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Iron in PDB 8ajz: Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser

Enzymatic activity of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser

All present enzymatic activity of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser:
1.9.3.1;

Protein crystallography data

The structure of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser, PDB code: 8ajz was solved by C.Safari, S.Ghosh, R.Andersson, J.Johannesson, A.V.Donoso, P.Bath, R.Bosman, P.Dahl, E.Nango, R.Tanaka, D.Zoric, E.Svensson, T.Nakane, S.Iwata, R.Neutze, G.Branden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.70 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.85, 100.32, 96.62, 90, 126.76, 90
R / Rfree (%) 19 / 21

Other elements in 8ajz:

The structure of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser (pdb code 8ajz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser, PDB code: 8ajz:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 8ajz

Go back to Iron Binding Sites List in 8ajz
Iron binding site 1 out of 3 in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:31.9
occ:1.00
 FE A:HEM602 0.0 31.9 1.0
ND A:HEM602 1.9 27.5 1.0
NE2 A:HIS386 1.9 28.3 1.0
NE2 A:HIS72 2.0 30.0 1.0
NA A:HEM602 2.0 28.4 1.0
NC A:HEM602 2.1 29.1 1.0
NB A:HEM602 2.1 28.9 1.0
CE1 A:HIS386 2.9 29.6 1.0
C1D A:HEM602 3.0 27.8 1.0
C4D A:HEM602 3.0 27.9 1.0
C1A A:HEM602 3.0 29.2 1.0
CE1 A:HIS72 3.0 31.4 1.0
CD2 A:HIS72 3.0 28.9 1.0
C4C A:HEM602 3.0 31.4 1.0
C4B A:HEM602 3.0 27.2 1.0
C4A A:HEM602 3.1 27.3 1.0
CD2 A:HIS386 3.1 25.9 1.0
C1C A:HEM602 3.1 31.6 1.0
C1B A:HEM602 3.1 31.6 1.0
CHD A:HEM602 3.4 28.3 1.0
CHA A:HEM602 3.4 28.3 1.0
CHC A:HEM602 3.4 28.5 1.0
CHB A:HEM602 3.5 28.7 1.0
ND1 A:HIS386 4.0 27.3 1.0
CG A:HIS386 4.1 28.3 1.0
ND1 A:HIS72 4.1 30.2 1.0
CG A:HIS72 4.2 27.7 1.0
C2A A:HEM602 4.2 28.4 1.0
C3A A:HEM602 4.2 28.3 1.0
C2D A:HEM602 4.2 29.9 1.0
C3D A:HEM602 4.2 27.9 1.0
C3C A:HEM602 4.3 32.0 1.0
C2C A:HEM602 4.3 30.4 1.0
C3B A:HEM602 4.3 29.6 1.0
C2B A:HEM602 4.3 30.6 1.0
OE1 A:GLN42 4.6 34.3 1.0

Iron binding site 2 out of 3 in 8ajz

Go back to Iron Binding Sites List in 8ajz
Iron binding site 2 out of 3 in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:35.2
occ:0.70
 FE A:HAS603 0.0 35.2 0.7
FE A:HAS603 0.3 49.9 0.3
C A:CMO614 1.9 26.4 0.7
NC A:HAS603 2.1 45.8 0.3
NA A:HAS603 2.1 31.2 0.7
ND A:HAS603 2.1 32.2 0.7
NB A:HAS603 2.1 32.8 0.7
NC A:HAS603 2.1 32.1 0.7
NB A:HAS603 2.1 44.3 0.3
ND A:HAS603 2.2 48.0 0.3
NE2 A:HIS384 2.2 31.1 0.7
NA A:HAS603 2.2 45.3 0.3
NE2 A:HIS384 2.5 42.3 0.3
C A:CMO614 2.7 43.5 0.3
O A:CMO614 3.0 28.4 0.7
C4C A:HAS603 3.0 47.4 0.3
C1C A:HAS603 3.1 49.5 0.3
C1D A:HAS603 3.1 31.3 0.7
C1D A:HAS603 3.1 53.9 0.3
C1B A:HAS603 3.1 31.9 0.7
C1A A:HAS603 3.1 30.8 0.7
C4A A:HAS603 3.1 30.5 0.7
C1B A:HAS603 3.1 51.5 0.3
C4D A:HAS603 3.1 31.2 0.7
C4B A:HAS603 3.1 45.8 0.3
C4B A:HAS603 3.1 32.1 0.7
C1C A:HAS603 3.1 31.8 0.7
C4C A:HAS603 3.1 30.3 0.7
C4A A:HAS603 3.1 48.4 0.3
CE1 A:HIS384 3.2 32.5 0.7
C1A A:HAS603 3.2 44.8 0.3
C4D A:HAS603 3.3 44.9 0.3
CD2 A:HIS384 3.3 31.6 0.7
O A:CMO614 3.3 35.6 0.3
CHB A:HAS603 3.4 47.9 0.3
CHB A:HAS603 3.4 31.1 0.7
CHA A:HAS603 3.4 30.1 0.7
CHC A:HAS603 3.4 45.1 0.3
CHD A:HAS603 3.4 49.1 0.3
CHC A:HAS603 3.4 31.8 0.7
CD2 A:HIS384 3.4 42.0 0.3
CHD A:HAS603 3.5 29.9 0.7
CE1 A:HIS384 3.5 39.7 0.3
CHA A:HAS603 3.6 43.1 0.3
ND1 A:HIS384 4.3 31.2 0.7
C3C A:HAS603 4.3 48.4 0.3
C2D A:HAS603 4.4 30.3 0.7
C2C A:HAS603 4.4 50.6 0.3
CG A:HIS384 4.4 30.8 0.7
C2A A:HAS603 4.4 29.0 0.7
C2D A:HAS603 4.4 51.1 0.3
C3C A:HAS603 4.4 30.1 0.7
C2B A:HAS603 4.4 31.2 0.7
C3A A:HAS603 4.4 29.4 0.7
C3D A:HAS603 4.4 29.9 0.7
C3B A:HAS603 4.4 31.5 0.7
C2C A:HAS603 4.4 31.4 0.7
C3B A:HAS603 4.5 49.2 0.3
C2B A:HAS603 4.5 49.6 0.3
C3A A:HAS603 4.5 46.3 0.3
C2A A:HAS603 4.6 44.7 0.3
C3D A:HAS603 4.6 45.4 0.3
ND1 A:HIS384 4.6 36.2 0.3
CG A:HIS384 4.6 42.0 0.3
CU A:CU601 4.6 46.4 0.3
CE1 A:HIS233 4.9 37.6 0.3
CU A:CU601 4.9 30.6 0.7

