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Chlorine in PDB 5ogh: Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions

Enzymatic activity of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions

All present enzymatic activity of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions:
3.1.27.5;

Protein crystallography data

The structure of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions, PDB code: 5ogh was solved by J.A.Blanco, G.Prats-Ejarque, V.A.Salazar, M.Moussaoui, E.Boix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.65 / 1.16
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 64.060, 64.060, 64.058, 90.00, 90.00, 120.00
R / Rfree (%) 12.1 / 13.5

Other elements in 5ogh:

The structure of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions (pdb code 5ogh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions, PDB code: 5ogh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ogh

Go back to Chlorine Binding Sites List in 5ogh
Chlorine binding site 1 out of 5 in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:19.0
occ:0.66
 HZ2 A:LYS61 2.2 21.7 1.0
NZ A:LYS61 3.0 18.1 1.0
HZ1 A:LYS61 3.2 21.7 1.0
O A:HOH416 3.3 18.4 1.0
HE3 A:LYS61 3.4 20.1 1.0
HD2 A:LYS61 3.5 18.3 1.0
CE A:LYS61 3.7 16.7 1.0
HZ3 A:LYS61 3.7 21.7 1.0
CD A:LYS61 4.1 15.3 1.0
O A:HOH413 4.5 18.9 1.0
HD3 A:LYS61 4.5 18.3 1.0
HE2 A:LYS61 4.6 20.1 1.0
H A:ASN62 5.0 16.5 1.0

Chlorine binding site 2 out of 5 in 5ogh

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Chlorine binding site 2 out of 5 in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:21.0
occ:0.67
 NA A:NA209 2.8 22.4 1.0
O A:HOH437 2.9 38.7 0.8
HB3 A:SER15 2.9 19.3 1.0
HA A:SER50 3.1 14.5 1.0
O A:HOH477 3.2 51.9 0.9
O A:HOH472 3.2 53.9 1.0
O A:HOH479 3.3 47.8 1.0
HB3 A:SER50 3.4 15.8 1.0
HB2 A:SER50 3.5 15.8 1.0
CB A:SER15 3.7 16.1 1.0
CB A:SER50 3.8 13.2 1.0
HB2 A:SER15 3.9 19.3 1.0
CA A:SER50 3.9 12.1 1.0
O A:SER15 4.2 23.1 1.0
OG A:SER15 4.3 14.4 1.0
H A:LEU51 4.3 14.4 1.0
O A:HOH417 4.4 41.2 0.9
HG A:SER15 4.5 17.3 1.0
N A:SER50 4.6 11.6 1.0
CL A:CL206 4.8 20.6 0.6
CA A:SER15 4.8 15.9 1.0
C A:SER15 4.9 17.6 1.0
H A:SER50 4.9 13.9 1.0
N A:LEU51 4.9 12.1 1.0
HA A:SER15 5.0 19.1 1.0

Chlorine binding site 3 out of 5 in 5ogh

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Chlorine binding site 3 out of 5 in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:20.6
occ:0.60
 H A:ALA52 2.2 15.2 1.0
O A:HOH452 2.7 21.7 0.5
HB2 A:SER50 2.7 15.8 1.0
O A:HOH459 2.7 29.3 0.9
NA A:NA209 3.0 22.4 1.0
HB2 A:ALA52 3.0 17.5 1.0
N A:ALA52 3.0 12.7 1.0
HB3 A:LEU51 3.1 17.6 1.0
O A:HOH474 3.1 33.9 0.7
H A:LEU51 3.2 14.4 1.0
HB3 A:ALA52 3.3 17.5 1.0
CB A:ALA52 3.5 14.6 1.0
N A:LEU51 3.5 12.1 1.0
O A:HOH477 3.6 51.9 0.9
CB A:SER50 3.6 13.2 1.0
CA A:ALA52 3.8 13.1 1.0
CB A:LEU51 3.9 14.7 1.0
C A:LEU51 3.9 12.0 1.0
CA A:LEU51 3.9 12.2 1.0
OG A:SER50 4.1 13.5 1.0
C A:SER50 4.2 11.8 1.0
HB3 A:SER50 4.2 15.8 1.0
HA A:SER50 4.3 14.5 1.0
CA A:SER50 4.3 12.1 1.0
HA A:ALA52 4.3 15.7 1.0
HB2 A:LEU51 4.4 17.6 1.0
HB1 A:ALA52 4.4 17.5 1.0
O A:HOH479 4.5 47.8 1.0
O A:HOH472 4.5 53.9 1.0
O A:HOH335 4.6 35.6 1.0
H A:ASP53 4.6 14.0 1.0
CL A:CL205 4.8 21.0 0.7
HD23 A:LEU51 4.8 21.4 1.0
HG A:LEU51 4.9 17.6 1.0
HA A:LEU51 4.9 14.6 1.0
HG A:SER50 4.9 16.2 1.0
CG A:LEU51 5.0 14.7 1.0
O A:HOH343 5.0 37.7 1.0

