Bromine in PDB 9es9: Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site

Enzymatic activity of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site

All present enzymatic activity of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site:
7.1.1.6;

Other elements in 9es9:

The structure of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site 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 Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site (pdb code 9es9). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site, PDB code: 9es9:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 9es9

Go back to Bromine Binding Sites List in 9es9
Bromine binding site 1 out of 4 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br306

b:153.0
occ:1.00
 BRAH A:BNT306 0.0 153.0 1.0
CAG A:BNT306 1.9 126.9 1.0
CAL A:BNT306 2.8 126.2 1.0
CAF A:BNT306 2.8 125.7 1.0
OAB A:BNT306 2.9 128.0 1.0
CAM A:BNT306 3.2 127.3 1.0
CD1 A:ILE150 3.4 96.8 1.0
CE1 B:PHE85 3.5 57.8 1.0
CAK A:BNT306 4.2 126.9 1.0
CAE A:BNT306 4.2 124.5 1.0
CD1 B:PHE85 4.3 60.2 1.0
NE2 L:HIS128 4.3 61.8 1.0
CZ B:PHE85 4.4 56.0 1.0
CG2 B:ILE75 4.4 60.7 1.0
CE1 L:HIS128 4.6 67.0 1.0
O L:CYS127 4.6 74.5 1.0
CG2 A:ILE150 4.6 95.2 1.0
O B:ILE75 4.7 64.7 1.0
CG1 A:ILE150 4.7 91.8 1.0
CAJ A:BNT306 4.7 129.1 1.0
CB L:CYS127 4.7 70.3 1.0
SG L:CYS127 4.9 83.8 1.0
CB A:ILE150 5.0 93.2 1.0
CA L:CYS127 5.0 73.0 1.0

Bromine binding site 2 out of 4 in 9es9

Go back to Bromine Binding Sites List in 9es9
Bromine binding site 2 out of 4 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br306

b:164.8
occ:1.00
 BRAI A:BNT306 0.0 164.8 1.0
CAJ A:BNT306 1.9 129.1 1.0
CAK A:BNT306 2.8 126.9 1.0
CAE A:BNT306 2.9 124.5 1.0
OAN A:BNT306 2.9 126.9 1.0
CAD A:BNT306 3.3 122.4 1.0
CG2 A:VAL151 3.3 93.3 1.0
CAA A:BNT306 3.4 124.5 1.0
CAC A:BNT306 3.4 126.3 1.0
CAL A:BNT306 4.2 126.2 1.0
CAF A:BNT306 4.2 125.7 1.0
CB B:PRO77 4.2 53.4 1.0
CG B:PHE81 4.5 57.1 1.0
CD2 B:PHE81 4.5 58.0 1.0
CD1 B:PHE81 4.7 57.8 1.0
CAG A:BNT306 4.7 126.9 1.0
CB A:VAL151 4.8 96.0 1.0
CE2 B:PHE81 4.8 52.4 1.0
CB B:PHE81 4.9 51.9 1.0
CE1 B:PHE81 4.9 57.1 1.0
CG B:PRO77 5.0 51.6 1.0
CZ B:PHE81 5.0 56.0 1.0

Bromine binding site 3 out of 4 in 9es9

Go back to Bromine Binding Sites List in 9es9
Bromine binding site 3 out of 4 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Br306

b:158.9
occ:1.00
 BRAH I:BNT306 0.0 158.9 1.0
CAG I:BNT306 1.9 129.8 1.0
CAL I:BNT306 2.8 129.7 1.0
CAF I:BNT306 2.8 128.6 1.0
OAB I:BNT306 2.9 131.0 1.0
CAM I:BNT306 3.2 130.9 1.0
CD1 I:ILE150 3.4 96.8 1.0
CE1 J:PHE85 3.5 57.8 1.0
CAK I:BNT306 4.2 130.4 1.0
CAE I:BNT306 4.2 127.7 1.0
CD1 J:PHE85 4.3 60.2 1.0
NE2 D:HIS128 4.3 61.8 1.0
CZ J:PHE85 4.4 56.0 1.0
CG2 J:ILE75 4.4 60.7 1.0
CE1 D:HIS128 4.6 67.0 1.0
O D:CYS127 4.6 74.5 1.0
CG2 I:ILE150 4.6 95.2 1.0
O J:ILE75 4.7 64.7 1.0
CG1 I:ILE150 4.7 91.8 1.0
CAJ I:BNT306 4.7 132.9 1.0
CB D:CYS127 4.7 70.3 1.0
SG D:CYS127 4.9 83.8 1.0
CB I:ILE150 5.0 93.2 1.0
CA D:CYS127 5.0 73.0 1.0

Bromine binding site 4 out of 4 in 9es9

Go back to Bromine Binding Sites List in 9es9
Bromine binding site 4 out of 4 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Br306

b:170.9
occ:1.00
 BRAI I:BNT306 0.0 170.9 1.0
CAJ I:BNT306 1.9 132.9 1.0
CAK I:BNT306 2.8 130.4 1.0
CAE I:BNT306 2.9 127.7 1.0
OAN I:BNT306 2.9 129.8 1.0
CAD I:BNT306 3.3 125.1 1.0
CG2 I:VAL151 3.3 93.3 1.0
CAA I:BNT306 3.4 127.4 1.0
CAC I:BNT306 3.4 129.2 1.0
CAL I:BNT306 4.2 129.7 1.0
CAF I:BNT306 4.2 128.6 1.0
CB J:PRO77 4.2 53.4 1.0
CG J:PHE81 4.5 57.1 1.0
CD2 J:PHE81 4.5 58.0 1.0
CD1 J:PHE81 4.7 57.8 1.0
CAG I:BNT306 4.7 129.8 1.0
CB I:VAL151 4.8 96.0 1.0
CE2 J:PHE81 4.8 52.4 1.0
CB J:PHE81 4.9 51.9 1.0
CE1 J:PHE81 4.9 57.1 1.0
CG J:PRO77 5.0 51.6 1.0
CZ J:PHE81 5.0 56.0 1.0

Reference:

S.Pintscher, R.Pietras, B.Mielecki, M.Szwalec, A.Wojcik-Augustyn, P.Indyka, M.Rawski, L.Koziej, M.Jaciuk, G.Wazny, S.Glatt, A.Osyczka. Molecular Basis of Plastoquinone Reduction in Plant Cytochrome B 6 F. Nat.Plants 2024.
ISSN: ESSN 2055-0278
PubMed: 39362993
DOI: 10.1038/S41477-024-01804-X
Page generated: Thu Oct 31 16:52:19 2024

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