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Iron 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
Calcium (Ca) 8 atoms
Chlorine (Cl) 6 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 6 binding sites of Iron where determined in the Re-Refinement of Crystal Structure of Photosystem II Complex, PDB code: 5v2c:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5v2c

Go back to Iron Binding Sites List in 5v2c
Iron binding site 1 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe602

b:25.6
occ:1.00
NE2 D:HIS214 2.0 25.4 1.0
NE2 A:HIS215 2.1 25.6 1.0
NE2 A:HIS272 2.1 28.3 1.0
NE2 D:HIS268 2.1 26.1 1.0
O1 A:BCT605 2.2 27.1 1.0
O2 A:BCT605 2.2 31.6 1.0
C A:BCT605 2.5 35.3 1.0
CE1 A:HIS215 2.9 27.2 1.0
CE1 A:HIS272 3.0 29.6 1.0
CE1 D:HIS214 3.0 25.0 1.0
CE1 D:HIS268 3.0 28.6 1.0
CD2 D:HIS214 3.1 25.8 1.0
CD2 A:HIS215 3.2 24.4 1.0
CD2 A:HIS272 3.2 26.4 1.0
CD2 D:HIS268 3.2 25.0 1.0
O3 A:BCT605 3.9 52.0 1.0
ND1 A:HIS215 4.1 25.0 1.0
ND1 D:HIS214 4.1 22.8 1.0
ND1 A:HIS272 4.2 25.2 1.0
CG D:HIS214 4.2 23.5 1.0
ND1 D:HIS268 4.2 27.1 1.0
CG A:HIS215 4.2 24.3 1.0
CG A:HIS272 4.3 25.4 1.0
CG D:HIS268 4.3 22.7 1.0
CG2 A:VAL219 4.6 29.8 1.0
CG2 D:VAL218 4.8 22.9 1.0
O A:HOH702 4.8 57.7 1.0
OH D:TYR244 4.9 36.1 1.0

Iron binding site 2 out of 6 in 5v2c

Go back to Iron Binding Sites List in 5v2c
Iron binding site 2 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


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Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
E:Fe113

b:39.9
occ:1.00
FE E:HEM113 0.0 39.9 1.0
ND E:HEM113 1.9 40.4 1.0
NE2 F:HIS24 1.9 37.1 1.0
NE2 E:HIS23 2.0 43.6 1.0
NA E:HEM113 2.0 40.6 1.0
NC E:HEM113 2.1 38.9 1.0
NB E:HEM113 2.1 38.5 1.0
C4D E:HEM113 2.9 43.2 1.0
CD2 F:HIS24 2.9 44.6 1.0
C1D E:HEM113 2.9 41.5 1.0
CE1 E:HIS23 2.9 42.6 1.0
CE1 F:HIS24 2.9 45.3 1.0
C1A E:HEM113 3.0 46.2 1.0
C4B E:HEM113 3.0 38.8 1.0
C1B E:HEM113 3.0 41.9 1.0
CD2 E:HIS23 3.0 36.5 1.0
C4C E:HEM113 3.0 40.0 1.0
C4A E:HEM113 3.1 45.9 1.0
C1C E:HEM113 3.1 41.4 1.0
CHA E:HEM113 3.3 36.3 1.0
CHD E:HEM113 3.4 37.7 1.0
CHC E:HEM113 3.4 35.6 1.0
CHB E:HEM113 3.4 44.8 1.0
ND1 F:HIS24 4.0 42.9 1.0
CG F:HIS24 4.1 42.8 1.0
ND1 E:HIS23 4.1 41.8 1.0
CG E:HIS23 4.1 40.5 1.0
C3D E:HEM113 4.2 46.5 1.0
C2D E:HEM113 4.2 39.7 1.0
C2A E:HEM113 4.2 47.9 1.0
C3C E:HEM113 4.2 39.1 1.0
C2C E:HEM113 4.3 36.7 1.0
C3A E:HEM113 4.3 47.4 1.0
C2B E:HEM113 4.3 41.3 1.0
C3B E:HEM113 4.3 40.8 1.0
CE1 E:TYR19 4.8 39.3 1.0
NE1 F:TRP20 4.9 41.9 1.0

