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Bromine in PDB 2d2c: Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus

Enzymatic activity of Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus

All present enzymatic activity of Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus:
1.10.99.1;

Protein crystallography data

The structure of Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus, PDB code: 2d2c was solved by J.Yan, G.Kurisu, W.A.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.76 / 3.80
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 156.587, 156.587, 361.786, 90.00, 90.00, 120.00
R / Rfree (%) 27.6 / 37.8

Other elements in 2d2c:

The structure of Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 12 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus (pdb code 2d2c). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus, PDB code: 2d2c:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 2d2c

Go back to Bromine Binding Sites List in 2d2c
Bromine binding site 1 out of 4 in the Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br309

b:64.1
occ:1.00
 BRAH B:BNT309 0.0 64.1 1.0
CAG B:BNT309 1.9 64.1 1.0
CAF B:BNT309 2.8 64.1 1.0
CAL B:BNT309 2.8 64.1 1.0
OAB B:BNT309 3.0 64.1 1.0
CAM B:BNT309 3.1 64.1 1.0
CB B:MET61 3.6 77.1 1.0
CB C:LYS146 3.8 77.6 1.0
CB C:GLU246 4.0 1.0 1.0
CE C:LYS146 4.1 77.6 1.0
CAK B:BNT309 4.2 64.1 1.0
CAE B:BNT309 4.2 64.1 1.0
CG B:MET61 4.2 77.1 1.0
N C:TYR147 4.3 36.9 1.0
C C:LYS146 4.3 61.5 1.0
CG C:GLU246 4.3 1.0 1.0
C C:TYR147 4.4 36.9 1.0
N C:ALA148 4.4 79.1 1.0
O C:LYS146 4.5 61.5 1.0
CA C:TYR147 4.5 36.9 1.0
CE B:MET61 4.7 77.1 1.0
CAJ B:BNT309 4.7 64.1 1.0
CA C:LYS146 4.7 61.5 1.0
CD C:LYS146 4.8 77.6 1.0
O C:TYR147 4.8 36.9 1.0
CG C:LYS146 4.9 77.6 1.0
CA C:ALA148 4.9 79.1 1.0
CA B:MET61 4.9 57.6 1.0

Bromine binding site 2 out of 4 in 2d2c

Go back to Bromine Binding Sites List in 2d2c
Bromine binding site 2 out of 4 in the Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br309

b:64.1
occ:1.00
 BRAI B:BNT309 0.0 64.1 1.0
CAJ B:BNT309 1.9 64.1 1.0
CAE B:BNT309 2.9 64.1 1.0
CAK B:BNT309 3.0 64.1 1.0
OAN B:BNT309 3.2 64.1 1.0
CAD B:BNT309 3.2 64.1 1.0
N B:GLU64 3.2 98.3 1.0
CG B:GLU64 3.4 44.9 1.0
CD B:PRO65 3.5 17.5 1.0
OE2 B:GLU64 3.6 44.9 1.0
CA B:GLY63 3.7 15.8 1.0
CB B:GLU64 3.8 44.9 1.0
C B:GLY63 3.9 15.8 1.0
CAA B:BNT309 3.9 64.1 1.0
CD B:GLU64 3.9 44.9 1.0
CA B:GLU64 4.0 98.3 1.0
CAF B:BNT309 4.2 64.1 1.0
CG B:PRO65 4.2 17.5 1.0
CAL B:BNT309 4.2 64.1 1.0
CAC B:BNT309 4.4 64.1 1.0
N B:PRO65 4.5 72.1 1.0
C B:GLU64 4.7 98.3 1.0
O B:VAL62 4.7 31.1 1.0
CAG B:BNT309 4.7 64.1 1.0
O B:GLY63 5.0 15.8 1.0
CB A:GLN142 5.0 97.4 1.0

Bromine binding site 3 out of 4 in 2d2c

Go back to Bromine Binding Sites List in 2d2c
Bromine binding site 3 out of 4 in the Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Br1309

b:64.1
occ:1.00
 BRAH O:BNT1309 0.0 64.1 1.0
CAG O:BNT1309 1.9 64.1 1.0
CAF O:BNT1309 2.8 64.1 1.0
CAL O:BNT1309 2.9 64.1 1.0
OAB O:BNT1309 2.9 64.1 1.0
CAM O:BNT1309 3.1 64.1 1.0
CB O:MET61 3.6 88.6 1.0
CB P:GLU246 3.8 66.5 1.0
CB P:LYS146 3.8 41.8 1.0
CA O:MET61 4.0 24.9 1.0
CE P:LYS146 4.1 41.8 1.0
CG P:GLU246 4.1 66.5 1.0
CAE O:BNT1309 4.1 64.1 1.0
CAK O:BNT1309 4.2 64.1 1.0
N P:ALA148 4.2 60.2 1.0
N P:TYR147 4.2 35.9 1.0
N O:VAL62 4.2 77.2 1.0
C P:TYR147 4.3 35.9 1.0
C P:LYS146 4.3 57.4 1.0
CA P:TYR147 4.5 35.9 1.0
O P:LYS146 4.6 57.4 1.0
O P:TYR147 4.6 35.9 1.0
C O:MET61 4.7 24.9 1.0
CA P:ALA148 4.7 60.2 1.0
CAJ O:BNT1309 4.7 64.1 1.0
CD P:LYS146 4.7 41.8 1.0
CA P:LYS146 4.7 57.4 1.0
CG P:LYS146 4.9 41.8 1.0
CG O:MET61 4.9 88.6 1.0

Bromine binding site 4 out of 4 in 2d2c

Go back to Bromine Binding Sites List in 2d2c
Bromine binding site 4 out of 4 in the Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Cytochrome B6F Complex with Dbmib From M. Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Br1309

b:64.1
occ:1.00
 BRAI O:BNT1309 0.0 64.1 1.0
CAJ O:BNT1309 1.9 64.1 1.0
CAE O:BNT1309 2.9 64.1 1.0
CAK O:BNT1309 3.0 64.1 1.0
O O:GLY63 3.1 20.0 1.0
CAD O:BNT1309 3.1 64.1 1.0
OAN O:BNT1309 3.2 64.1 1.0
CAA O:BNT1309 3.9 64.1 1.0
CB O:GLU64 4.0 59.1 1.0
C O:GLY63 4.0 20.0 1.0
OE2 O:GLU74 4.1 67.0 1.0
CAF O:BNT1309 4.2 64.1 1.0
CAL O:BNT1309 4.2 64.1 1.0
CAC O:BNT1309 4.3 64.1 1.0
CA O:GLU64 4.5 56.4 1.0
N O:GLU64 4.6 56.4 1.0
OE1 O:GLU74 4.7 67.0 1.0
CAG O:BNT1309 4.7 64.1 1.0
CD O:GLU74 4.8 67.0 1.0
CG O:GLU64 4.9 59.1 1.0
O O:VAL62 4.9 77.2 1.0
CA O:GLY63 5.0 20.0 1.0

Reference:

J.Yan, G.Kurisu, W.A.Cramer. Intraprotein Transfer of the Quinone Analogue Inhibitor 2,5-Dibromo-3-Methyl-6-Isopropyl-P-Benzoquinone in the Cytochrome B6F Complex Proc.Natl.Acad.Sci.Usa V. 103 69 2006.
ISSN: ISSN 0027-8424
PubMed: 16371475
DOI: 10.1073/PNAS.0504909102
Page generated: Wed Jul 10 17:55:11 2024

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