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Bromine in PDB 5odq: Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate.

Enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate.

All present enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate.:
1.12.99.6; 1.8.98.1;

Protein crystallography data

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate., PDB code: 5odq was solved by T.Wagner, J.Koch, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.68 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 366.325, 97.352, 133.276, 90.00, 108.37, 90.00
R / Rfree (%) 19.6 / 21.9

Other elements in 5odq:

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate. also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Iron (Fe) 113 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate. (pdb code 5odq). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate., PDB code: 5odq:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 5odq

Go back to Bromine Binding Sites List in 5odq
Bromine binding site 1 out of 4 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br303

b:60.4
occ:1.00
 BR1 B:9SB303 0.0 60.4 1.0
C1 B:9SB303 2.0 54.6 1.0
C2 B:9SB303 2.9 49.8 1.0
FE6 B:9S8302 3.4 24.9 1.0
CA B:GLY80 3.4 17.2 1.0
S7 B:9S8302 3.6 24.7 1.0
N B:GLY80 3.6 16.8 1.0
SG B:CYS231 3.7 27.5 1.0
S5 B:9S8302 3.7 24.6 1.0
FE4 B:9S8302 3.8 25.4 1.0
CB B:PHE233 3.9 26.1 1.0
CD2 B:HIS154 3.9 35.0 1.0
CG B:PHE233 4.2 28.4 1.0
S2 B:9SB303 4.4 45.9 1.0
CD2 B:PHE233 4.5 31.2 1.0
C B:ASN79 4.5 19.6 1.0
NE2 B:HIS154 4.5 34.9 1.0
CG B:HIS154 4.6 32.6 1.0
CB B:ASN79 4.8 11.0 1.0
O2S B:9SB303 4.8 46.2 1.0
C B:GLY80 4.9 22.2 1.0
CD1 B:PHE233 4.9 32.6 1.0
O1S B:9SB303 4.9 45.9 1.0
CB B:HIS154 4.9 28.7 1.0

Bromine binding site 2 out of 4 in 5odq

Go back to Bromine Binding Sites List in 5odq
Bromine binding site 2 out of 4 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br304

b:72.4
occ:1.00
 BR1 B:9SB304 0.0 72.4 1.0
C1 B:9SB304 2.0 70.8 1.0
C2 B:9SB304 2.9 69.6 1.0
CD1 B:LEU236 3.9 23.7 1.0
CG B:ARG14 3.9 38.2 1.0
CD2 B:LEU236 3.9 26.4 1.0
CG1 C:VAL128 3.9 34.1 1.0
CG2 C:VAL128 4.2 33.6 1.0
NE B:ARG14 4.2 52.0 1.0
CD B:ARG14 4.3 47.0 1.0
S2 B:9SB304 4.3 68.5 1.0
CG1 B:ILE10 4.5 26.1 1.0
O2S B:9SB304 4.6 68.0 1.0
CG B:LEU236 4.6 23.5 1.0
CB B:ARG14 4.6 25.9 1.0
CG2 B:ILE10 4.7 26.7 1.0
CB C:VAL128 4.7 33.8 1.0
CD1 B:ILE10 4.9 33.7 1.0

Bromine binding site 3 out of 4 in 5odq

Go back to Bromine Binding Sites List in 5odq
Bromine binding site 3 out of 4 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br303

b:67.7
occ:1.00
 BR1 H:9SB303 0.0 67.7 1.0
C1 H:9SB303 2.0 64.8 1.0
C2 H:9SB303 2.9 62.5 1.0
CA H:GLY80 3.4 25.0 1.0
FE6 H:9S8302 3.5 25.3 1.0
S7 H:9S8302 3.5 27.3 1.0
SG H:CYS231 3.7 27.8 1.0
CB H:PHE233 3.7 25.7 1.0
N H:GLY80 3.7 25.0 1.0
S5 H:9S8302 3.7 27.1 1.0
FE4 H:9S8302 3.7 29.0 1.0
CG H:PHE233 4.0 27.7 1.0
CD2 H:HIS154 4.2 35.8 1.0
CD2 H:PHE233 4.2 30.2 1.0
S2 H:9SB303 4.2 60.9 1.0
O3S H:9SB303 4.3 60.1 1.0
CD1 H:PHE233 4.6 31.0 1.0
C H:ASN79 4.7 26.8 1.0
NE2 H:HIS154 4.8 35.8 1.0
CG H:HIS154 4.8 33.3 1.0
C H:GLY80 4.9 28.3 1.0
CB H:ASN79 5.0 19.2 1.0

Bromine binding site 4 out of 4 in 5odq

Go back to Bromine Binding Sites List in 5odq
Bromine binding site 4 out of 4 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Bromoethanesulfonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br304

b:67.6
occ:1.00
 BR1 H:9SB304 0.0 67.6 1.0
C1 H:9SB304 2.0 65.5 1.0
C2 H:9SB304 2.9 63.6 1.0
CZ H:PHE233 3.5 31.7 1.0
CB I:ALA127 3.6 27.6 1.0
CG2 I:THR117 3.7 44.0 1.0
CE2 H:PHE233 3.9 33.3 1.0
S2 H:9SB304 4.1 62.3 1.0
O2S H:9SB304 4.2 62.1 1.0
O3S H:9SB304 4.5 62.2 1.0
S5 H:9S8301 4.6 32.0 1.0
CE1 H:PHE233 4.6 32.2 1.0
CG2 I:VAL128 4.6 33.1 1.0
CB H:ALA44 4.6 29.4 1.0
CG2 H:VAL47 4.7 36.5 1.0
OG1 I:THR117 4.8 46.3 1.0
CB I:THR117 4.9 44.3 1.0
CA I:ALA127 4.9 27.4 1.0

Reference:

T.Wagner, J.Koch, U.Ermler, S.Shima. Methanogenic Heterodisulfide Reductase (Hdrabc-Mvhagd) Uses Two Noncubane [4FE-4S] Clusters For Reduction. Science V. 357 699 2017.
ISSN: ESSN 1095-9203
PubMed: 28818947
DOI: 10.1126/SCIENCE.AAN0425
Page generated: Thu Jul 11 00:35:50 2024

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