.1 1.0
CB A:ASP170 4.4 18.8 1.0
NH2 C:ARG357 4.4 21.2 1.0
O A:HOH571 4.6 27.0 1.0
OE1 A:GLN165 4.6 26.0 1.0
O A:HOH608 4.6 30.3 1.0
OH A:TYR161 4.7 21.1 1.0
CA A:ALA344 4.8 27.7 1.0
CZ C:ARG357 4.8 30.7 1.0

Calcium binding site 2 out of 9 in 4ub8

Go back to Calcium Binding Sites List in 4ub8
Calcium binding site 2 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:79.1
occ:1.00
 O O:HOH564 2.6 55.7 1.0
OD1 B:ASN438 2.7 28.3 1.0
O B:HOH860 2.8 53.4 1.0
O B:HOH842 2.8 30.0 1.0
O B:HOH855 3.1 61.5 1.0
O O:HOH551 3.2 69.0 1.0
CG B:ASN438 3.9 35.0 1.0
OE2 B:GLU435 4.2 52.7 0.5
O B:HOH776 4.5 38.2 1.0
O B:SER439 4.6 18.1 1.0
ND2 B:ASN438 4.6 30.4 1.0
O B:HOH800 4.7 28.8 1.0
CA B:ASN438 4.8 27.4 1.0
OE2 O:GLU181 4.8 99.7 1.0
CB B:ASN438 5.0 26.0 1.0
C B:ASN438 5.0 30.3 1.0

Calcium binding site 3 out of 9 in 4ub8

Go back to Calcium Binding Sites List in 4ub8
Calcium binding site 3 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:72.8
occ:1.00
 O V:HOH321 2.5 38.8 1.0
O F:HOH202 2.5 55.7 1.0
OXT F:ARG45 2.5 27.2 1.0
O F:HOH207 2.7 48.9 1.0
O F:HOH203 2.7 69.0 1.0
O2 F:GOL103 2.8 68.3 1.0
O3 F:GOL103 2.8 52.6 1.0
O F:ARG45 3.0 30.4 1.0
C F:ARG45 3.2 39.9 1.0
C3 F:GOL103 3.3 65.0 1.0
C2 F:GOL103 3.6 65.8 1.0
O F:HOH201 3.9 51.4 1.0
O V:HOH322 4.3 36.1 1.0
OE2 V:GLU23 4.4 66.1 1.0
OE1 V:GLU23 4.5 79.3 1.0
O F:HOH205 4.5 42.2 1.0
C1 F:GOL103 4.6 56.0 1.0
O1 F:GOL103 4.6 59.8 1.0
CA F:ARG45 4.7 33.5 1.0
CD V:GLU23 4.7 75.6 1.0

Calcium binding site 4 out of 9 in 4ub8

Go back to Calcium Binding Sites List in 4ub8
Calcium binding site 4 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:57.0
occ:1.00
 O O:VAL201 2.3 51.8 1.0
O O:THR138 2.4 44.3 1.0
O O:HOH518 2.4 53.9 1.0
OD1 O:ASN200 2.5 49.5 1.0
O O:HOH419 2.7 52.3 1.0
O O:HOH519 2.8 44.0 1.0
O O:HOH427 2.9 47.7 1.0
C O:VAL201 3.5 44.5 1.0
C O:THR138 3.5 44.2 1.0
CG O:ASN200 3.6 53.4 1.0
ND2 O:ASN200 4.1 60.6 1.0
N O:VAL201 4.1 34.0 1.0
CA O:VAL201 4.3 38.6 1.0
CA O:THR138 4.4 52.2 1.0
N O:SER139 4.4 38.7 1.0
N O:ALA202 4.4 42.3 1.0
CA O:SER139 4.4 37.6 1.0
C O:ASN200 4.5 37.2 1.0
O O:THR140 4.5 46.7 1.0
CA O:ALA202 4.5 38.0 1.0
CB O:THR138 4.7 57.2 1.0
C O:SER139 4.8 39.9 1.0
CB O:ASN200 4.8 43.9 1.0
CB O:VAL201 4.9 43.5 1.0
CA O:ASN200 5.0 41.1 1.0

Calcium binding site 5 out of 9 in 4ub8

Go back to Calcium Binding Sites List in 4ub8
Calcium binding site 5 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca415

b:37.4
occ:1.00
 CA1 a:OEX415 0.0 37.4 1.0
OD1 a:ASP170 2.3 39.1 1.0
O a:HOH525 2.4 46.4 1.0
O a:ALA344 2.4 29.1 1.0
O5 a:OEX415 2.5 20.2 1.0
O a:HOH526 2.6 36.8 1.0
O1 a:OEX415 2.6 24.0 1.0
O2 a:OEX415 2.7 22.9 1.0
O a:HOH560 3.1 45.6 1.0
OE1 a:GLU189 3.1 30.9 1.0
CG a:ASP170 3.3 30.3 1.0
MN2 a:OEX415 3.3 25.3 1.0
MN3 a:OEX415 3.3 25.0 1.0
MN1 a:OEX415 3.4 27.4 1.0
C a:ALA344 3.5 34.1 1.0
OD2 a:ASP170 3.6 25.0 1.0
MN4 a:OEX415 3.8 25.2 1.0
O4 a:OEX415 3.8 20.3 1.0
OXT a:ALA344 3.8 21.9 1.0
OE2 a:GLU189 3.9 31.2 1.0
CD a:GLU189 3.9 35.4 1.0
O3 a:OEX415 4.0 35.8 1.0
NH1 c:ARG357 4.3 26.6 1.0
CB a:ASP170 4.6 26.4 1.0
NH2 c:ARG357 4.6 24.5 1.0
OE1 a:GLN165 4.6 26.2 1.0
O a:HOH565 4.6 26.9 1.0
O a:HOH527 4.6 31.5 1.0
OH a:TYR161 4.7 24.0 1.0
CA a:ALA344 4.8 33.2 1.0
CZ c:ARG357 4.9 30.5 1.0
OE2 c:GLU354 5.0 24.0 1.0

