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Calcium 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
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-1) By A Femtosecond X-Ray Laser (pdb code 4ub6). 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-1) By A Femtosecond X-Ray Laser, PDB code: 4ub6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4ub6

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Calcium binding site 1 out of 9 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 Calcium with other atoms in the Ca 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:Ca418

b:28.3
occ:1.00
 CA1 A:OEX418 0.0 28.3 1.0
OD1 A:ASP170 2.3 28.3 1.0
O A:ALA344 2.4 29.2 1.0
O A:HOH568 2.5 39.6 1.0
O1 A:OEX418 2.6 20.9 1.0
O5 A:OEX418 2.6 15.1 1.0
O A:HOH569 2.6 18.4 1.0
O2 A:OEX418 2.7 24.2 1.0
OE1 A:GLU189 3.1 30.1 1.0
CG A:ASP170 3.2 19.9 1.0
MN2 A:OEX418 3.4 22.1 1.0
MN3 A:OEX418 3.5 19.6 1.0
C A:ALA344 3.5 29.2 1.0
MN1 A:OEX418 3.5 20.2 1.0
OD2 A:ASP170 3.6 21.1 1.0
MN4 A:OEX418 3.8 21.5 1.0
OXT A:ALA344 3.8 27.9 1.0
O4 A:OEX418 3.8 20.0 1.0
CD A:GLU189 3.9 15.2 1.0
OE2 A:GLU189 4.0 16.0 1.0
O A:HOH601 4.0 40.4 1.0
O3 A:OEX418 4.1 24.6 1.0
NH1 C:ARG357 4.4 27.0 1.0
CB A:ASP170 4.5 15.2 1.0
O A:HOH570 4.5 26.3 1.0
NH2 C:ARG357 4.5 20.2 1.0
O A:HOH607 4.7 15.8 1.0
OE1 A:GLN165 4.7 25.9 1.0
OH A:TYR161 4.7 15.2 1.0
CA A:ALA344 4.8 28.3 1.0
CZ C:ARG357 4.9 29.1 1.0
CG1 A:VAL185 5.0 17.5 1.0

Calcium binding site 2 out of 9 in 4ub6

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Calcium binding site 2 out of 9 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 Calcium with other atoms in the Ca 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
B:Ca601

b:83.2
occ:1.00
 O O:HOH565 2.7 55.1 1.0
O B:HOH847 2.7 33.2 1.0
OD1 B:ASN438 2.8 35.8 1.0
O B:HOH865 2.9 35.1 1.0
O B:HOH989 3.1 56.9 1.0
O O:HOH555 3.1 62.2 1.0
O B:HOH860 3.4 55.1 1.0
CG B:ASN438 4.0 30.1 1.0
OE2 B:GLU435 4.1 32.6 0.5
O B:HOH778 4.5 27.2 1.0
OE2 O:GLU181 4.6 60.5 0.5
O B:SER439 4.8 16.4 1.0
O B:HOH803 4.8 31.8 1.0
O B:HOH973 4.8 54.0 1.0
ND2 B:ASN438 4.8 29.4 1.0
CA B:ASN438 4.9 23.9 1.0

Calcium binding site 3 out of 9 in 4ub6

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Calcium binding site 3 out of 9 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 Calcium with other atoms in the Ca 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
F:Ca102

b:69.4
occ:1.00
 O F:HOH203 2.6 47.6 1.0
O2 F:GOL103 2.6 67.2 1.0
OXT F:ARG45 2.6 30.4 1.0
O V:HOH322 2.6 62.4 1.0
O F:HOH202 2.8 49.5 1.0
O V:HOH320 2.8 55.6 1.0
O F:ARG45 2.8 28.6 1.0
O3 F:GOL103 2.9 71.4 1.0
C F:ARG45 3.1 27.6 1.0
C3 F:GOL103 3.3 71.9 1.0
C2 F:GOL103 3.5 65.8 1.0
O F:HOH201 4.0 42.1 1.0
O V:HOH321 4.3 29.5 1.0
OE1 V:GLU23 4.4 72.0 1.0
C1 F:GOL103 4.5 60.4 1.0
OE2 V:GLU23 4.5 88.9 1.0
CA F:ARG45 4.6 22.4 1.0
O1 F:GOL103 4.7 60.7 1.0
O F:HOH205 4.8 41.0 1.0
CD V:GLU23 4.8 80.9 1.0

