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Sodium in PDB 6enp: Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group.

Protein crystallography data

The structure of Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group., PDB code: 6enp was solved by G.Prats-Ejarque, M.Moussaoui, E.Boix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.93 / 1.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 27.734, 38.557, 98.965, 90.00, 90.00, 90.00
R / Rfree (%) 12.2 / 14.5

Other elements in 6enp:

The structure of Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group. also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group. (pdb code 6enp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group., PDB code: 6enp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6enp

Go back to Sodium Binding Sites List in 6enp
Sodium binding site 1 out of 3 in the Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:43.4
occ:1.00
O A:HOH516 2.4 39.4 0.9
HH11 A:ARG4 2.5 74.4 0.0
HH12 A:ARG4 2.8 74.4 0.0
NH1 A:ARG4 2.9 62.0 0.0
HD2 A:ARG4 3.8 66.1 0.0
CZ A:ARG4 4.1 61.0 0.0
CD A:ARG4 4.6 55.1 0.0
NE A:ARG4 4.8 58.6 0.0
HH22 A:ARG4 4.9 73.8 0.0
HD3 A:ARG4 4.9 66.1 0.0
NH2 A:ARG4 5.0 61.5 0.0

Sodium binding site 2 out of 3 in 6enp

Go back to Sodium Binding Sites List in 6enp
Sodium binding site 2 out of 3 in the Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:22.7
occ:0.53
CB A:PRO18 0.4 13.8 0.4
CA A:PRO18 1.4 13.8 0.4
CG A:PRO18 1.8 14.1 0.4
C A:PRO18 2.4 13.6 0.4
N A:PRO18 2.5 12.5 0.4
CD A:PRO18 2.7 13.3 0.4
O A:HOH430 2.7 18.7 0.6
CL A:CL208 2.9 24.1 0.4
O A:PRO18 2.9 14.7 0.4
N A:SER19 3.3 14.3 0.4
HA A:ASP46 3.4 21.0 1.0
C A:ASP46 3.6 17.3 1.0
N A:ASP46 3.6 16.2 1.0
C A:GLN17 3.7 10.1 0.4
CA A:ASP46 3.7 17.5 1.0
O A:ASP46 3.8 17.9 1.0
C A:HIS45 3.8 14.2 1.0
CB A:PRO18 3.9 13.4 0.6
H A:ASP46 3.9 19.4 1.0
CA A:PRO18 3.9 11.1 0.6
HA A:HIS45 4.0 16.0 1.0
N A:SER47 4.0 21.0 1.0
O A:GLN17 4.1 12.8 0.4
O A:HIS45 4.1 15.3 1.0
HA A:SER47 4.1 24.5 1.0
H A:SER47 4.3 25.1 1.0
HB3 A:HIS45 4.4 17.1 1.0
CA A:HIS45 4.4 13.3 1.0
N A:PRO18 4.6 10.5 0.6
CA A:SER47 4.6 20.4 1.0
CA A:SER19 4.6 15.6 0.4
HB3 A:SER47 4.6 27.8 1.0
CA A:GLN17 4.9 13.1 0.4
CB A:HIS45 5.0 14.2 1.0
O A:GLN17 5.0 10.5 0.6
C A:GLN17 5.0 10.3 0.6

Sodium binding site 3 out of 3 in 6enp

Go back to Sodium Binding Sites List in 6enp
Sodium binding site 3 out of 3 in the Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:14.4
occ:0.53
O A:GLN71 2.6 10.7 0.4
O A:GLN71 2.7 11.1 0.6
O A:HOH505 2.8 23.1 0.8
O A:HOH332 2.8 13.9 1.0
HB3 A:GLN71 3.0 12.9 0.6
HD13 A:LEU57 3.0 15.5 1.0
HD23 A:LEU58 3.0 29.1 0.5
HB3 A:GLN71 3.0 13.9 0.4
HB3 A:LEU57 3.1 13.8 1.0
HD21 A:LEU58 3.2 29.1 0.5
CD2 A:LEU58 3.4 24.2 0.5
H A:GLN71 3.5 11.7 0.4
H A:GLN71 3.6 10.6 0.6
C A:GLN71 3.6 10.3 0.4
C A:GLN71 3.6 9.4 0.6
HD22 A:LEU58 3.6 29.1 0.5
HD12 A:LEU57 3.7 15.5 1.0
HB2 A:LEU57 3.7 13.8 1.0
CD1 A:LEU57 3.8 12.9 1.0
CB A:LEU57 3.8 11.5 1.0
CB A:GLN71 3.9 10.7 0.6
O A:HOH493 3.9 34.4 0.5
CB A:GLN71 3.9 11.6 0.4
CA A:GLN71 4.1 8.6 0.6
CA A:GLN71 4.1 11.1 0.4
HA A:SER73 4.1 21.7 1.0
N A:GLN71 4.1 9.7 0.4
N A:GLN71 4.1 8.8 0.6
HB2 A:LEU58 4.2 17.7 0.5
H A:LEU58 4.3 15.9 0.5
O A:SER72 4.3 13.2 1.0
CG A:LEU57 4.4 12.2 1.0
H A:LEU58 4.4 14.4 0.5
HG2 A:GLN71 4.4 14.1 0.4
HB2 A:GLN71 4.4 12.9 0.6
C A:SER72 4.5 13.0 1.0
O A:HOH333 4.5 22.9 0.4
HB2 A:GLN71 4.5 13.9 0.4
O A:HOH379 4.5 17.6 0.6
HD11 A:LEU57 4.5 15.5 1.0
HE21 A:GLN71 4.5 18.6 0.6
HB3 A:SER73 4.6 26.9 1.0
NE2 A:GLN71 4.6 15.5 0.6
HD22 A:LEU57 4.6 17.0 1.0
CD A:GLN71 4.6 13.8 0.6
CG A:GLN71 4.7 12.7 0.6
N A:SER73 4.7 14.0 1.0
HG2 A:GLN71 4.7 15.2 0.6
N A:SER72 4.7 9.5 1.0
CG A:GLN71 4.8 11.8 0.4
CA A:SER73 4.8 18.1 1.0
N A:LEU58 4.8 12.0 0.5
N A:LEU58 4.8 13.3 0.5
HE22 A:GLN71 4.9 18.6 0.6
CG A:LEU58 4.9 20.8 0.5
O A:LEU58 4.9 10.9 0.5
OE1 A:GLN71 5.0 23.5 0.4
O A:LEU58 5.0 12.3 0.5

Reference:

G.Prats-Ejarque, J.A.Blanco, V.A.Salazar, V.M.Nogues, M.Moussaoui, E.Boix. Characterization of An Rnase with Two Catalytic Centers. Human RNASE6 Catalytic and Phosphate-Binding Site Arrangement Favors the Endonuclease Cleavage of Polymeric Substrates. Biochim Biophys Acta Gen V.1863 105 2019SUBJ.
ISSN: ISSN 1872-8006
PubMed: 30287244
DOI: 10.1016/J.BBAGEN.2018.09.021
Page generated: Tue Oct 8 08:26:50 2024

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