Atomistry » Calcium » PDB 5b4y-5bx5 » 5b5e
Atomistry »
  Calcium »
    PDB 5b4y-5bx5 »
      5b5e »

Calcium in PDB 5b5e: Crystal Structure Analysis of Photosystem II Complex

Enzymatic activity of Crystal Structure Analysis of Photosystem II Complex

All present enzymatic activity of Crystal Structure Analysis of Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Crystal Structure Analysis of Photosystem II Complex, PDB code: 5b5e was solved by A.Tanaka, Y.Fukushima, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.98 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.404, 228.224, 286.429, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.2

Other elements in 5b5e:

The structure of Crystal Structure Analysis of Photosystem II Complex also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of Photosystem II Complex (pdb code 5b5e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure Analysis of Photosystem II Complex, PDB code: 5b5e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5b5e

Go back to Calcium Binding Sites List in 5b5e
Calcium binding site 1 out of 7 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:23.4
occ:1.00
 CA1 A:OEX401 0.0 23.4 1.0
O A:HOH619 2.3 24.5 1.0
O1 A:OEX401 2.4 20.3 1.0
OD2 A:ASP170 2.4 23.1 1.0
O A:HOH549 2.4 20.9 1.0
O5 A:OEX401 2.4 21.8 1.0
O A:ALA344 2.5 22.9 1.0
O2 A:OEX401 2.5 23.4 1.0
OE1 A:GLU189 3.0 23.9 1.0
CG A:ASP170 3.1 22.1 1.0
MN2 A:OEX401 3.4 21.1 1.0
MN3 A:OEX401 3.4 21.3 1.0
OD1 A:ASP170 3.4 20.5 1.0
MN1 A:OEX401 3.5 19.1 1.0
C A:ALA344 3.5 20.6 1.0
MN4 A:OEX401 3.7 22.3 1.0
OXT A:ALA344 3.8 21.7 1.0
CD A:GLU189 3.8 19.1 1.0
OE2 A:GLU189 3.9 19.0 1.0
O4 A:OEX401 3.9 24.7 1.0
O3 A:OEX401 4.1 21.7 1.0
O A:HOH575 4.1 26.7 1.0
NH1 C:ARG357 4.2 18.6 1.0
CB A:ASP170 4.3 20.5 1.0
O A:HOH578 4.4 25.8 1.0
NH2 C:ARG357 4.5 17.2 1.0
O A:HOH515 4.5 19.8 1.0
OH A:TYR161 4.7 19.2 1.0
OE1 A:GLN165 4.8 21.2 1.0
CA A:ALA344 4.8 21.3 1.0
CZ C:ARG357 4.8 22.4 1.0
CG1 A:VAL185 5.0 21.5 1.0

Calcium binding site 2 out of 7 in 5b5e

Go back to Calcium Binding Sites List in 5b5e
Calcium binding site 2 out of 7 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:41.4
occ:1.00
 O B:HOH766 2.3 48.6 1.0
O B:HOH993 2.4 44.1 1.0
OD1 B:ASN438 2.4 30.0 1.0
O B:HOH896 2.4 22.9 1.0
O B:HOH1012 2.5 57.1 1.0
O B:HOH996 2.7 56.8 1.0
CG B:ASN438 3.6 27.8 1.0
OE2 B:GLU435 3.9 60.8 1.0
CA B:ASN438 4.3 22.8 1.0
O B:HOH709 4.4 39.2 1.0
O B:SER439 4.5 20.5 1.0
ND2 B:ASN438 4.5 30.8 1.0
CB B:ASN438 4.5 25.4 1.0
C B:ASN438 4.6 23.4 1.0
O B:HOH803 4.6 49.0 1.0
OE1 B:GLU435 4.6 57.9 1.0
O D:HOH654 4.7 54.6 1.0
CD B:GLU435 4.7 52.7 1.0
O B:HOH892 4.8 38.1 1.0
C1 D:DMS417 4.8 55.0 1.0
O O:HOH581 4.8 72.2 1.0
O B:THR434 4.8 23.4 1.0
O B:ASN438 5.0 21.3 1.0

