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Sodium in PDB 6gl6: Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H

Enzymatic activity of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H

All present enzymatic activity of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H:
1.18.99.1;

Protein crystallography data

The structure of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H, PDB code: 6gl6 was solved by L.Kertess, T.Happe, E.Hofmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.730, 70.730, 155.900, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 19.7

Other elements in 6gl6:

The structure of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H (pdb code 6gl6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H, PDB code: 6gl6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6gl6

Go back to Sodium Binding Sites List in 6gl6
Sodium binding site 1 out of 2 in the Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:49.2
occ:1.00
O A:HOH733 2.4 48.3 1.0
O A:HOH767 2.4 45.1 1.0
O A:HOH647 2.5 44.5 1.0
O A:TRP236 2.6 29.1 1.0
H A:GLY245 3.0 56.9 1.0
OE2 A:GLU235 3.2 88.1 1.0
HA A:ASP237 3.2 30.8 1.0
HA A:SER244 3.3 67.0 1.0
O A:HOH604 3.6 51.2 1.0
N A:GLY245 3.7 47.4 1.0
C A:TRP236 3.8 31.6 1.0
HB2 A:GLU235 3.8 49.2 1.0
HG3 A:GLU235 3.8 61.2 1.0
CD A:GLU235 3.9 84.8 1.0
OD1 A:ASP237 4.1 31.2 1.0
CA A:ASP237 4.1 25.6 1.0
CA A:SER244 4.2 55.8 1.0
CG A:GLU235 4.2 51.0 1.0
HB2 A:SER244 4.3 72.9 1.0
N A:ASP237 4.4 30.4 1.0
C A:SER244 4.4 48.3 1.0
H A:ASN238 4.5 32.9 1.0
O A:GLY245 4.5 34.2 1.0
O A:GLY243 4.5 66.2 1.0
CB A:GLU235 4.5 41.0 1.0
HA2 A:GLY245 4.6 46.4 1.0
CA A:GLY245 4.7 38.6 1.0
OE1 A:GLU235 4.7 64.6 1.0
CB A:SER244 4.8 60.7 1.0
CG A:ASP237 4.8 31.1 1.0
N A:TRP236 4.8 30.0 1.0
H A:TRP236 4.9 36.0 1.0
CA A:TRP236 4.9 26.6 1.0
C A:GLY245 5.0 33.3 1.0
O A:HOH912 5.0 58.5 1.0
CB A:ASP237 5.0 27.5 1.0

Sodium binding site 2 out of 2 in 6gl6

Go back to Sodium Binding Sites List in 6gl6
Sodium binding site 2 out of 2 in the Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:39.2
occ:0.86
O A:ASP85 2.3 28.6 1.0
O A:HOH696 2.4 38.6 1.0
O A:HOH701 2.5 41.7 1.0
O A:HOH792 2.5 46.9 1.0
O A:HOH665 2.7 47.1 1.0
HA A:ASP85 3.2 31.3 1.0
C A:ASP85 3.3 30.2 1.0
O A:HOH937 3.4 42.4 1.0
HH11 A:ARG80 3.6 41.1 1.0
HH12 A:ARG80 3.6 41.1 1.0
HB3 A:ASP85 3.7 32.8 1.0
CA A:ASP85 3.7 26.1 1.0
NH1 A:ARG80 3.9 34.3 1.0
CB A:ASP85 4.2 27.3 1.0
OE2 A:GLU86 4.4 35.1 1.0
HA A:GLU86 4.4 29.5 1.0
N A:GLU86 4.5 24.0 1.0
CD A:GLU86 4.6 32.1 1.0
HE1 A:HIS46 4.7 43.6 1.0
OE1 A:GLU86 4.8 34.1 1.0
OD1 A:ASP85 4.9 31.4 1.0
O A:PHE84 4.9 24.6 1.0
HB2 A:ASP85 4.9 32.8 1.0
HD3 A:ARG80 4.9 51.9 1.0
HG2 A:GLU86 4.9 34.5 1.0
CA A:GLU86 5.0 24.6 1.0
O A:HOH912 5.0 58.5 1.0

Reference:

P.Rodriguez-Macia, L.Kertess, J.Burnik, J.A.Birrell, E.Hofmann, W.Lubitz, T.Happe, O.Rudiger. His-Ligation to the [4FE-4S] Subcluster Tunes the Catalytic Bias of [Fefe] Hydrogenase. J.Am.Chem.Soc. V. 141 472 2019.
ISSN: ESSN 1520-5126
PubMed: 30545220
DOI: 10.1021/JACS.8B11149
Page generated: Tue Dec 15 12:17:31 2020

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