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Calcium 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
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 of the Psbm-Deletion Mutant of Photosystem II (pdb code 5h2f). 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 of the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5h2f

Go back to Calcium Binding Sites List in 5h2f
Calcium binding site 1 out of 7 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca401

b:28.6
occ:1.00
 CA1 A:OEX401 0.0 28.6 1.0
O A:HOH521 2.3 25.8 1.0
O1 A:OEX401 2.3 25.9 1.0
O A:ALA344 2.3 28.9 1.0
O2 A:OEX401 2.4 30.0 1.0
OD2 A:ASP170 2.4 26.8 1.0
O A:HOH604 2.4 30.4 1.0
O5 A:OEX401 2.7 31.9 1.0
OE1 A:GLU189 3.0 30.4 1.0
CG A:ASP170 3.1 26.1 1.0
MN2 A:OEX401 3.4 26.8 1.0
C A:ALA344 3.4 25.9 1.0
OD1 A:ASP170 3.4 23.7 1.0
MN3 A:OEX401 3.5 27.7 1.0
MN1 A:OEX401 3.7 25.5 1.0
OXT A:ALA344 3.8 24.5 1.0
MN4 A:OEX401 3.8 29.9 1.0
CD A:GLU189 3.9 28.2 1.0
O4 A:OEX401 3.9 32.0 1.0
O A:HOH519 4.0 33.1 1.0
OE2 A:GLU189 4.1 27.1 1.0
O3 A:OEX401 4.3 26.4 1.0
NH2 C:ARG357 4.3 29.8 1.0
NH1 C:ARG357 4.3 27.9 1.0
CB A:ASP170 4.3 25.2 1.0
O A:HOH503 4.5 27.8 1.0
O A:HOH591 4.6 27.3 1.0
OH A:TYR161 4.6 30.9 1.0
OE1 A:GLN165 4.7 28.1 1.0
CA A:ALA344 4.7 27.8 1.0
CZ C:ARG357 4.8 28.9 1.0

Calcium binding site 2 out of 7 in 5h2f

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Calcium binding site 2 out of 7 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca601

b:64.9
occ:1.00
 O B:HOH932 2.3 55.5 1.0
OD1 B:ASN438 2.6 34.5 1.0
O O:HOH518 2.6 56.0 1.0
O B:HOH850 2.6 64.2 1.0
O B:HOH720 2.7 42.6 1.0
CG B:ASN438 3.8 38.4 1.0
OE1 B:GLU435 3.8 66.4 1.0
O B:HOH742 3.8 46.5 1.0
CA B:ASN438 4.3 34.9 1.0
O B:SER439 4.5 29.3 1.0
OE2 B:GLU435 4.5 66.1 1.0
C1 D:DMS417 4.5 72.9 1.0
CB B:ASN438 4.6 34.3 1.0
CD B:GLU435 4.6 60.4 1.0
C B:ASN438 4.6 34.3 1.0
O B:HOH752 4.7 51.9 1.0
ND2 B:ASN438 4.8 38.6 1.0
O B:THR434 4.8 36.2 1.0
O B:ASN438 4.9 37.3 1.0

Calcium binding site 3 out of 7 in 5h2f

Go back to Calcium Binding Sites List in 5h2f
Calcium binding site 3 out of 7 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
O:Ca302

b:59.3
occ:1.00
 O O:HOH459 2.2 47.0 1.0
O O:VAL201 2.3 48.4 1.0
O O:THR138 2.5 59.1 1.0
OD1 O:ASN200 2.5 54.2 1.0
O O:HOH533 2.9 59.5 1.0
C O:VAL201 3.5 42.5 1.0
C O:THR138 3.6 49.7 1.0
CG O:ASN200 3.6 56.0 1.0
ND2 O:ASN200 4.1 58.2 1.0
CA O:ALA202 4.3 43.1 1.0
N O:VAL201 4.4 42.7 1.0
N O:ALA202 4.4 42.8 1.0
CA O:THR138 4.5 50.9 1.0
N O:SER139 4.5 47.0 1.0
CA O:SER139 4.5 48.1 1.0
CA O:VAL201 4.5 39.4 1.0
OD1 O:ASP141 4.5 69.5 1.0
C O:ASN200 4.6 43.9 1.0
CB O:THR138 4.7 49.5 1.0
O O:THR140 4.8 46.2 1.0
CB O:ALA202 4.9 42.9 1.0
CB O:ASN200 4.9 51.8 1.0
O O:ASN200 4.9 44.3 1.0
C O:SER139 4.9 45.0 1.0

Calcium binding site 4 out of 7 in 5h2f

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Calcium binding site 4 out of 7 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca403

b:33.1
occ:1.00
 CA1 a:OEX403 0.0 33.1 1.0
O a:HOH506 2.4 23.9 1.0
OD1 a:ASP170 2.5 36.5 1.0
O1 a:OEX403 2.5 31.1 1.0
O a:ALA344 2.6 30.3 1.0
O a:HOH599 2.6 36.0 1.0
O5 a:OEX403 2.6 29.3 1.0
O2 a:OEX403 2.8 32.4 1.0
OE1 a:GLU189 2.9 30.0 1.0
CG a:ASP170 3.3 35.8 1.0
MN2 a:OEX403 3.4 32.4 1.0
MN3 a:OEX403 3.4 31.0 1.0
C a:ALA344 3.5 29.8 1.0
MN1 a:OEX403 3.5 31.3 1.0
OD2 a:ASP170 3.5 34.0 1.0
OXT a:ALA344 3.7 30.0 1.0
CD a:GLU189 3.8 29.9 1.0
O3 a:OEX403 3.8 30.4 1.0
MN4 a:OEX403 3.8 31.1 1.0
OE2 a:GLU189 3.9 27.4 1.0
O a:HOH579 4.2 58.0 1.0
O4 a:OEX403 4.2 29.7 1.0
NH1 c:ARG357 4.3 30.6 1.0
NH2 c:ARG357 4.4 28.2 1.0
O a:HOH540 4.5 36.9 1.0
CB a:ASP170 4.5 34.9 1.0
OH a:TYR161 4.6 26.7 1.0
OE1 a:GLN165 4.6 30.4 1.0
O a:HOH597 4.6 23.4 1.0
CA a:ALA344 4.8 31.6 1.0
CZ c:ARG357 4.9 30.4 1.0
CG1 a:VAL185 5.0 23.9 1.0
OD1 a:ASP342 5.0 26.7 1.0