Calcium binding site 3 out of 7 in 5b5e

Go back to Calcium Binding Sites List in 5b5e
Calcium binding site 3 out of 7 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:42.4
occ:1.00
 O O:HOH558 2.1 46.6 1.0
O O:VAL201 2.2 37.4 1.0
O O:HOH497 2.3 42.1 1.0
O O:HOH472 2.3 37.6 1.0
O O:THR138 2.4 36.4 1.0
OD1 O:ASN200 2.5 42.2 1.0
O O:HOH550 2.5 47.3 1.0
C O:VAL201 3.4 34.6 1.0
CG O:ASN200 3.6 43.0 1.0
C O:THR138 3.6 38.8 1.0
ND2 O:ASN200 4.1 42.2 1.0
N O:VAL201 4.2 32.6 1.0
O O:HOH635 4.2 57.0 1.0
N O:ALA202 4.3 35.0 1.0
CA O:VAL201 4.3 31.2 1.0
CA O:ALA202 4.3 38.0 1.0
CA O:THR138 4.4 40.2 1.0
C O:ASN200 4.4 30.8 1.0
N O:SER139 4.5 37.4 1.0
CA O:SER139 4.5 39.2 1.0
O O:HOH645 4.6 58.2 1.0
CB O:THR138 4.6 42.7 1.0
OD2 O:ASP141 4.6 53.6 1.0
O O:THR140 4.8 35.4 1.0
O O:ASN200 4.8 32.4 1.0
CB O:VAL201 4.8 32.8 1.0
CB O:ASN200 4.8 37.5 1.0
O O:HOH518 4.9 24.1 0.5
CA O:ASN200 4.9 34.1 1.0
O O:HOH511 4.9 44.8 1.0
C O:SER139 5.0 37.5 1.0

Calcium binding site 4 out of 7 in 5b5e

Go back to Calcium Binding Sites List in 5b5e
Calcium binding site 4 out of 7 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca402

b:24.4
occ:1.00
 CA1 a:OEX402 0.0 24.4 1.0
OD2 a:ASP170 2.3 23.3 1.0
O a:HOH539 2.5 23.8 1.0
O a:HOH632 2.5 19.0 1.0
O a:ALA344 2.5 24.8 1.0
O2 a:OEX402 2.6 23.8 1.0
O5 a:OEX402 2.6 24.5 1.0
O1 a:OEX402 2.6 21.4 1.0
OE1 a:GLU189 3.0 24.7 1.0
CG a:ASP170 3.2 22.1 1.0
MN2 a:OEX402 3.3 23.0 1.0
MN3 a:OEX402 3.4 22.0 1.0
MN1 a:OEX402 3.5 21.5 1.0
C a:ALA344 3.5 25.1 1.0
OD1 a:ASP170 3.5 20.8 1.0
MN4 a:OEX402 3.8 23.4 1.0
OXT a:ALA344 3.8 27.5 1.0
CD a:GLU189 3.8 22.8 1.0
O3 a:OEX402 3.9 24.3 1.0
OE2 a:GLU189 4.0 20.0 1.0
O4 a:OEX402 4.0 23.2 1.0
O a:HOH569 4.1 27.4 1.0
NH1 c:ARG357 4.4 22.9 1.0
CB a:ASP170 4.4 20.4 1.0
NH2 c:ARG357 4.5 19.9 1.0
O a:HOH595 4.6 21.3 1.0
O a:HOH545 4.6 22.9 1.0
OH a:TYR161 4.7 19.6 1.0
OE1 a:GLN165 4.7 19.7 1.0
CA a:ALA344 4.8 23.6 1.0
CZ c:ARG357 4.9 20.4 1.0
OD1 a:ASP342 5.0 17.9 1.0
CG1 a:VAL185 5.0 17.4 1.0

Calcium binding site 5 out of 7 in 5b5e

Go back to Calcium Binding Sites List in 5b5e
Calcium binding site 5 out of 7 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca601

b:41.9
occ:1.00
 OD1 b:ASN438 2.3 30.9 1.0
O b:HOH947 2.3 43.4 1.0
O b:HOH706 2.4 30.8 0.5
O b:HOH937 2.4 48.0 1.0
O b:HOH706 2.5 27.6 0.5
O b:HOH751 2.5 23.9 1.0
O b:HOH1044 2.7 62.4 1.0
CG b:ASN438 3.5 27.2 1.0
O d:HOH675 4.3 51.5 1.0
CA b:ASN438 4.3 22.7 1.0
ND2 b:ASN438 4.4 28.8 1.0
CB b:ASN438 4.5 23.6 1.0
O b:SER439 4.5 24.8 1.0
O b:HOH1055 4.6 38.3 1.0
O b:HOH785 4.6 54.0 1.0
C b:ASN438 4.6 21.5 1.0
O m:HOH205 4.6 48.1 1.0
O b:HOH791 4.7 47.8 1.0
O b:THR434 4.7 22.2 1.0
OE1 b:GLU435 4.7 52.7 1.0
OE2 b:GLU435 4.8 55.1 1.0
O b:ASN438 5.0 21.6 1.0

