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Sodium in PDB 3f47: The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme From Methanocaldococcus Jannaschii

Enzymatic activity of The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme From Methanocaldococcus Jannaschii

All present enzymatic activity of The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme From Methanocaldococcus Jannaschii:
1.12.98.2;

Protein crystallography data

The structure of The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme From Methanocaldococcus Jannaschii, PDB code: 3f47 was solved by T.Hiromoto, O.Pilak, E.Warkentin, R.K.Thauer, S.Shima, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.75
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 95.930, 95.930, 165.810, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.5

Other elements in 3f47:

The structure of The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme From Methanocaldococcus Jannaschii also contains other interesting chemical elements:

Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme From Methanocaldococcus Jannaschii (pdb code 3f47). 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 The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme From Methanocaldococcus Jannaschii, PDB code: 3f47:

Sodium binding site 1 out of 1 in 3f47

Go back to Sodium Binding Sites List in 3f47
Sodium binding site 1 out of 1 in the The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme From Methanocaldococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na363

b:32.1
occ:1.00
 O A:VAL57 2.6 33.1 1.0
O A:VAL54 2.7 31.4 1.0
O A:LEU51 2.7 32.5 1.0
O A:HOH524 3.1 51.5 1.0
O A:PRO55 3.3 33.2 1.0
C A:VAL54 3.6 31.5 1.0
C A:VAL57 3.7 32.6 1.0
C A:PRO55 3.7 33.1 1.0
C A:LEU51 3.8 31.9 1.0
CA A:PRO55 3.8 32.5 1.0
N A:VAL57 4.1 32.5 1.0
N A:PRO55 4.2 32.1 1.0
CA A:VAL57 4.3 32.5 1.0
CA A:LEU51 4.4 30.7 1.0
O A:LEU50 4.5 30.3 1.0
CB A:VAL57 4.5 32.9 1.0
N A:ASP56 4.7 32.8 0.5
N A:ASP56 4.7 32.5 0.5
CD1 A:LEU51 4.7 33.5 1.0
N A:VAL54 4.7 31.5 1.0
N A:LYS58 4.8 31.1 1.0
CA A:VAL54 4.8 31.1 1.0
N A:HIS52 4.8 32.3 1.0
C A:ASP56 4.9 32.8 0.5

Reference:

T.Hiromoto, K.Ataka, O.Pilak, S.Vogt, M.S.Stagni, W.Meyer-Klaucke, E.Warkentin, R.K.Thauer, S.Shima, U.Ermler. The Crystal Structure of C176A Mutated [Fe]-Hydrogenase Suggests An Acyl-Iron Ligation in the Active Site Iron Complex. Febs Lett. V. 583 585 2009.
ISSN: ISSN 0014-5793
PubMed: 19162018
DOI: 10.1016/J.FEBSLET.2009.01.017
Page generated: Tue Dec 15 06:10:17 2020

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