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Calcium in PDB 6jlm: Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2):
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2), PDB code: 6jlm was solved by M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.040, 228.840, 286.980, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 20.9

Other elements in 6jlm:

The structure of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) 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:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) (pdb code 6jlm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2), PDB code: 6jlm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 6jlm

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Calcium binding site 1 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:51.2
occ:1.00
 CA1 A:OEX416 0.0 51.2 1.0
OD1 A:ASP170 2.4 50.2 1.0
O A:ALA344 2.4 55.3 1.0
O A:HOH543 2.5 47.4 1.0
O1 A:OEX416 2.6 56.5 1.0
O A:HOH639 2.6 50.3 1.0
O5 A:OEX416 2.6 61.3 1.0
O2 A:OEX416 2.7 45.1 1.0
OE1 A:GLU189 3.1 54.4 1.0
CG A:ASP170 3.1 51.3 1.0
OD2 A:ASP170 3.4 49.6 1.0
C A:ALA344 3.4 56.3 1.0
MN2 A:OEX416 3.5 43.0 1.0
MN3 A:OEX416 3.5 42.9 1.0
MN1 A:OEX416 3.6 42.8 1.0
OXT A:ALA344 3.7 45.8 1.0
MN4 A:OEX416 3.7 50.9 1.0
O4 A:OEX416 3.9 40.0 1.0
CD A:GLU189 3.9 41.5 1.0
OE2 A:GLU189 3.9 58.8 1.0
O3 A:OEX416 4.2 77.6 1.0
O A:HOH526 4.2 53.9 1.0
O A:HOH504 4.3 39.5 1.0
NH1 C:ARG357 4.3 34.4 1.0
CB A:ASP170 4.4 46.7 1.0
NH2 C:ARG357 4.4 36.0 1.0
O A:HOH536 4.6 33.5 1.0
OH A:TYR161 4.6 38.4 1.0
OE1 A:GLN165 4.8 44.2 1.0
CA A:ALA344 4.8 57.3 1.0
CZ C:ARG357 4.9 51.9 1.0

Calcium binding site 2 out of 11 in 6jlm

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Calcium binding site 2 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:0.9
occ:1.00
 O B:HOH896 2.4 0.8 1.0
O O:HOH458 2.6 87.0 1.0
O M:HOH212 2.8 77.2 1.0
O B:HOH752 2.8 80.7 1.0
O B:HOH845 2.9 56.3 1.0
OD1 B:ASN438 3.2 51.3 1.0
O D:HOH620 3.5 96.0 1.0
OE1 O:GLU181 4.3 72.0 0.5
CG B:ASN438 4.4 45.3 1.0
O M:HOH203 4.6 93.8 1.0
OE2 O:GLU181 4.6 87.8 0.5
O B:HOH795 4.6 50.1 1.0
OE2 B:GLU435 4.9 72.4 0.5
OE2 M:GLU2 4.9 0.7 1.0
O B:SER439 4.9 38.2 1.0
O B:HOH715 5.0 61.4 1.0
OE1 O:GLU181 5.0 64.6 0.5

Calcium binding site 3 out of 11 in 6jlm

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Calcium binding site 3 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca525