Iron binding site 3 out of 6 in 5v2c

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Iron binding site 3 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
V:Fe203

b:24.8
occ:1.00
FE V:HEM203 0.0 24.8 1.0
NE2 V:HIS41 1.9 25.1 1.0
ND V:HEM203 1.9 27.1 1.0
NE2 V:HIS92 2.0 23.4 1.0
NC V:HEM203 2.0 21.2 1.0
NA V:HEM203 2.0 24.7 1.0
NB V:HEM203 2.1 20.6 1.0
CE1 V:HIS41 2.9 26.1 1.0
C4D V:HEM203 2.9 25.0 1.0
CE1 V:HIS92 2.9 26.1 1.0
CD2 V:HIS41 3.0 24.2 1.0
C1D V:HEM203 3.0 21.4 1.0
CD2 V:HIS92 3.0 27.1 1.0
C4C V:HEM203 3.0 22.6 1.0
C1C V:HEM203 3.0 24.3 1.0
C1A V:HEM203 3.0 22.7 1.0
C4B V:HEM203 3.0 22.8 1.0
C1B V:HEM203 3.1 24.1 1.0
C4A V:HEM203 3.1 25.1 1.0
CHA V:HEM203 3.4 23.5 1.0
CHC V:HEM203 3.4 23.5 1.0
CHD V:HEM203 3.4 22.2 1.0
CHB V:HEM203 3.4 25.7 1.0
ND1 V:HIS92 4.1 27.5 1.0
ND1 V:HIS41 4.1 22.8 1.0
CG V:HIS41 4.1 22.8 1.0
CG V:HIS92 4.1 25.5 1.0
C2D V:HEM203 4.2 23.2 1.0
C3D V:HEM203 4.2 23.5 1.0
C3C V:HEM203 4.3 23.6 1.0
C2C V:HEM203 4.3 22.8 1.0
C2A V:HEM203 4.3 25.5 1.0
C2B V:HEM203 4.3 24.3 1.0
C3A V:HEM203 4.3 25.3 1.0
C3B V:HEM203 4.3 24.6 1.0
CE1 V:TYR75 4.7 24.3 1.0

Iron binding site 4 out of 6 in 5v2c

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Iron binding site 4 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe403

b:25.8
occ:1.00
NE2 d:HIS214 2.0 26.1 1.0
NE2 a:HIS215 2.0 26.4 1.0
NE2 d:HIS268 2.1 25.6 1.0
NE2 a:HIS272 2.1 26.8 1.0
O2 a:BCT406 2.1 28.9 1.0
O1 a:BCT406 2.2 27.0 1.0
C a:BCT406 2.5 31.7 1.0
CE1 a:HIS215 2.9 27.1 1.0
CE1 d:HIS268 3.0 26.4 1.0
CE1 d:HIS214 3.0 27.8 1.0
CD2 d:HIS214 3.0 25.5 1.0
CE1 a:HIS272 3.0 27.6 1.0
CD2 a:HIS215 3.2 26.1 1.0
CD2 a:HIS272 3.2 24.9 1.0
CD2 d:HIS268 3.2 23.1 1.0
O3 a:BCT406 3.8 50.0 1.0
ND1 a:HIS215 4.1 27.7 1.0
ND1 d:HIS214 4.1 22.6 1.0
ND1 d:HIS268 4.2 24.6 1.0
CG d:HIS214 4.2 23.8 1.0
ND1 a:HIS272 4.2 25.0 1.0
CG a:HIS215 4.2 25.9 1.0
CG a:HIS272 4.3 26.0 1.0
CG d:HIS268 4.3 22.3 1.0
O a:HOH501 4.6 58.6 1.0
CG2 a:VAL219 4.7 25.5 1.0
CG2 d:VAL218 4.9 23.3 1.0
OH d:TYR244 5.0 38.3 1.0

