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Sodium in PDB 7sxm: Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis

Enzymatic activity of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis

All present enzymatic activity of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis:
2.8.4.1;

Protein crystallography data

The structure of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis, PDB code: 7sxm was solved by P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.63 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.956, 115.741, 123.4, 90, 92.53, 90
R / Rfree (%) 17.8 / 21.8

Other elements in 7sxm:

The structure of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Nickel (Ni) 2 atoms
Xenon (Xe) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis (pdb code 7sxm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis, PDB code: 7sxm:

Sodium binding site 1 out of 1 in 7sxm

Go back to Sodium Binding Sites List in 7sxm
Sodium binding site 1 out of 1 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:20.9
occ:1.00
 O A:ARG216 2.8 24.9 1.0
O A:CYS218 2.8 24.6 1.0
O D:CYS218 2.8 24.2 1.0
O D:ARG216 2.8 22.1 1.0
O A:SER215 3.4 25.4 1.0
O D:SER215 3.5 21.1 1.0
C A:ARG216 3.5 23.8 1.0
C D:ARG216 3.6 24.3 1.0
NH1 D:ARG102 3.6 25.0 1.0
NH1 A:ARG102 3.7 23.3 1.0
C A:CYS218 3.8 24.0 1.0
CA A:ARG216 3.8 22.4 1.0
O A:HOH789 3.8 23.5 1.0
C D:CYS218 3.9 22.8 1.0
CA D:ARG216 3.9 22.3 1.0
O A:HOH858 3.9 23.4 1.0
CZ D:ARG102 4.1 21.4 1.0
NH2 D:ARG102 4.1 21.0 1.0
CZ A:ARG102 4.2 26.3 1.0
NH2 A:ARG102 4.3 26.2 1.0
N A:CYS218 4.4 22.2 1.0
C A:SER215 4.4 24.1 1.0
N D:CYS218 4.5 22.2 1.0
C D:SER215 4.5 23.2 1.0
CA D:ASP219 4.5 24.5 1.0
C A:THR217 4.5 20.7 1.0
CA A:ASP219 4.5 22.5 1.0
N A:THR217 4.6 23.2 1.0
N A:ASP219 4.6 21.2 1.0
N D:ASP219 4.6 19.0 1.0
C D:THR217 4.6 22.2 1.0
N D:THR217 4.6 21.1 1.0
N A:ARG216 4.6 23.1 1.0
N D:ARG216 4.7 25.2 1.0
CA A:CYS218 4.7 24.0 1.0
CA D:CYS218 4.8 21.9 1.0
O A:THR217 4.8 20.1 1.0
O D:THR217 4.9 22.2 1.0

Reference:

C.J.Ohmer, M.Dasgupta, A.Patwardhan, I.Bogacz, C.Kaminsky, M.D.Doyle, P.Y.Chen, S.M.Keable, H.Makita, P.S.Simon, R.Massad, T.Fransson, R.Chatterjee, A.Bhowmick, D.W.Paley, N.W.Moriarty, A.S.Brewster, L.B.Gee, R.Alonso-Mori, F.Moss, F.D.Fuller, A.Batyuk, N.K.Sauter, U.Bergmann, C.L.Drennan, V.K.Yachandra, J.Yano, J.F.Kern, S.W.Ragsdale. Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase. J.Inorg.Biochem. V. 230 11768 2022.
ISSN: ISSN 0162-0134
PubMed: 35202981
DOI: 10.1016/J.JINORGBIO.2022.111768
Page generated: Wed Oct 9 09:03:16 2024

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