b:79.1
occ:1.00
 O C:HIS251 2.7 68.5 1.0
O C:THR254 2.7 68.1 1.0
OG1 C:THR159 2.8 77.0 1.0
O C:ASN155 2.8 78.5 1.0
O C:ILE252 2.8 73.6 1.0
OG1 C:THR158 2.9 61.7 1.0
OD1 C:ASN155 2.9 86.9 1.0
C C:ILE252 3.5 79.4 1.0
N C:THR159 3.6 60.5 1.0
C C:ASN155 3.7 74.4 1.0
CG C:ASN155 3.7 89.8 1.0
C C:HIS251 3.8 78.0 1.0
CB C:THR159 3.9 68.6 1.0
CA C:ILE252 3.9 77.2 1.0
CA C:THR159 3.9 66.2 1.0
C C:THR254 3.9 68.3 1.0
CA C:ASN155 4.0 81.6 1.0
CB C:THR158 4.0 60.0 1.0
C C:THR158 4.1 65.8 1.0
N C:THR254 4.2 77.3 1.0
N C:ILE252 4.4 78.6 1.0
O C:HOH622 4.4 70.5 1.0
N C:LEU253 4.5 77.6 1.0
ND2 C:ASN155 4.5 0.3 1.0
CB C:ASN155 4.5 82.8 1.0
CA C:THR158 4.5 65.1 1.0
O C:THR158 4.6 64.3 1.0
CA C:THR254 4.7 69.5 1.0
C C:LEU253 4.8 78.3 1.0
N C:LYS156 4.9 66.3 1.0
N C:THR255 4.9 67.8 1.0
N C:THR158 4.9 57.0 1.0

Calcium binding site 4 out of 11 in 6jlm

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Calcium binding site 4 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca104

b:0.5
occ:1.00
 O2 V:GOL201 2.6 0.7 1.0
O V:HOH386 2.9 98.7 1.0
O V:HOH370 3.0 84.7 1.0
O F:HOH210 3.1 75.9 1.0
O3 V:GOL201 3.1 0.7 1.0
C3 V:GOL201 3.2 0.9 1.0
O F:ARG45 3.2 70.0 1.0
O V:HOH381 3.2 68.5 1.0
OXT F:ARG45 3.4 74.7 1.0
C2 V:GOL201 3.4 96.9 1.0
C F:ARG45 3.7 62.6 1.0
OE2 V:GLU23 4.3 0.7 1.0
O F:HOH204 4.4 71.4 1.0
OE1 V:GLU23 4.6 0.8 1.0
C1 V:GOL201 4.6 88.0 1.0
CD V:GLU23 4.9 0.4 1.0
O F:HOH201 4.9 72.8 1.0
CB A:ALA309 5.0 42.7 1.0

Calcium binding site 5 out of 11 in 6jlm

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Calcium binding site 5 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:89.3
occ:1.00
 O O:HOH480 2.4 0.9 1.0
O O:VAL201 2.6 67.0 1.0
O O:HOH442 2.7 53.2 1.0
OD1 O:ASN200 2.7 99.0 1.0
O O:THR138 2.7 86.8 1.0
O O:HOH556 2.9 85.6 1.0
O O:HOH570 3.0 94.8 1.0
CG O:ASN200 3.4 0.1 1.0
ND2 O:ASN200 3.6 0.9 1.0
C O:THR138 3.7 70.7 1.0
C O:VAL201 3.7 58.4 1.0
CA O:ALA202 4.3 61.2 1.0
N O:ALA202 4.5 63.1 1.0
CA O:THR138 4.5 66.1 1.0
N O:SER139 4.5 77.1 1.0
CA O:SER139 4.6 77.0 1.0
N O:VAL201 4.7 61.5 1.0
C O:ASN200 4.7 74.8 1.0
CA O:VAL201 4.8 51.5 1.0
CB O:THR138 4.8 74.2 1.0
CB O:ASN200 4.8 84.2 1.0
O O:ASN200 5.0 81.9 1.0
CB O:ALA202 5.0 51.3 1.0

Calcium binding site 6 out of 11 in 6jlm

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Calcium binding site 6 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca416