Iron binding site 5 out of 6 in 5v2c

Go back to Iron Binding Sites List in 5v2c
Iron binding site 5 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
e:Fe107

b:43.9
occ:1.00
FE e:HEM107 0.0 43.9 1.0
ND e:HEM107 1.9 41.9 1.0
NE2 f:HIS24 1.9 46.1 1.0
NE2 e:HIS23 1.9 48.8 1.0
NA e:HEM107 2.0 43.6 1.0
NC e:HEM107 2.1 42.3 1.0
NB e:HEM107 2.1 50.1 1.0
CE1 e:HIS23 2.9 43.6 1.0
C4D e:HEM107 2.9 45.1 1.0
C1D e:HEM107 2.9 42.8 1.0
CD2 f:HIS24 2.9 41.0 1.0
CE1 f:HIS24 2.9 45.5 1.0
C1A e:HEM107 3.0 50.8 1.0
CD2 e:HIS23 3.0 47.3 1.0
C4A e:HEM107 3.0 49.3 1.0
C4C e:HEM107 3.1 41.3 1.0
C4B e:HEM107 3.1 47.3 1.0
C1C e:HEM107 3.1 45.3 1.0
C1B e:HEM107 3.1 44.3 1.0
CHA e:HEM107 3.4 42.8 1.0
CHD e:HEM107 3.4 40.5 1.0
CHC e:HEM107 3.4 46.0 1.0
CHB e:HEM107 3.4 46.3 1.0
ND1 e:HIS23 4.0 44.9 1.0
ND1 f:HIS24 4.1 43.2 1.0
CG f:HIS24 4.1 43.5 1.0
CG e:HIS23 4.1 45.1 1.0
C3D e:HEM107 4.2 45.0 1.0
C2D e:HEM107 4.2 46.6 1.0
C2A e:HEM107 4.2 47.1 1.0
C3A e:HEM107 4.2 50.4 1.0
C3C e:HEM107 4.3 44.0 1.0
C2C e:HEM107 4.3 42.6 1.0
C2B e:HEM107 4.3 53.3 1.0
C3B e:HEM107 4.4 50.6 1.0
CE1 e:TYR19 4.7 44.3 1.0
NE1 f:TRP20 4.8 52.4 1.0

Iron binding site 6 out of 6 in 5v2c

Go back to Iron Binding Sites List in 5v2c
Iron binding site 6 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
v:Fe202

b:31.8
occ:1.00
FE v:HEM202 0.0 31.8 1.0
NE2 v:HIS41 1.9 33.7 1.0
NE2 v:HIS92 1.9 26.8 1.0
ND v:HEM202 2.0 34.2 1.0
NA v:HEM202 2.0 29.6 1.0
NC v:HEM202 2.1 33.4 1.0
NB v:HEM202 2.1 29.7 1.0
CE1 v:HIS41 2.9 31.5 1.0
CE1 v:HIS92 2.9 27.7 1.0
C4D v:HEM202 3.0 29.6 1.0
CD2 v:HIS92 3.0 29.0 1.0
CD2 v:HIS41 3.0 30.6 1.0
C1A v:HEM202 3.0 34.2 1.0
C1D v:HEM202 3.0 30.4 1.0
C4B v:HEM202 3.0 34.3 1.0
C1B v:HEM202 3.0 30.5 1.0
C1C v:HEM202 3.1 32.0 1.0
C4C v:HEM202 3.1 29.0 1.0
C4A v:HEM202 3.1 29.7 1.0
CHA v:HEM202 3.4 30.6 1.0
CHC v:HEM202 3.4 32.9 1.0
CHB v:HEM202 3.4 26.2 1.0
CHD v:HEM202 3.5 29.9 1.0
ND1 v:HIS41 4.0 31.1 1.0
ND1 v:HIS92 4.0 29.2 1.0
CG v:HIS92 4.1 29.1 1.0
CG v:HIS41 4.1 30.2 1.0
C3D v:HEM202 4.2 28.3 1.0
C2D v:HEM202 4.2 31.3 1.0
C2C v:HEM202 4.2 27.6 1.0
C2A v:HEM202 4.3 30.9 1.0
C2B v:HEM202 4.3 31.4 1.0
C3A v:HEM202 4.3 30.6 1.0
C3C v:HEM202 4.3 30.4 1.0
C3B v:HEM202 4.3 32.1 1.0
CE1 v:TYR75 4.9 35.5 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: Tue Aug 6 10:06:26 2024

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