Calcium binding site 4 out of 9 in 4ub6

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Calcium binding site 4 out of 9 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 Calcium with other atoms in the Ca 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
O:Ca301

b:53.7
occ:1.00
 OD1 O:ASN200 2.3 53.5 1.0
O O:THR138 2.4 45.1 1.0
O O:VAL201 2.5 44.0 1.0
O O:HOH522 2.5 44.1 1.0
O O:HOH523 2.8 47.7 1.0
O O:HOH427 2.9 45.0 1.0
O O:HOH419 2.9 52.5 1.0
CG O:ASN200 3.4 56.1 1.0
C O:THR138 3.6 44.2 1.0
C O:VAL201 3.6 45.6 1.0
ND2 O:ASN200 3.8 53.7 1.0
N O:VAL201 4.1 31.4 1.0
O O:HOH580 4.4 71.7 1.0
CA O:VAL201 4.4 36.4 1.0
C O:ASN200 4.4 30.8 1.0
CA O:THR138 4.5 51.3 1.0
N O:SER139 4.5 40.3 1.0
CA O:SER139 4.5 45.4 1.0
N O:ALA202 4.5 40.4 1.0
CA O:ALA202 4.6 33.6 1.0
CB O:ASN200 4.6 44.0 1.0
O O:THR140 4.7 41.7 1.0
CB O:THR138 4.7 47.3 1.0
C O:SER139 4.8 34.9 1.0
CA O:ASN200 4.8 38.2 1.0
O O:ASN200 4.9 46.8 1.0
CB O:VAL201 4.9 39.8 1.0

Calcium binding site 5 out of 9 in 4ub6

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Calcium binding site 5 out of 9 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 Calcium with other atoms in the Ca 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:Ca416

b:34.0
occ:1.00
 CA1 a:OEX416 0.0 34.0 1.0
O a:ALA344 2.4 21.8 1.0
OD1 a:ASP170 2.5 37.8 1.0
O a:HOH526 2.5 39.4 1.0
O2 a:OEX416 2.6 19.6 1.0
O5 a:OEX416 2.6 18.8 1.0
O a:HOH527 2.6 39.4 1.0
O1 a:OEX416 2.6 20.3 1.0
OE1 a:GLU189 3.0 28.2 1.0
O a:HOH561 3.1 47.5 1.0
MN2 a:OEX416 3.3 22.9 1.0
CG a:ASP170 3.3 27.9 1.0
MN3 a:OEX416 3.4 21.5 1.0
C a:ALA344 3.4 37.0 1.0
MN1 a:OEX416 3.5 24.7 1.0
OD2 a:ASP170 3.6 26.2 1.0
OXT a:ALA344 3.7 20.4 1.0
OE2 a:GLU189 3.8 26.3 1.0
CD a:GLU189 3.8 29.0 1.0
MN4 a:OEX416 3.9 22.7 1.0
O4 a:OEX416 3.9 18.9 1.0
O3 a:OEX416 4.1 24.0 1.0
NH1 c:ARG357 4.3 25.8 1.0
O a:HOH528 4.4 27.7 1.0
O a:HOH566 4.5 17.9 1.0
CB a:ASP170 4.6 23.4 1.0
NH2 c:ARG357 4.6 22.6 1.0
OH a:TYR161 4.7 19.3 1.0
OE1 a:GLN165 4.7 32.0 1.0
CA a:ALA344 4.8 31.0 1.0
CZ c:ARG357 5.0 32.0 1.0

Calcium binding site 6 out of 9 in 4ub6

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Calcium binding site 6 out of 9 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 Calcium with other atoms in the Ca 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
b:Ca604

b:0.1
occ:1.00
 OD1 b:ASN438 2.6 43.1 1.0
O b:HOH746 2.9 27.6 1.0
O b:HOH756 3.0 53.9 1.0
O o:HOH531 3.0 77.7 1.0
O b:HOH764 3.1 59.5 1.0
CG b:ASN438 3.8 27.2 1.0
O b:HOH723 4.1 33.3 1.0
O d:HOH629 4.4 50.1 1.0
ND2 b:ASN438 4.4 28.3 1.0
O b:SER439 4.5 19.4 1.0
CA b:ASN438 5.0 24.2 1.0
CB b:ASN438 5.0 19.4 1.0
OE1 o:GLU181 5.0 74.3 0.5

