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Sodium in PDB 7b2c: Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon

Enzymatic activity of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon

All present enzymatic activity of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon:
2.8.4.1;

Protein crystallography data

The structure of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon, PDB code: 7b2c was solved by T.Wagner, O.N.Lemaire, S.Engilberge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.90 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.791, 147.186, 113.376, 90, 107.2, 90
R / Rfree (%) 17.4 / 20.1

Other elements in 7b2c:

The structure of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Potassium (K) 17 atoms
Nickel (Ni) 2 atoms
Xenon (Xe) 16 atoms
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon (pdb code 7b2c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon, PDB code: 7b2c:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7b2c

Go back to Sodium Binding Sites List in 7b2c
Sodium binding site 1 out of 5 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1203

b:15.2
occ:1.00
 O A:HOH1671 3.0 3.6 0.5
O A:HOH1724 3.1 39.2 1.0
O E:HOH785 3.2 17.5 1.0
N A:TYR412 3.3 11.6 1.0
CB A:THR411 3.5 12.7 1.0
OE1 A:GLU413 3.6 31.5 0.5
CA A:THR411 3.6 11.5 1.0
CE1 E:PHE174 3.6 15.2 1.0
O A:HOH1760 3.7 22.7 1.0
O2 A:GOL1211 3.8 50.5 1.0
CG2 A:THR411 3.9 12.3 1.0
O3 A:GOL1211 3.9 50.5 1.0
C A:THR411 4.0 11.7 1.0
CZ E:PHE174 4.1 14.2 1.0
CB A:TYR412 4.3 12.1 1.0
C2 A:GOL1211 4.4 50.5 1.0
CA A:TYR412 4.4 11.6 1.0
O A:HOH1698 4.5 37.6 1.0
O E:HOH637 4.5 29.6 1.0
CD A:GLU413 4.7 29.9 0.5
C3 A:GOL1211 4.7 50.5 1.0
CD1 E:PHE174 4.8 14.3 1.0
OG1 A:THR411 4.8 12.5 1.0
N A:THR411 4.9 12.4 1.0
N A:GLU413 5.0 11.7 0.5
N A:GLU413 5.0 11.8 0.5
O A:ASN410 5.0 15.6 1.0

Sodium binding site 2 out of 5 in 7b2c

Go back to Sodium Binding Sites List in 7b2c
Sodium binding site 2 out of 5 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:10.5
occ:1.00
 OG C:SER35 3.0 23.6 1.0
O C:HOH486 3.4 30.1 1.0
CB C:SER35 3.5 19.4 1.0
CB C:LYS37 4.1 20.4 1.0
CD C:LYS37 4.2 33.2 1.0
OD1 C:ASP38 4.3 24.3 1.0
CG C:ASP38 4.5 22.6 1.0
OD2 C:ASP38 4.6 21.3 1.0
O C:HOH617 4.6 29.8 1.0
CG C:LYS37 4.7 24.4 1.0
N C:ASP38 4.8 17.6 1.0
CE C:LYS37 4.9 39.4 1.0

Sodium binding site 3 out of 5 in 7b2c

Go back to Sodium Binding Sites List in 7b2c
Sodium binding site 3 out of 5 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na704

b:9.4
occ:1.00
 O D:HOH1048 2.5 18.2 1.0
O D:HOH1160 2.6 27.4 1.0
O D:GLN212 2.6 19.5 1.0
O D:HOH1239 2.6 37.7 1.0
O D:LEU215 3.0 16.4 1.0
O D:HOH866 3.1 13.6 1.0
C D:GLN212 3.7 17.4 1.0
C D:LEU215 4.1 15.7 1.0
CA D:ARG213 4.3 14.5 1.0
N D:LEU215 4.4 15.8 1.0
O D:HOH1177 4.4 18.2 1.0
C D:ARG213 4.4 14.3 1.0
O D:ARG213 4.4 14.9 1.0
N D:ARG213 4.5 14.5 1.0
CA D:LEU215 4.7 17.5 1.0
NZ D:LYS198 4.7 12.2 1.0
O A:HOH1330 4.7 33.0 1.0
CA D:GLN212 4.8 17.3 1.0
O D:HOH856 4.8 26.0 1.0
CB D:LEU215 4.9 19.1 1.0
CB D:GLN212 4.9 17.3 1.0
O D:HOH878 4.9 29.4 1.0

Sodium binding site 4 out of 5 in 7b2c

Go back to Sodium Binding Sites List in 7b2c
Sodium binding site 4 out of 5 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na705

b:14.3
occ:1.00
 O B:HOH814 2.9 17.6 1.0
N D:TYR412 3.3 12.7 1.0
O D:HOH1268 3.4 37.6 1.0
OE1 D:GLU413 3.5 35.0 1.0
CE1 B:PHE174 3.5 17.6 1.0
O F:HOH1450 3.6 25.3 1.0
CA D:THR411 3.6 13.2 1.0
CB D:THR411 3.6 15.3 1.0
CZ B:PHE174 4.0 16.1 1.0
C D:THR411 4.0 12.9 1.0
CG2 D:THR411 4.0 14.4 1.0
CB D:TYR412 4.3 12.7 1.0
O2 F:GOL1107 4.3 45.1 1.0
CA D:TYR412 4.4 12.9 1.0
O B:HOH732 4.5 25.1 1.0
CD D:GLU413 4.6 40.4 1.0
CD1 B:PHE174 4.7 16.2 1.0
C2 F:GOL1107 4.7 45.3 1.0
NE2 B:HIS175 4.8 15.3 1.0
OG1 D:THR411 4.9 17.5 1.0
N D:THR411 4.9 13.2 1.0
OE2 D:GLU413 5.0 48.4 1.0
O D:ASN410 5.0 13.2 1.0

Sodium binding site 5 out of 5 in 7b2c

Go back to Sodium Binding Sites List in 7b2c
Sodium binding site 5 out of 5 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na706

b:18.1
occ:1.00
 O D:HOH1211 2.7 40.0 1.0
O D:ASN219 2.8 20.1 1.0
O D:PHE222 2.8 16.1 1.0
O D:HOH1215 3.0 47.0 1.0
O D:LYS220 3.3 19.0 1.0
O D:HOH997 3.6 19.2 1.0
C D:PHE222 3.6 16.4 1.0
C D:LYS220 3.7 18.8 1.0
C D:ASN219 3.9 18.6 1.0
CA D:LYS220 4.0 19.4 1.0
N D:PHE222 4.2 16.4 1.0
N D:PRO223 4.4 16.0 1.0
N D:LYS220 4.4 18.2 1.0
CA D:PRO223 4.4 16.7 1.0
CA D:PHE222 4.5 15.6 1.0
O D:HOH1265 4.5 32.5 1.0
N D:MET221 4.6 17.2 1.0
C D:MET221 4.6 15.7 1.0
C D:PRO223 5.0 17.3 1.0

Reference:

C.J.Hahn, O.N.Lemaire, J.Kahnt, S.Engilberge, G.Wegener, T.Wagner. Crystal Structure of A Key Enzyme For Anaerobic Ethane Activation. Science V. 373 118 2021.
ISSN: ESSN 1095-9203
PubMed: 34210888
DOI: 10.1126/SCIENCE.ABG1765
Page generated: Tue Oct 8 16:05:01 2024

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