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Iron in PDB 2zt9: Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120

Enzymatic activity of Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120

All present enzymatic activity of Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120:
1.10.99.1;

Protein crystallography data

The structure of Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120, PDB code: 2zt9 was solved by W.A.Craner, D.Baniulis, E.Yamashita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.69 / 3.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 159.225, 159.225, 365.886, 90.00, 90.00, 120.00
R / Rfree (%) 23 / 25.9

Other elements in 2zt9:

The structure of Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120 (pdb code 2zt9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120, PDB code: 2zt9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 2zt9

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Iron binding site 1 out of 6 in the Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:38.8
occ:1.00
 FE A:HEM301 0.0 38.8 1.0
ND A:HEM301 2.0 41.0 1.0
NE2 A:HIS187 2.0 32.4 1.0
NE2 A:HIS86 2.1 41.2 1.0
NA A:HEM301 2.1 40.2 1.0
NB A:HEM301 2.1 40.3 1.0
NC A:HEM301 2.1 40.5 1.0
CE1 A:HIS86 2.9 41.8 1.0
CE1 A:HIS187 2.9 32.8 1.0
C4D A:HEM301 3.0 41.0 1.0
C1A A:HEM301 3.0 39.9 1.0
C1D A:HEM301 3.0 41.5 1.0
C4B A:HEM301 3.1 40.6 1.0
CD2 A:HIS187 3.1 33.1 1.0
C4C A:HEM301 3.1 40.9 1.0
C1C A:HEM301 3.1 41.0 1.0
C4A A:HEM301 3.1 40.0 1.0
C1B A:HEM301 3.1 40.2 1.0
CD2 A:HIS86 3.2 42.4 1.0
CHA A:HEM301 3.3 40.4 1.0
CHD A:HEM301 3.4 41.2 1.0
CHC A:HEM301 3.4 40.8 1.0
CHB A:HEM301 3.5 40.2 1.0
ND1 A:HIS187 4.0 32.8 1.0
ND1 A:HIS86 4.1 42.9 1.0
CG A:HIS187 4.2 34.1 1.0
C3D A:HEM301 4.2 41.3 1.0
CG A:HIS86 4.2 43.4 1.0
C2D A:HEM301 4.3 40.8 1.0
C2A A:HEM301 4.3 40.0 1.0
C3B A:HEM301 4.3 40.3 1.0
C3A A:HEM301 4.3 39.8 1.0
C2B A:HEM301 4.3 39.4 1.0
C3C A:HEM301 4.3 42.3 1.0
C2C A:HEM301 4.4 41.8 1.0
OE1 A:GLN47 4.8 39.2 1.0
CA A:GLY135 5.0 46.6 1.0

Iron binding site 2 out of 6 in 2zt9

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Iron binding site 2 out of 6 in the Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:42.4
occ:1.00
 FE A:HEM302 0.0 42.4 1.0
NA A:HEM302 2.0 42.4 1.0
NE2 A:HIS100 2.0 46.6 1.0
NB A:HEM302 2.1 42.4 1.0
ND A:HEM302 2.1 43.1 1.0
NC A:HEM302 2.1 43.3 1.0
NE2 A:HIS202 2.1 45.3 1.0
CE1 A:HIS100 3.0 46.5 1.0
C1A A:HEM302 3.0 43.2 1.0
C4D A:HEM302 3.0 43.9 1.0
CD2 A:HIS100 3.0 46.8 1.0
C4A A:HEM302 3.0 42.4 1.0
CE1 A:HIS202 3.0 44.4 1.0
C1C A:HEM302 3.1 44.1 1.0
C4C A:HEM302 3.1 43.8 1.0
C4B A:HEM302 3.1 42.4 1.0
C1B A:HEM302 3.1 42.3 1.0
C1D A:HEM302 3.1 44.2 1.0
CD2 A:HIS202 3.2 45.4 1.0
CHA A:HEM302 3.3 43.5 1.0
CHC A:HEM302 3.4 43.3 1.0
CHB A:HEM302 3.4 42.7 1.0
CHD A:HEM302 3.5 44.0 1.0
ND1 A:HIS100 4.1 47.5 1.0
CG A:HIS100 4.1 47.6 1.0
ND1 A:HIS202 4.2 45.3 1.0
C2A A:HEM302 4.2 43.5 1.0
C3A A:HEM302 4.2 42.8 1.0
C3D A:HEM302 4.3 44.5 1.0
C2C A:HEM302 4.3 44.5 1.0
C3C A:HEM302 4.3 43.9 1.0
CG A:HIS202 4.3 46.4 1.0
C2D A:HEM302 4.3 44.9 1.0
C2B A:HEM302 4.3 42.0 1.0
C3B A:HEM302 4.3 41.9 1.0
CD1 A:ILE206 5.0 49.8 1.0

