Atomistry » Sodium » PDB 4w96-4wxb » 4wcx
Atomistry »
  Sodium »
    PDB 4w96-4wxb »
      4wcx »

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

Protein crystallography data

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

Other elements in 4wcx:

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

Iron (Fe) 17 atoms

Sodium Binding Sites:

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 4wcx

Go back to Sodium Binding Sites List in 4wcx
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 4wcx

Go back to Sodium Binding Sites List in 4wcx
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 4wcx

Go back to Sodium Binding Sites List in 4wcx
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

Reference:

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
Page generated: Tue Dec 15 09:24:57 2020

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy