Sodium in PDB 4wcx: Crystal Structure of Hydg: A Maturase of the [Fefe]-Hydrogenase

The structure of Crystal Structure of Hydg: A Maturase of the [Fefe]-Hydrogenase, PDB code: 4wcx was solved by P.C.Dinis, J.E.Harmer, R.C.Driesener, P.L.Roach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.33 / 1.59
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.130, 56.190, 84.920, 89.59, 83.62, 66.84
R / Rfree (%)	18 / 21.3

The structure of Crystal Structure of Hydg: A Maturase of the [Fefe]-Hydrogenase also contains other interesting chemical elements:

Iron

(Fe)

17 atoms

The binding sites of Sodium atom in the Crystal Structure of Hydg: A Maturase of the [Fefe]-Hydrogenase (pdb code 4wcx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Hydg: A Maturase of the [Fefe]-Hydrogenase, PDB code: 4wcx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Hydg: A Maturase of the [Fefe]-Hydrogenase


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 Hydg: A Maturase of the [Fefe]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:65.4 occ:1.00 OE2 A:GLU343 2.5 62.3 1.0 CD A:GLU343 3.5 67.6 1.0 OE1 A:GLU343 3.8 73.0 1.0 N A:LYS352 4.0 58.2 1.0 O A:VAL338 4.1 45.1 1.0 HD3 A:LYS108 4.5 60.5 1.0 HD2 A:LYS108 4.9 60.5 1.0 CG A:GLU343 4.9 57.5 1.0 HA A:LYS352 4.9 71.3 1.0 O A:HOH928 5.0 52.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Hydg: A Maturase of the [Fefe]-Hydrogenase


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 Hydg: A Maturase of the [Fefe]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na505 b:39.5 occ:1.00 OH C:TYR240 2.3 27.5 1.0 O C:HOH610 2.4 35.4 1.0 HE1 C:TYR240 3.1 24.5 1.0 CZ C:TYR240 3.4 21.3 1.0 CE1 C:TYR240 3.6 20.4 1.0 HH C:TYR285 3.8 26.8 1.0 O C:HOH609 4.0 31.4 1.0 HH22 C:ARG15 4.0 49.4 1.0 HH21 C:ARG15 4.2 49.4 1.0 OH C:TYR285 4.2 22.3 1.0 NH2 C:ARG15 4.3 41.2 1.0 CE2 C:TYR240 4.6 17.6 1.0 HE2 C:TYR240 4.8 21.1 1.0 HE2 C:HIS197 4.9 20.1 1.0 CD1 C:TYR240 5.0 18.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Hydg: A Maturase of the [Fefe]-Hydrogenase


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 Hydg: A Maturase of the [Fefe]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na506 b:53.4 occ:1.00 OE2 C:GLU19 2.3 48.2 1.0 OE1 C:GLU19 2.5 43.6 1.0 CD C:GLU19 2.6 47.1 1.0 HE3 C:LYS22 2.7 52.4 1.0 HE2 C:LYS22 3.3 52.4 1.0 CE C:LYS22 3.4 43.6 1.0 HZ1 C:LYS22 3.5 68.8 1.0 NZ C:LYS22 3.9 57.4 1.0 CG C:GLU19 3.9 37.8 1.0 HG3 C:GLU19 4.1 45.3 1.0 HG2 C:GLU19 4.2 45.3 1.0 HZ2 C:LYS22 4.3 68.8 1.0 HD2 C:ARG15 4.4 47.9 1.0 HH11 C:ARG15 4.6 53.2 1.0 HD2 C:LYS22 4.6 54.7 1.0 HA C:GLU19 4.6 28.1 1.0 CD C:LYS22 4.6 45.6 1.0 HZ3 C:LYS22 4.7 68.8 1.0

P.Dinis, D.L.Suess, S.J.Fox, J.E.Harmer, R.C.Driesener, L.De La Paz, J.R.Swartz, J.W.Essex, R.D.Britt, P.L.Roach. X-Ray Crystallographic and Epr Spectroscopic Analysis of Hydg, A Maturase in [Fefe]-Hydrogenase H-Cluster Assembly. Proc.Natl.Acad.Sci.Usa V. 112 1362 2015.
ISSN: ESSN 1091-6490
PubMed: 25605932
DOI: 10.1073/PNAS.1417252112