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Calcium in PDB 5v2c: Re-Refinement of Crystal Structure of Photosystem II Complex

Enzymatic activity of Re-Refinement of Crystal Structure of Photosystem II Complex

All present enzymatic activity of Re-Refinement of Crystal Structure of Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Re-Refinement of Crystal Structure of Photosystem II Complex, PDB code: 5v2c was solved by J.Wang, J.M.Wiwczar, G.W.Brudvig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 178.62 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.190, 228.510, 286.400, 90.00, 90.00, 90.00
R / Rfree (%) 9.2 / 16.3

Other elements in 5v2c:

The structure of Re-Refinement of Crystal Structure of Photosystem II Complex also contains other interesting chemical elements:

Magnesium (Mg) 74 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Re-Refinement of Crystal Structure of Photosystem II Complex (pdb code 5v2c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Re-Refinement of Crystal Structure of Photosystem II Complex, PDB code: 5v2c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5v2c

Go back to Calcium Binding Sites List in 5v2c
Calcium binding site 1 out of 8 in the Re-Refinement of Crystal Structure of Photosystem II Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:24.0
occ:1.00
 CA1 A:OEX601 0.0 24.0 1.0
O1 A:OEX601 2.3 22.0 1.0
O A:HOH840 2.4 27.4 1.0
O A:HOH777 2.4 27.7 1.0
O5 A:OEX601 2.4 21.7 1.0
OD1 A:ASP170 2.5 25.6 1.0
O2 A:OEX601 2.5 22.5 1.0
O A:ALA344 2.5 24.7 1.0
CG A:ASP170 3.2 22.0 1.0
OE1 A:GLU189 3.3 28.9 1.0
MN2 A:OEX601 3.3 20.7 1.0
OD2 A:ASP170 3.4 23.3 1.0
MN3 A:OEX601 3.4 21.2 1.0
C A:ALA344 3.5 26.3 1.0
MN1 A:OEX601 3.5 20.6 1.0
OXT A:ALA344 3.8 21.1 1.0
MN4 A:OEX601 3.8 24.3 1.0
O3 A:OEX601 3.9 20.2 1.0
O4 A:OEX601 3.9 26.5 1.0
O A:HOH798 4.0 31.6 1.0
CD A:GLU189 4.1 27.7 1.0
OE2 A:GLU189 4.2 21.5 1.0
NH1 C:ARG357 4.2 27.5 1.0
CB A:ASP170 4.4 19.7 1.0
NH2 C:ARG357 4.4 24.4 1.0
O A:HOH803 4.6 26.1 1.0
OH A:TYR161 4.7 19.5 1.0
OE1 A:GLN165 4.7 25.7 1.0
O A:HOH773 4.8 23.3 1.0
CA A:ALA344 4.8 26.6 1.0
CZ C:ARG357 4.8 21.9 1.0
OD1 A:ASP342 5.0 21.7 1.0

Calcium binding site 2 out of 8 in 5v2c

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Calcium binding site 2 out of 8 in the Re-Refinement of Crystal Structure of Photosystem II Complex


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Stereo pair view

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

b:82.4
occ:1.00
 O B:HOH1076 2.3 92.7 1.0
O B:HOH915 2.3 35.3 1.0
O B:HOH955 2.3 85.4 1.0
OD1 B:ASN438 2.6 38.6 1.0
O M:HOH231 3.6 49.1 1.0
CG B:ASN438 3.9 32.3 1.0
O B:SER439 4.4 20.1 1.0
O B:HOH858 4.4 32.0 1.0
O B:HOH708 4.5 42.0 1.0
ND2 B:ASN438 4.6 34.0 1.0
CA B:ASN438 4.7 23.5 1.0
C B:ASN438 4.8 21.2 1.0
CB B:ASN438 4.9 27.3 1.0
O B:ASN438 5.0 21.2 1.0
O B:HOH886 5.0 29.6 1.0

Calcium binding site 3 out of 8 in 5v2c

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Calcium binding site 3 out of 8 in the Re-Refinement of Crystal Structure of Photosystem II Complex