Iron binding site 3 out of 6 in 2zt9

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Iron binding site 3 out of 6 in the Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:55.5
occ:1.00
 FE A:HEM303 0.0 55.5 1.0
O A:HOH401 1.7 27.4 1.0
NA A:HEM303 2.0 56.9 1.0
NB A:HEM303 2.0 56.1 1.0
ND A:HEM303 2.1 55.2 1.0
NC A:HEM303 2.1 57.0 1.0
C1A A:HEM303 3.0 56.6 1.0
C4B A:HEM303 3.0 56.7 1.0
C4A A:HEM303 3.1 57.7 1.0
C4D A:HEM303 3.1 55.3 1.0
C1B A:HEM303 3.1 56.7 1.0
C1C A:HEM303 3.1 57.1 1.0
C1D A:HEM303 3.2 55.0 1.0
C4C A:HEM303 3.2 56.5 1.0
CHA A:HEM303 3.3 56.0 1.0
CHC A:HEM303 3.4 57.0 1.0
CHB A:HEM303 3.4 57.2 1.0
CHD A:HEM303 3.6 55.9 1.0
CZ B:PHE40 3.7 52.1 1.0
CE2 B:PHE40 3.9 53.3 1.0
C2A A:HEM303 4.2 57.7 1.0
C3A A:HEM303 4.2 57.4 1.0
C3B A:HEM303 4.3 57.4 1.0
C2B A:HEM303 4.3 57.2 1.0
O2A A:HEM302 4.3 53.3 1.0
O A:TYR34 4.3 53.0 1.0
C3D A:HEM303 4.3 55.4 1.0
C2C A:HEM303 4.3 56.4 1.0
C2D A:HEM303 4.4 55.3 1.0
C3C A:HEM303 4.4 57.0 1.0
CMA A:HEM302 4.5 40.7 1.0
CA A:GLY38 4.6 46.0 1.0
CE1 B:PHE40 4.7 51.7 1.0
CAA A:HEM302 4.7 44.7 1.0
N A:GLY38 4.8 46.5 1.0

Iron binding site 4 out of 6 in 2zt9

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Iron binding site 4 out of 6 in the Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:55.6
occ:1.00
 FE C:HEM301 0.0 55.6 1.0
NA C:HEM301 2.0 55.4 1.0
NC C:HEM301 2.0 53.9 1.0
ND C:HEM301 2.1 56.3 1.0
N C:TYR1 2.1 60.0 1.0
NB C:HEM301 2.1 55.1 1.0
NE2 C:HIS26 2.3 62.7 1.0
C4A C:HEM301 3.0 55.9 1.0
C4C C:HEM301 3.0 53.5 1.0
C1B C:HEM301 3.0 55.0 1.0
C1A C:HEM301 3.0 56.9 1.0
C1D C:HEM301 3.0 56.2 1.0
C4D C:HEM301 3.1 57.2 1.0
C1C C:HEM301 3.1 53.8 1.0
CD2 C:HIS26 3.1 62.9 1.0
CA C:TYR1 3.1 60.1 1.0
C4B C:HEM301 3.1 54.2 1.0
CHB C:HEM301 3.3 56.0 1.0
CE1 C:HIS26 3.4 62.4 1.0
CHD C:HEM301 3.4 55.3 1.0
CHA C:HEM301 3.4 56.3 1.0
CHC C:HEM301 3.5 54.0 1.0
C C:TYR1 3.8 60.2 1.0
O C:TYR1 4.1 60.4 1.0
C3A C:HEM301 4.2 57.1 1.0
C2A C:HEM301 4.2 57.2 1.0
C3C C:HEM301 4.3 53.3 1.0
C2B C:HEM301 4.3 53.9 1.0
C2D C:HEM301 4.3 57.1 1.0
C3D C:HEM301 4.3 58.0 1.0
C2C C:HEM301 4.3 53.8 1.0
C3B C:HEM301 4.3 54.5 1.0
CG C:HIS26 4.3 63.0 1.0
ND1 C:HIS26 4.4 62.5 1.0
CB C:TYR1 4.4 60.1 1.0
N C:PRO2 4.6 60.0 1.0
CG C:TYR1 4.7 59.9 1.0
CE3 C:TRP4 4.8 65.5 1.0
CD C:PRO2 5.0 60.0 1.0