Calcium binding site 7 out of 9 in 4ub6

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Calcium binding site 7 out of 9 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 Calcium with other atoms in the Ca 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
c:Ca901

b:44.6
occ:1.00
 O c:HOH1170 2.3 34.5 1.0
O c:THR24 2.3 40.3 1.0
OG c:SER30 2.4 45.0 1.0
OE1 c:GLU29 2.4 42.5 1.0
O c:PHE22 2.5 72.9 1.0
OD2 c:ASP27 2.5 38.5 1.0
OD1 c:ASP27 2.7 32.1 1.0
CG c:ASP27 3.0 51.2 1.0
C c:PHE22 3.4 34.5 1.0
CD c:GLU29 3.5 32.9 1.0
CB c:SER30 3.5 38.3 1.0
C c:THR24 3.6 34.2 1.0
OE2 c:GLU29 4.0 48.4 1.0
N c:THR24 4.1 59.9 1.0
O c:HOH1187 4.2 34.2 1.0
N c:SER30 4.2 37.6 1.0
N c:ALA23 4.2 35.1 1.0
C c:ALA23 4.2 62.9 1.0
CA c:PHE22 4.3 48.0 1.0
CA c:ASN25 4.3 52.1 1.0
N c:ASN25 4.4 51.7 1.0
CA c:SER30 4.4 34.7 1.0
CA c:ALA23 4.5 35.6 1.0
CB c:ASP27 4.5 52.7 1.0
CA c:THR24 4.5 55.1 1.0
CB c:PHE22 4.6 33.9 1.0
O c:ALA23 4.7 65.6 1.0
CG c:GLU29 4.7 39.3 1.0
C c:ASN25 4.8 47.6 1.0
CB c:GLU29 4.8 36.5 1.0

Calcium binding site 8 out of 9 in 4ub6

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Calcium binding site 8 out of 9 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 Calcium with other atoms in the Ca 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
f:Ca104

b:77.8
occ:1.00
 OXT f:ARG45 2.5 35.7 1.0
O3 f:GOL101 2.6 44.5 1.0
O2 f:GOL101 2.6 64.4 1.0
O f:HOH205 2.6 62.1 1.0
O v:HOH312 2.7 44.5 1.0
O f:ARG45 2.7 37.2 1.0
C f:ARG45 3.0 32.1 1.0
O v:HOH307 3.4 78.7 1.0
C3 f:GOL101 3.6 62.2 1.0
C2 f:GOL101 3.6 60.4 1.0
O v:HOH306 3.9 46.8 1.0
O v:HOH313 3.9 55.6 1.0
O f:HOH201 3.9 43.4 1.0
OE1 v:GLU23 4.4 71.5 1.0
CA f:ARG45 4.5 31.4 1.0
OE2 v:GLU23 4.5 89.2 1.0
C1 f:GOL101 4.6 50.9 1.0
O1 f:GOL101 4.7 44.7 1.0
O a:ALA309 4.7 36.6 1.0
CD v:GLU23 4.8 80.2 1.0
CG f:ARG45 5.0 33.0 1.0

Calcium binding site 9 out of 9 in 4ub6

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Calcium binding site 9 out of 9 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 Calcium with other atoms in the Ca binding site number 9 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
o:Ca301

b:54.7
occ:1.00
 OD1 o:ASN200 2.3 53.6 1.0
O o:VAL201 2.6 42.7 1.0
O o:HOH501 2.6 58.9 1.0
O o:HOH488 2.7 53.4 1.0
O o:THR138 2.7 59.2 1.0
O o:HOH506 2.7 58.2 1.0
O o:HOH487 2.7 39.4 1.0
CG o:ASN200 3.3 57.8 1.0
C o:VAL201 3.7 45.6 1.0
C o:THR138 3.7 47.2 1.0
ND2 o:ASN200 3.8 52.8 1.0
N o:VAL201 4.3 35.0 1.0
CA o:ALA202 4.5 39.5 1.0
N o:ALA202 4.5 44.9 1.0
CA o:THR138 4.5 48.0 1.0
N o:SER139 4.5 57.5 1.0
C o:ASN200 4.6 31.1 1.0
CA o:VAL201 4.6 38.5 1.0
CA o:SER139 4.6 59.0 1.0
O o:THR140 4.6 43.3 1.0
CB o:ASN200 4.7 42.4 1.0
CB o:THR138 4.8 48.7 1.0
C o:SER139 4.9 65.8 1.0
O o:HOH544 4.9 52.8 1.0
CA o:ASN200 5.0 39.2 1.0
O o:ASN200 5.0 48.2 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 13:40:01 2024

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