Calcium binding site 5 out of 7 in 5h2f

Go back to Calcium Binding Sites List in 5h2f
Calcium binding site 5 out of 7 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
b:Ca601

b:59.5
occ:1.00
 O b:HOH787 2.1 54.7 1.0
OD1 b:ASN438 2.4 42.5 1.0
O b:HOH861 2.5 58.2 1.0
O b:HOH755 2.6 34.3 1.0
CG b:ASN438 3.6 36.9 1.0
O o:HOH455 3.8 64.7 1.0
O b:HOH846 4.3 41.9 1.0
OE2 b:GLU435 4.4 61.5 1.0
O b:SER439 4.5 30.5 1.0
CA b:ASN438 4.5 32.0 1.0
ND2 b:ASN438 4.5 42.3 1.0
CB b:ASN438 4.6 34.3 1.0
C b:ASN438 4.8 32.4 1.0
O b:HOH804 4.8 56.1 1.0
OE1 b:GLU435 4.8 58.3 1.0
OE1 o:GLU181 4.9 83.3 1.0
CD b:GLU435 5.0 52.7 1.0

Calcium binding site 6 out of 7 in 5h2f

Go back to Calcium Binding Sites List in 5h2f
Calcium binding site 6 out of 7 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
c:Ca901

b:48.7
occ:1.00
 OE2 c:GLU29 1.8 37.6 1.0
O c:THR24 2.2 51.7 1.0
OG c:SER30 2.3 50.0 1.0
O c:PHE22 2.4 53.5 1.0
O c:HOH1158 2.5 43.5 1.0
OD2 c:ASP27 2.5 46.7 1.0
OD1 c:ASP27 2.8 42.1 1.0
CG c:ASP27 3.0 49.5 1.0
CD c:GLU29 3.1 45.8 1.0
C c:THR24 3.4 52.3 1.0
CB c:SER30 3.4 47.5 1.0
C c:PHE22 3.5 49.5 1.0
CG c:GLU29 3.9 48.0 1.0
OE1 c:GLU29 3.9 48.2 1.0
O c:HOH1022 4.0 36.6 1.0
N c:THR24 4.0 61.1 1.0
N c:SER30 4.2 39.1 1.0
C c:ALA23 4.2 53.6 1.0
CA c:ASN25 4.2 47.1 1.0
N c:ASN25 4.3 49.9 1.0
CA c:PHE22 4.3 47.2 1.0
CA c:THR24 4.4 53.8 1.0
CA c:SER30 4.4 44.4 1.0
N c:ALA23 4.4 47.7 1.0
O c:ALA23 4.5 51.6 1.0
CB c:ASP27 4.6 43.4 1.0
CB c:PHE22 4.6 47.8 1.0
CA c:ALA23 4.6 51.4 1.0
O c:HOH1142 4.6 62.8 1.0
C c:ASN25 4.8 47.0 1.0
OG1 c:THR24 5.0 48.2 1.0

Calcium binding site 7 out of 7 in 5h2f

Go back to Calcium Binding Sites List in 5h2f
Calcium binding site 7 out of 7 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
o:Ca301

b:55.2
occ:1.00
 O o:HOH489 2.3 56.6 1.0
OD1 o:ASN200 2.3 50.4 1.0
O o:VAL201 2.4 48.6 1.0
O o:HOH447 2.4 55.8 1.0
O o:THR138 2.5 60.8 1.0
O o:HOH416 2.5 44.9 1.0
O o:HOH441 2.6 51.1 1.0
C o:VAL201 3.4 46.4 1.0
CG o:ASN200 3.5 50.2 1.0
C o:THR138 3.6 54.2 1.0
ND2 o:ASN200 4.0 48.4 1.0
N o:VAL201 4.1 43.9 1.0
N o:ALA202 4.2 46.7 1.0
CA o:ALA202 4.3 48.0 1.0
O o:HOH406 4.3 54.6 1.0
CA o:VAL201 4.4 43.3 1.0
CA o:THR138 4.4 48.8 1.0
N o:SER139 4.5 51.3 1.0
C o:ASN200 4.5 46.7 1.0
CA o:SER139 4.5 53.6 1.0
CB o:THR138 4.6 48.4 1.0
O o:HOH509 4.6 60.8 1.0
OD1 o:ASP141 4.6 61.5 1.0
O o:HOH472 4.7 51.0 1.0
CB o:ASN200 4.7 47.9 1.0
O o:THR140 4.8 57.7 1.0
O o:ASN200 4.9 49.0 1.0
CA o:ASN200 4.9 45.9 1.0
CB o:ALA202 5.0 43.3 1.0
C o:SER139 5.0 50.9 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 Jul 14 19:50:59 2024

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