b:53.0
occ:1.00
 CA1 a:OEX416 0.0 53.0 1.0
OD1 a:ASP170 2.4 56.1 1.0
O a:ALA344 2.4 53.2 1.0
O a:HOH520 2.5 45.3 1.0
O1 a:OEX416 2.6 63.8 1.0
O a:HOH632 2.6 57.9 1.0
O5 a:OEX416 2.6 47.6 1.0
O2 a:OEX416 2.6 74.3 1.0
OE1 a:GLU189 3.1 54.4 1.0
CG a:ASP170 3.2 42.9 1.0
MN2 a:OEX416 3.5 43.2 1.0
C a:ALA344 3.5 56.5 1.0
OD2 a:ASP170 3.5 51.3 1.0
MN3 a:OEX416 3.6 45.7 1.0
MN1 a:OEX416 3.7 45.5 1.0
OXT a:ALA344 3.8 45.3 1.0
OE2 a:GLU189 3.8 40.7 1.0
CD a:GLU189 3.8 47.5 1.0
MN4 a:OEX416 3.9 45.2 1.0
O4 a:OEX416 4.1 35.5 1.0
O3 a:OEX416 4.2 60.0 1.0
O a:HOH579 4.3 44.6 1.0
NH1 c:ARG357 4.3 42.2 1.0
CB a:ASP170 4.4 59.8 1.0
OH a:TYR161 4.5 41.1 1.0
O a:HOH541 4.5 37.1 1.0
O a:HOH574 4.6 43.2 1.0
OE1 a:GLN165 4.6 42.2 1.0
NH2 c:ARG357 4.8 49.0 1.0
CA a:ALA344 4.8 57.4 1.0
CB a:GLN165 4.9 39.2 1.0
CG a:GLN165 5.0 41.6 1.0

Calcium binding site 7 out of 11 in 6jlm

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Calcium binding site 7 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca605

b:0.3
occ:1.00
 O o:HOH432 2.5 88.9 1.0
O m:HOH215 2.8 51.1 1.0
O b:HOH725 2.9 64.2 1.0
O b:HOH894 3.0 53.1 1.0
OD1 b:ASN438 3.2 55.6 1.0
O m:HOH208 4.0 59.3 1.0
O b:HOH874 4.1 54.3 1.0
CG b:ASN438 4.3 44.7 1.0
OE1 o:GLU181 4.4 82.0 0.5
O b:SER439 4.6 40.6 1.0
O b:HOH840 4.7 65.9 1.0
OE2 m:GLU2 4.8 75.6 1.0
O b:HOH835 4.9 45.5 1.0
ND2 b:ASN438 4.9 54.4 1.0
OE2 o:GLU181 4.9 78.8 0.5
O o:HOH449 4.9 60.8 1.0
O b:HOH856 5.0 49.4 1.0

Calcium binding site 8 out of 11 in 6jlm

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Calcium binding site 8 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca901

b:74.4
occ:1.00
 O c:THR24 2.3 73.1 1.0
OE1 c:GLU29 2.4 74.2 1.0
O c:PHE22 2.5 98.3 1.0
OG c:SER30 2.5 78.8 1.0
OD2 c:ASP27 2.5 65.3 1.0
OD1 c:ASP27 2.9 56.7 1.0
O c:HOH1137 3.0 60.5 1.0
CG c:ASP27 3.1 71.4 1.0
C c:PHE22 3.3 62.0 1.0
C c:THR24 3.5 73.1 1.0
CD c:GLU29 3.6 69.2 1.0
CB c:SER30 3.7 67.5 1.0
CA c:PHE22 3.9 55.8 1.0
CB c:PHE22 4.0 52.7 1.0
O c:HOH1099 4.1 56.1 1.0
OE2 c:GLU29 4.2 84.8 1.0
N c:THR24 4.2 95.2 1.0
N c:SER30 4.3 67.1 1.0
C c:ALA23 4.3 92.6 1.0
N c:ALA23 4.3 64.4 1.0
N c:ASN25 4.4 79.0 1.0
CA c:ASN25 4.4 74.7 1.0
O c:ALA23 4.5 85.8 1.0
CA c:THR24 4.5 86.2 1.0
CA c:SER30 4.5 72.6 1.0
CB c:ASP27 4.6 74.7 1.0
CB c:GLU29 4.7 76.6 1.0
CG c:GLU29 4.7 60.9 1.0
CA c:ALA23 4.7 93.0 1.0
C c:ASN25 4.8 73.9 1.0