Calcium binding site 6 out of 9 in 4ub8

Go back to Calcium Binding Sites List in 4ub8
Calcium binding site 6 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca605

b:95.7
occ:1.00
 OD1 b:ASN438 2.5 31.5 1.0
O b:HOH747 2.5 33.9 1.0
O o:HOH533 2.6 61.1 1.0
O b:HOH763 2.8 73.4 1.0
CG b:ASN438 3.7 32.8 1.0
O m:HOH203 4.0 38.1 1.0
O b:HOH718 4.5 44.0 1.0
O b:SER439 4.5 23.0 1.0
O b:HOH722 4.5 39.1 1.0
CA b:ASN438 4.6 25.5 1.0
ND2 b:ASN438 4.6 29.9 1.0
CB b:ASN438 4.7 25.8 1.0
C b:ASN438 4.7 31.1 1.0
O b:ASN438 4.9 22.4 1.0

Calcium binding site 7 out of 9 in 4ub8

Go back to Calcium Binding Sites List in 4ub8
Calcium binding site 7 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca502

b:44.9
occ:1.00
 OG c:SER30 2.4 46.8 1.0
O c:HOH768 2.4 38.9 1.0
O c:PHE22 2.4 52.9 1.0
OE1 c:GLU29 2.4 35.0 1.0
O c:THR24 2.4 43.3 1.0
OD2 c:ASP27 2.4 40.5 1.0
OD1 c:ASP27 2.7 35.0 1.0
CG c:ASP27 2.9 39.1 1.0
C c:PHE22 3.4 36.5 1.0
CB c:SER30 3.5 35.7 1.0
CD c:GLU29 3.6 44.7 1.0
C c:THR24 3.7 36.1 1.0
N c:SER30 4.1 45.5 1.0
O c:HOH786 4.2 44.1 1.0
OE2 c:GLU29 4.2 56.6 1.0
CA c:PHE22 4.2 41.1 1.0
N c:THR24 4.2 48.1 1.0
CB c:PHE22 4.4 38.5 1.0
CA c:SER30 4.4 37.5 1.0
N c:ALA23 4.4 37.1 1.0
C c:ALA23 4.4 50.0 1.0
CB c:ASP27 4.4 48.6 1.0
CA c:ASN25 4.5 48.7 1.0
N c:ASN25 4.5 48.5 1.0
CA c:THR24 4.6 44.8 1.0
CA c:ALA23 4.7 37.7 1.0
CB c:GLU29 4.7 39.7 1.0
CG c:GLU29 4.7 52.3 1.0
C c:ASN25 4.9 42.0 1.0
C c:GLU29 4.9 43.1 1.0
O c:ALA23 5.0 53.2 1.0

Calcium binding site 8 out of 9 in 4ub8

Go back to Calcium Binding Sites List in 4ub8
Calcium binding site 8 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Ca103

b:72.1
occ:1.00
 O f:HOH207 2.5 65.8 1.0
OXT f:ARG45 2.5 34.4 1.0
O3 f:GOL104 2.6 45.6 1.0
O f:HOH205 2.7 61.1 1.0
O v:HOH311 2.7 50.4 1.0
O2 f:GOL104 2.9 61.6 1.0
O f:ARG45 2.9 40.3 1.0
C f:ARG45 3.1 38.9 1.0
O f:HOH204 3.2 59.3 1.0
C3 f:GOL104 3.7 55.4 1.0
O f:HOH203 3.7 47.1 1.0
C2 f:GOL104 3.8 59.9 1.0
O v:HOH312 4.2 51.7 1.0
O v:HOH378 4.3 80.3 1.0
OE1 v:GLU23 4.5 78.5 1.0
OE2 v:GLU23 4.5 66.0 1.0
CA f:ARG45 4.6 32.8 1.0
C1 f:GOL104 4.6 51.0 1.0
O a:ALA309 4.7 33.5 1.0
CB a:ALA309 4.9 34.6 1.0
CD v:GLU23 4.9 75.4 1.0
O1 f:GOL104 4.9 49.7 1.0

Calcium binding site 9 out of 9 in 4ub8

Go back to Calcium Binding Sites List in 4ub8
Calcium binding site 9 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:62.0
occ:1.00
 OD1 o:ASN200 2.3 49.3 1.0
O o:HOH506 2.5 52.1 1.0
O o:VAL201 2.5 48.9 1.0
O o:HOH491 2.6 45.3 1.0
O o:HOH511 2.6 72.7 1.0
O o:THR138 2.6 48.6 1.0
O o:HOH492 2.6 50.5 1.0
CG o:ASN200 3.4 53.4 1.0
C o:VAL201 3.6 47.6 1.0
C o:THR138 3.7 46.6 1.0
ND2 o:ASN200 3.9 58.5 1.0
N o:VAL201 4.2 37.9 1.0
CA o:THR138 4.5 44.0 1.0
N o:ALA202 4.5 45.4 1.0
CA o:VAL201 4.5 45.1 1.0
N o:SER139 4.5 53.8 1.0
CA o:ALA202 4.6 39.0 1.0
CA o:SER139 4.6 51.9 1.0
C o:ASN200 4.6 43.8 1.0
O o:THR140 4.7 39.0 1.0
CB o:ASN200 4.7 42.7 1.0
CB o:THR138 4.7 55.5 1.0
C o:SER139 4.9 56.6 1.0
CA o:ASN200 5.0 33.8 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: Sun Jul 14 13:40:20 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