Iron binding site 5 out of 6 in 2zt9

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Iron binding site 5 out of 6 in the Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:0.9
occ:1.00
 FE1 D:FES200 0.0 0.9 1.0
SG D:CYS108 1.7 0.6 1.0
S1 D:FES200 2.2 0.4 1.0
S2 D:FES200 2.2 0.4 1.0
SG D:CYS126 2.4 0.3 1.0
FE2 D:FES200 3.0 0.2 1.0
CB D:CYS126 3.3 0.1 1.0
CB D:HIS110 3.5 95.9 1.0
CB D:CYS108 3.6 0.5 1.0
OG D:SER131 3.6 0.2 1.0
ND1 D:HIS110 4.2 94.3 1.0
CG D:HIS110 4.3 95.0 1.0
O D:CYS108 4.3 0.0 1.0
C D:CYS108 4.5 99.8 1.0
N D:HIS110 4.5 96.9 1.0
CB D:CYS128 4.6 99.0 1.0
N D:LEU111 4.6 96.2 1.0
CA D:HIS110 4.6 96.2 1.0
CA D:CYS108 4.6 0.4 1.0
CB D:SER131 4.7 0.3 1.0
ND1 D:HIS129 4.7 98.0 1.0
CA D:CYS126 4.8 0.1 1.0
N D:HIS129 4.8 99.1 1.0
CB D:ALA144 4.9 0.1 1.0
SG D:CYS113 5.0 97.2 1.0

Iron binding site 6 out of 6 in 2zt9

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Iron binding site 6 out of 6 in the Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Cytochrome B6F Complex From Nostoc Sp. Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:0.2
occ:1.00
 FE2 D:FES200 0.0 0.2 1.0
ND1 D:HIS129 2.0 98.0 1.0
S2 D:FES200 2.2 0.4 1.0
ND1 D:HIS110 2.2 94.3 1.0
S1 D:FES200 2.2 0.4 1.0
CG D:HIS129 2.9 98.5 1.0
FE1 D:FES200 3.0 0.9 1.0
CE1 D:HIS110 3.0 93.9 1.0
CE1 D:HIS129 3.0 98.1 1.0
CG D:HIS110 3.2 95.0 1.0
CB D:HIS129 3.2 99.0 1.0
CB D:HIS110 3.6 95.9 1.0
N D:HIS129 3.8 99.1 1.0
CD2 D:HIS129 4.1 98.3 1.0
NE2 D:HIS129 4.1 98.2 1.0
CA D:HIS129 4.1 99.1 1.0
CB D:CYS128 4.1 99.0 1.0
NE2 D:HIS110 4.1 94.5 1.0
CD2 D:HIS110 4.2 94.7 1.0
CG D:PRO143 4.3 0.7 1.0
C D:CYS128 4.4 99.2 1.0
CD1 D:LEU111 4.6 94.7 1.0
N D:LEU111 4.7 96.2 1.0
CB D:LEU111 4.7 95.6 1.0
SG D:CYS108 4.7 0.6 1.0
CG D:LEU111 4.7 94.8 1.0
SG D:CYS126 4.9 0.3 1.0
CA D:CYS128 4.9 99.2 1.0
CA D:HIS110 4.9 96.2 1.0
C D:HIS129 4.9 99.3 1.0

Reference:

D.Baniulis, E.Yamashita, J.P.Whitelegge, A.I.Zatsman, M.P.Hendrich, S.S.Hasan, C.M.Ryan, W.A.Cramer. Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome B6F Complex From Nostoc Sp. Pcc 7120 J.Biol.Chem. V. 284 9861 2009.
ISSN: ISSN 0021-9258
PubMed: 19189962
DOI: 10.1074/JBC.M809196200
Page generated: Sun Aug 4 06:22:44 2024

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