Calcium binding site 9 out of 11 in 6jlm

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Calcium binding site 9 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca926

b:77.1
occ:1.00
 O c:ASN155 2.5 75.8 1.0
O c:HIS251 2.6 77.2 1.0
OG1 c:THR159 2.6 71.7 1.0
O c:THR254 2.7 65.3 1.0
OG1 c:THR158 2.7 62.2 1.0
O c:ILE252 3.2 72.6 1.0
OD1 c:ASN155 3.2 92.1 1.0
N c:THR159 3.3 66.6 1.0
C c:ASN155 3.5 73.8 1.0
CB c:THR159 3.7 69.9 1.0
CA c:THR159 3.7 67.4 1.0
C c:ILE252 3.7 77.4 1.0
C c:HIS251 3.7 83.6 1.0
CB c:THR158 3.8 58.9 1.0
C c:THR158 3.8 67.4 1.0
CA c:ASN155 3.9 81.0 1.0
CG c:ASN155 3.9 88.6 1.0
CA c:ILE252 3.9 75.6 1.0
C c:THR254 4.0 62.7 1.0
CA c:THR158 4.3 61.4 1.0
N c:ILE252 4.3 79.9 1.0
N c:THR254 4.4 77.1 1.0
O c:THR158 4.5 69.7 1.0
CB c:ASN155 4.5 80.9 1.0
O c:HOH1053 4.5 53.8 1.0
N c:THR158 4.6 54.3 1.0
N c:LEU253 4.6 72.8 1.0
ND2 c:ASN155 4.7 0.2 1.0
N c:LYS156 4.7 66.0 1.0
CA c:THR254 4.8 64.4 1.0
CG2 c:THR159 4.9 51.8 1.0
N c:THR255 4.9 64.6 1.0
O c:LYS154 4.9 81.0 1.0
CA c:HIS251 4.9 79.4 1.0
CA c:THR255 5.0 69.7 1.0
C c:LEU253 5.0 77.2 1.0

Calcium binding site 10 out of 11 in 6jlm

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Calcium binding site 10 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2) within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Ca103

b:0.1
occ:1.00
 O a:HOH602 2.4 73.9 1.0
O3 a:GOL419 2.5 94.1 1.0
O f:HOH204 2.6 73.3 1.0
OXT f:ARG45 2.9 72.6 1.0
O f:ARG45 3.1 66.8 1.0
O f:HOH203 3.2 65.0 1.0
O2 a:GOL419 3.2 95.9 1.0
C f:ARG45 3.4 61.2 1.0
O v:HOH345 3.6 0.1 1.0
O f:HOH206 3.7 86.7 1.0
C3 a:GOL419 3.7 81.5 1.0
O a:HOH612 3.8 71.5 1.0
O f:HOH201 4.0 61.5 1.0
C2 a:GOL419 4.0 90.8 1.0
OE2 v:GLU23 4.3 0.1 1.0
OE1 v:GLU23 4.7 0.1 1.0
CD v:GLU23 4.9 0.3 1.0
CA f:ARG45 4.9 62.1 1.0

Reference:

M.Suga, F.Akita, K.Yamashita, Y.Nakajima, G.Ueno, H.Li, T.Yamane, K.Hirata, Y.Umena, S.Yonekura, L.J.Yu, H.Murakami, T.Nomura, T.Kimura, M.Kubo, S.Baba, T.Kumasaka, K.Tono, M.Yabashi, H.Isobe, K.Yamaguchi, M.Yamamoto, H.Ago, J.R.Shen. An Oxyl/Oxo Mechanism For Oxygen-Oxygen Coupling in Psii Revealed By An X-Ray Free-Electron Laser. Science V. 366 334 2019.
ISSN: ESSN 1095-9203
PubMed: 31624207
DOI: 10.1126/SCIENCE.AAX6998
Page generated: Tue Jul 16 10:00:22 2024

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