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Sodium in PDB 4ras: Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation

Protein crystallography data

The structure of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation, PDB code: 4ras was solved by C.P.Quezada, K.A.P.Payne, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.90 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.340, 171.510, 109.020, 90.00, 98.87, 90.00
R / Rfree (%) 18.1 / 20.7

Other elements in 4ras:

The structure of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation also contains other interesting chemical elements:

Cobalt (Co) 3 atoms
Iron (Fe) 24 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation (pdb code 4ras). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation, PDB code: 4ras:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4ras

Go back to Sodium Binding Sites List in 4ras
Sodium binding site 1 out of 3 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na805

b:33.2
occ:1.00
O A:HOH1010 2.5 33.3 1.0
O A:ASN571 2.7 36.4 1.0
O A:HOH1011 2.8 41.0 1.0
O A:CYS568 2.8 34.2 1.0
O A:LYS566 3.4 37.1 1.0
C A:CYS568 3.7 31.6 1.0
C A:ASN571 3.8 34.0 1.0
CA A:PRO569 4.1 31.7 1.0
CB A:ASN571 4.1 38.0 1.0
ND2 A:ASN571 4.2 50.5 1.0
N A:PRO569 4.2 31.5 1.0
C A:MET567 4.3 35.1 1.0
O A:MET567 4.3 34.8 1.0
CA A:ASN571 4.3 34.7 1.0
C A:PRO569 4.4 31.6 1.0
CB A:ASN604 4.4 43.0 1.0
N A:CYS568 4.4 34.4 1.0
O A:PRO569 4.4 34.4 1.0
N A:ASN571 4.4 34.2 1.0
CG A:ASN571 4.5 37.9 1.0
C A:LYS566 4.6 35.6 1.0
CA A:CYS568 4.7 32.1 1.0
OD2 A:ASP599 4.7 43.1 1.0
CA A:MET567 4.8 36.3 1.0
N A:GLY605 4.8 41.1 1.0
OD1 A:ASP599 4.8 44.5 1.0
C A:ASN604 5.0 39.5 1.0
N A:ARG572 5.0 33.4 1.0

Sodium binding site 2 out of 3 in 4ras

Go back to Sodium Binding Sites List in 4ras
Sodium binding site 2 out of 3 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na805

b:38.8
occ:1.00
O B:HOH980 2.6 52.4 1.0
O B:ASN571 2.7 41.8 1.0
O B:HOH981 2.8 42.4 1.0
O B:CYS568 2.9 42.0 1.0
O B:LYS566 3.3 46.9 1.0
C B:CYS568 3.8 42.4 1.0
C B:ASN571 3.8 41.8 1.0
ND2 B:ASN571 4.0 48.4 1.0
CB B:ASN571 4.0 43.5 1.0
C B:MET567 4.2 44.9 1.0
CG B:ASN571 4.3 45.7 1.0
CA B:PRO569 4.3 41.2 1.0
CA B:ASN571 4.3 42.3 1.0
N B:CYS568 4.3 42.5 1.0
CB B:ASN604 4.4 48.6 1.0
O B:MET567 4.4 47.5 1.0
N B:PRO569 4.4 42.0 1.0
C B:LYS566 4.4 45.1 1.0
N B:ASN571 4.5 40.5 1.0
C B:PRO569 4.6 40.9 1.0
O B:PRO569 4.6 40.5 1.0
CA B:CYS568 4.7 43.2 1.0
CA B:MET567 4.7 47.9 1.0
N B:GLY605 4.8 48.4 1.0
OD1 B:ASP599 4.9 57.0 1.0
OD2 B:ASP599 4.9 53.7 1.0
OE1 B:GLU409 5.0 74.7 1.0
C B:ASN604 5.0 49.4 1.0
N B:ARG572 5.0 41.6 1.0

Sodium binding site 3 out of 3 in 4ras

Go back to Sodium Binding Sites List in 4ras
Sodium binding site 3 out of 3 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na805

b:42.9
occ:1.00
O C:ASN571 2.7 49.0 1.0
O C:CYS568 2.8 46.8 1.0
O C:LYS566 3.3 51.3 1.0
C C:ASN571 3.8 49.1 1.0
C C:CYS568 3.8 47.4 1.0
ND2 C:ASN571 4.0 63.5 1.0
CB C:ASN571 4.0 50.6 1.0
CA C:ASN571 4.2 49.3 1.0
CG C:ASN571 4.2 55.1 1.0
CA C:PRO569 4.2 48.0 1.0
C C:MET567 4.3 47.5 1.0
N C:PRO569 4.4 47.1 1.0
O C:MET567 4.4 47.9 1.0
N C:ASN571 4.4 46.4 1.0
N C:CYS568 4.4 46.4 1.0
C C:LYS566 4.5 49.3 1.0
O C:PRO569 4.5 47.7 1.0
C C:PRO569 4.5 47.1 1.0
CB C:ASN604 4.5 57.5 1.0
CA C:MET567 4.8 50.0 1.0
CA C:CYS568 4.8 47.2 1.0
N C:GLY605 4.8 53.4 1.0
N C:ARG572 4.9 51.2 1.0
OD2 C:ASP599 4.9 59.5 1.0
OD1 C:ASP599 5.0 55.8 1.0
OE1 C:GLU409 5.0 77.5 1.0

Reference:

K.A.P.Payne, C.P.Quezada, K.Fisher, M.S.Dunstan, F.A.Collins, H.Sjuts, C.Levy, S.Hay, S.E.J.Rigby, D.Leys. Reductive Dehalogenase Structure Suggests A Mechanism For B12-Dependent Dehalogenation Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13901
Page generated: Tue Dec 15 07:09:58 2020

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