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Stereo pair view

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

b:53.8
occ:1.00
 O O:HOH475 2.3 53.0 1.0
O O:HOH565 2.3 60.8 1.0
O O:HOH617 2.3 73.1 1.0
O O:HOH579 2.3 73.8 1.0
O O:THR138 2.5 44.8 1.0
O O:VAL201 2.5 40.4 1.0
OD1 O:ASN200 2.5 57.7 1.0
C O:VAL201 3.6 37.4 1.0
C O:THR138 3.6 44.6 1.0
CG O:ASN200 3.6 53.9 1.0
ND2 O:ASN200 4.1 61.3 1.0
N O:VAL201 4.3 36.7 1.0
N O:ALA202 4.3 38.7 1.0
CA O:ALA202 4.3 36.1 1.0
CA O:THR138 4.4 46.5 1.0
CA O:VAL201 4.5 34.2 1.0
CB O:THR138 4.5 41.9 1.0
C O:ASN200 4.6 36.6 1.0
N O:SER139 4.6 44.0 1.0
CA O:SER139 4.7 41.2 1.0
O O:HOH506 4.8 50.5 1.0
O O:THR140 4.8 40.5 1.0
O O:ASN200 4.9 39.9 1.0
O O:HOH647 4.9 67.2 1.0
CB O:ASN200 4.9 46.2 1.0

Calcium binding site 4 out of 8 in 5v2c

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Calcium binding site 4 out of 8 in the Re-Refinement of Crystal Structure of Photosystem II Complex


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Stereo pair view

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

b:26.4
occ:1.00
 CA1 a:OEX402 0.0 26.4 1.0
O a:HOH649 2.4 29.6 1.0
OD1 a:ASP170 2.4 26.0 1.0
O a:HOH586 2.4 28.8 1.0
O1 a:OEX402 2.4 23.2 1.0
O a:ALA344 2.5 30.4 1.0
O5 a:OEX402 2.5 25.8 1.0
O2 a:OEX402 2.6 26.3 1.0
CG a:ASP170 3.2 23.6 1.0
OE1 a:GLU189 3.3 32.1 1.0
MN2 a:OEX402 3.3 23.9 1.0
OD2 a:ASP170 3.4 28.5 1.0
MN3 a:OEX402 3.5 23.7 1.0
C a:ALA344 3.5 32.0 1.0
MN1 a:OEX402 3.5 24.4 1.0
MN4 a:OEX402 3.8 27.6 1.0
OXT a:ALA344 3.8 27.5 1.0
O3 a:OEX402 3.9 24.7 1.0
O4 a:OEX402 3.9 26.2 1.0
O a:HOH587 4.0 34.3 1.0
CD a:GLU189 4.1 30.8 1.0
OE2 a:GLU189 4.1 24.1 1.0
NH1 c:ARG357 4.3 35.3 1.0
CB a:ASP170 4.4 24.4 1.0
NH2 c:ARG357 4.4 35.3 1.0
OH a:TYR161 4.7 23.6 1.0
OE1 a:GLN165 4.7 27.2 1.0
O a:HOH616 4.7 30.1 1.0
O a:HOH512 4.7 25.8 1.0
CA a:ALA344 4.8 30.3 1.0
CZ c:ARG357 4.9 30.8 1.0
OD1 a:ASP342 4.9 25.1 1.0

Calcium binding site 5 out of 8 in 5v2c

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Calcium binding site 5 out of 8 in the Re-Refinement of Crystal Structure 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 Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca601

b:72.1
occ:1.00
 O o:HOH530 2.3 75.6 1.0
O b:HOH1092 2.3 75.3 1.0
O b:HOH929 2.3 66.5 1.0
O b:HOH962 2.4 39.9 1.0
OD1 b:ASN438 2.6 43.5 1.0
O b:HOH784 2.7 0.5 1.0
CG b:ASN438 3.9 31.2 1.0
O m:HOH223 4.1 54.6 1.0
O b:HOH736 4.4 48.0 1.0
ND2 b:ASN438 4.6 30.6 1.0
O b:SER439 4.7 20.5 1.0
CA b:ASN438 4.8 23.3 1.0
O b:HOH822 4.8 36.8 1.0
OE1 o:GLU181 4.8 86.7 0.6
CB b:ASN438 4.9 27.4 1.0
OE1 b:GLU435 4.9 46.6 0.5
O b:HOH766 4.9 56.1 1.0
OE2 o:GLU181 5.0 91.8 0.6

Calcium binding site 6 out of 8 in 5v2c

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Calcium binding site 6 out of 8 in the Re-Refinement of Crystal Structure of Photosystem II Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca524

b:45.4
occ:1.00
 O c:PHE22 2.3 50.9 1.0
OE1 c:GLU29 2.3 46.2 1.0
OG c:SER30 2.4 44.8 1.0
OD2 c:ASP27 2.4 47.9 1.0
OD1 c:ASP27 2.4 48.3 1.0
O c:THR24 2.5 50.3 1.0
O c:HOH710 2.6 48.7 1.0
CG c:ASP27 2.7 45.5 1.0
C c:PHE22 3.4 48.4 1.0
CD c:GLU29 3.4 45.9 1.0
CB c:SER30 3.5 41.9 1.0
C c:THR24 3.7 47.2 1.0
OE2 c:GLU29 4.0 54.1 1.0
CA c:PHE22 4.0 54.5 1.0
N c:SER30 4.0 37.2 1.0
CB c:PHE22 4.1 53.9 1.0
O c:HOH649 4.2 44.5 1.0
N c:THR24 4.2 50.0 1.0
CB c:ASP27 4.2 44.9 1.0
CA c:SER30 4.3 36.3 1.0
O c:HOH609 4.3 68.6 1.0
C c:ALA23 4.4 49.6 1.0
N c:ALA23 4.4 46.8 1.0
CA c:ASN25 4.5 40.8 1.0
N c:ASN25 4.6 42.6 1.0
CG c:GLU29 4.6 50.2 1.0
CA c:THR24 4.7 47.8 1.0
CA c:ALA23 4.7 48.4 1.0
CB c:GLU29 4.8 42.3 1.0
C c:GLU29 4.8 36.1 1.0
O c:ALA23 4.8 64.4 1.0
C c:ASN25 4.9 46.3 1.0

Calcium binding site 7 out of 8 in 5v2c

Go back to Calcium Binding Sites List in 5v2c
Calcium binding site 7 out of 8 in the Re-Refinement of Crystal Structure of Photosystem II Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
h:Ca102

b:97.4
occ:1.00
 OE2 h:GLU17 3.1 52.2 1.0
OE1 h:GLU17 3.3 62.3 1.0
CD h:GLU17 3.6 48.9 1.0
O b:LEU218 3.9 43.0 1.0
CD b:ARG220 4.0 33.4 1.0
O b:HOH990 4.0 53.7 1.0
CG b:ARG220 4.3 38.0 1.0
O b:ILE217 4.6 38.0 1.0
C b:LEU218 4.6 38.6 1.0
O b:HOH936 4.7 51.8 1.0
CE h:LYS20 4.9 67.1 1.0

Calcium binding site 8 out of 8 in 5v2c

Go back to Calcium Binding Sites List in 5v2c
Calcium binding site 8 out of 8 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca302

b:55.2
occ:1.00
 O o:HOH583 2.2 64.8 1.0
O o:HOH454 2.3 69.3 1.0
O o:HOH406 2.3 53.9 1.0
O o:THR138 2.4 46.2 1.0
O o:HOH596 2.5 64.0 1.0
OD1 o:ASN200 2.5 55.1 1.0
O o:VAL201 2.6 47.0 1.0
CG o:ASN200 3.5 43.2 1.0
C o:VAL201 3.6 45.2 1.0
C o:THR138 3.6 50.9 1.0
ND2 o:ASN200 3.7 46.9 1.0
CA o:ALA202 4.3 41.5 1.0
N o:ALA202 4.3 40.0 1.0
CA o:THR138 4.4 50.6 1.0
N o:VAL201 4.4 35.8 1.0
CB o:THR138 4.5 44.0 1.0
N o:SER139 4.6 49.9 1.0
CA o:VAL201 4.6 36.0 1.0
CA o:SER139 4.7 45.3 1.0
C o:ASN200 4.8 32.8 1.0
O o:THR140 4.8 45.6 1.0
CB o:ASN200 4.9 37.4 1.0
O o:HOH432 4.9 50.4 1.0

Reference:

J.M.Wiwczar, A.M.Lafountain, J.Wang, H.A.Frank, G.W.Brudvig. Chlorophyll A with A Farnesyl Tail in Thermophilic Cyanobacteria. Photosyn. Res. V. 134 175 2017.
ISSN: ISSN 1573-5079
PubMed: 28741056
DOI: 10.1007/S11120-017-0425-4
Page generated: Wed Jul 9 10:41:56 2025

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