Calcium binding site 6 out of 7 in 5b5e

Go back to Calcium Binding Sites List in 5b5e
Calcium binding site 6 out of 7 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca901

b:39.7
occ:1.00
 OE1 c:GLU29 1.9 39.8 1.0
O c:THR24 2.2 36.1 1.0
OG c:SER30 2.2 35.3 1.0
O c:HOH1211 2.4 38.2 1.0
OD2 c:ASP27 2.5 39.2 1.0
O c:PHE22 2.5 41.9 1.0
OD1 c:ASP27 2.6 30.9 1.0
CG c:ASP27 2.9 36.8 1.0
CD c:GLU29 3.1 41.0 1.0
CB c:SER30 3.4 36.6 1.0
C c:THR24 3.4 37.8 1.0
C c:PHE22 3.6 39.8 1.0
OE2 c:GLU29 4.0 41.0 1.0
CG c:GLU29 4.0 44.8 1.0
N c:SER30 4.0 31.1 1.0
N c:THR24 4.0 44.4 1.0
O c:HOH1207 4.1 50.6 1.0
O c:HOH1019 4.1 34.5 1.0
CA c:SER30 4.2 34.5 1.0
CA c:ASN25 4.2 35.4 1.0
C c:ALA23 4.2 42.5 1.0
N c:ASN25 4.3 35.4 1.0
CA c:PHE22 4.4 43.2 1.0
CA c:THR24 4.4 39.1 1.0
CB c:ASP27 4.4 35.4 1.0
N c:ALA23 4.5 38.4 1.0
O c:HOH1148 4.5 55.4 1.0
CA c:ALA23 4.6 41.8 1.0
CB c:PHE22 4.7 42.3 1.0
C c:ASN25 4.7 34.3 1.0
O c:ALA23 4.7 42.9 1.0
O c:HOH1271 4.7 40.0 0.5
O c:HOH1198 4.9 55.6 1.0
C c:GLU29 4.9 32.5 1.0

Calcium binding site 7 out of 7 in 5b5e

Go back to Calcium Binding Sites List in 5b5e
Calcium binding site 7 out of 7 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca302

b:43.6
occ:1.00
 O o:HOH523 2.1 50.6 1.0
O o:HOH501 2.3 43.2 1.0
O o:VAL201 2.3 35.9 1.0
O o:HOH406 2.4 41.2 1.0
OD1 o:ASN200 2.4 35.4 1.0
O o:THR138 2.5 45.9 1.0
O o:HOH441 2.7 46.8 1.0
C o:VAL201 3.4 38.5 1.0
CG o:ASN200 3.5 41.4 1.0
C o:THR138 3.6 48.1 1.0
ND2 o:ASN200 4.1 41.5 1.0
N o:VAL201 4.1 36.6 1.0
N o:ALA202 4.3 35.6 1.0
CA o:VAL201 4.3 35.0 1.0
C o:ASN200 4.4 39.3 1.0
CA o:ALA202 4.4 39.3 1.0
CA o:THR138 4.4 44.3 1.0
N o:SER139 4.4 48.5 1.0
CA o:SER139 4.5 48.6 1.0
O o:THR140 4.5 38.4 1.0
OD2 o:ASP141 4.6 60.6 1.0
CB o:THR138 4.7 46.5 1.0
O o:HOH453 4.7 55.0 1.0
O o:ASN200 4.7 41.8 1.0
CB o:ASN200 4.8 35.9 1.0
O o:HOH527 4.8 46.7 1.0
O o:HOH554 4.9 49.8 1.0
CA o:ASN200 4.9 37.3 1.0
C o:SER139 4.9 43.6 1.0
CB o:VAL201 5.0 37.9 1.0

Reference:

A.Tanaka, Y.Fukushima, N.Kamiya. Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II J. Am. Chem. Soc. V. 139 1718 2017.
ISSN: ESSN 1520-5126
PubMed: 28102667
DOI: 10.1021/JACS.6B09666
Page generated: Sun Jul 14 16:49:59 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