Iron binding site 3 out of 3 in 8ajz

Go back to Iron Binding Sites List in 8ajz
Iron binding site 3 out of 3 in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:49.9
occ:0.30
 FE A:HAS603 0.0 49.9 0.3
FE A:HAS603 0.3 35.2 0.7
NE2 A:HIS384 1.9 31.1 0.7
ND A:HAS603 2.1 32.2 0.7
NB A:HAS603 2.1 44.3 0.3
NA A:HAS603 2.1 31.2 0.7
NC A:HAS603 2.1 45.8 0.3
NB A:HAS603 2.1 32.8 0.7
ND A:HAS603 2.2 48.0 0.3
NE2 A:HIS384 2.2 42.3 0.3
NC A:HAS603 2.2 32.1 0.7
NA A:HAS603 2.2 45.3 0.3
C A:CMO614 2.2 26.4 0.7
CE1 A:HIS384 2.9 32.5 0.7
CD2 A:HIS384 3.0 31.6 0.7
C A:CMO614 3.0 43.5 0.3
C1D A:HAS603 3.1 31.3 0.7
C1D A:HAS603 3.1 53.9 0.3
C4D A:HAS603 3.1 31.2 0.7
C1A A:HAS603 3.1 30.8 0.7
C4C A:HAS603 3.1 47.4 0.3
C1B A:HAS603 3.1 31.9 0.7
C1B A:HAS603 3.1 51.5 0.3
C1C A:HAS603 3.1 49.5 0.3
C4B A:HAS603 3.1 45.8 0.3
C4B A:HAS603 3.1 32.1 0.7
C4A A:HAS603 3.2 30.5 0.7
CD2 A:HIS384 3.2 42.0 0.3
C1C A:HAS603 3.2 31.8 0.7
C4C A:HAS603 3.2 30.3 0.7
C4A A:HAS603 3.2 48.4 0.3
CE1 A:HIS384 3.2 39.7 0.3
O A:CMO614 3.2 28.4 0.7
C1A A:HAS603 3.3 44.8 0.3
C4D A:HAS603 3.3 44.9 0.3
CHA A:HAS603 3.4 30.1 0.7
CHB A:HAS603 3.4 47.9 0.3
CHB A:HAS603 3.5 31.1 0.7
CHC A:HAS603 3.5 45.1 0.3
CHC A:HAS603 3.5 31.8 0.7
CHD A:HAS603 3.5 49.1 0.3
CHD A:HAS603 3.5 29.9 0.7
O A:CMO614 3.6 35.6 0.3
CHA A:HAS603 3.6 43.1 0.3
ND1 A:HIS384 4.0 31.2 0.7
CG A:HIS384 4.1 30.8 0.7
ND1 A:HIS384 4.3 36.2 0.3
CG A:HIS384 4.3 42.0 0.3
C2D A:HAS603 4.4 30.3 0.7
C3C A:HAS603 4.4 48.4 0.3
C2A A:HAS603 4.4 29.0 0.7
C2D A:HAS603 4.4 51.1 0.3
C3D A:HAS603 4.4 29.9 0.7
C2B A:HAS603 4.4 31.2 0.7
C3B A:HAS603 4.5 31.5 0.7
C3A A:HAS603 4.5 29.4 0.7
C2C A:HAS603 4.5 50.6 0.3
C3C A:HAS603 4.5 30.1 0.7
C2B A:HAS603 4.5 49.6 0.3
C3B A:HAS603 4.5 49.2 0.3
C2C A:HAS603 4.5 31.4 0.7
C3A A:HAS603 4.6 46.3 0.3
C2A A:HAS603 4.6 44.7 0.3
C3D A:HAS603 4.6 45.4 0.3
ND2 A:ASN366 4.8 33.1 1.0
CA A:GLY363 4.9 28.7 1.0
CU A:CU601 4.9 46.4 0.3

Reference:

C.Safari, S.Ghosh, R.Andersson, J.Johannesson, A.V.Donoso, P.Bath, R.Bosman, P.Dahl, E.Nango, R.Tanaka, D.Zoric, E.Svensson, T.Nakane, S.Iwata, R.Neutze, G.Branden. Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser To Be Published.
Page generated: Fri Aug 9 17:35:48 2024

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