Chlorine binding site 4 out of 5 in 5ogh

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Chlorine binding site 4 out of 5 in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:19.9
occ:0.61
 HG A:SER59 2.7 27.4 0.7
OG A:SER59 2.8 22.9 0.7
O A:HOH363 2.9 26.9 0.8
O A:HOH447 2.9 21.2 1.0
HA A:ALA56 3.0 14.7 1.0
OG A:SER59 3.2 17.4 0.3
O A:HOH457 3.2 36.3 0.7
HB3 A:SER59 3.2 19.7 0.3
HG A:SER59 3.2 20.9 0.3
HB2 A:SER59 3.3 21.6 0.7
HB2 A:CYS58 3.5 17.0 1.0
CB A:SER59 3.6 18.0 0.7
H A:SER59 3.6 15.8 0.3
H A:SER59 3.6 14.7 0.7
O A:GLN55 3.6 13.1 1.0
CB A:SER59 3.7 16.5 0.3
N A:SER59 3.8 12.2 0.7
N A:SER59 3.9 13.2 0.3
CA A:ALA56 3.9 12.2 1.0
O A:ALA56 3.9 12.5 1.0
C A:ALA56 4.2 11.5 1.0
O A:HOH318 4.2 14.9 0.7
CA A:SER59 4.3 12.9 0.7
C A:CYS58 4.3 12.5 1.0
HB3 A:SER59 4.3 21.6 0.7
H A:CYS58 4.4 14.4 1.0
CA A:SER59 4.4 13.8 0.3
C A:GLN55 4.4 12.0 1.0
CB A:CYS58 4.4 14.2 1.0
O A:HOH451 4.5 24.5 0.9
HB2 A:SER59 4.5 19.7 0.3
O A:HOH435 4.5 37.9 0.8
N A:ALA56 4.5 11.6 1.0
O A:HOH471 4.6 44.6 0.9
N A:CYS58 4.7 12.0 1.0
CA A:CYS58 4.7 12.7 1.0
HB3 A:CYS58 4.7 17.0 1.0
HA A:SER59 4.8 15.4 0.7
O A:HOH337 4.8 40.9 0.8
HB1 A:ALA56 4.8 15.8 1.0
CB A:ALA56 4.9 13.2 1.0
HA A:SER59 5.0 16.5 0.3
O A:TYR115 5.0 16.5 1.0
O A:CYS58 5.0 14.0 1.0

Chlorine binding site 5 out of 5 in 5ogh

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Chlorine binding site 5 out of 5 in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:15.1
occ:0.47
 O A:HOH445 2.2 30.2 1.0
HE21 A:GLN74 2.6 22.1 1.0
NE2 A:GLN74 3.3 18.4 1.0
NE2 A:HIS105 3.3 17.0 1.0
CD2 A:HIS105 3.4 12.3 1.0
HE22 A:GLN74 3.6 22.1 1.0
O A:HOH460 3.6 22.0 0.9
HD2 A:HIS105 3.6 14.8 1.0
HG2 A:GLN74 3.7 17.0 1.0
CE1 A:HIS105 3.8 16.4 1.0
CG A:HIS105 3.9 13.2 1.0
O A:SER75 3.9 12.4 1.0
HA A:TYR76 4.1 14.5 1.0
ND1 A:HIS105 4.1 15.9 1.0
HE1 A:HIS105 4.2 19.7 1.0
O A:TYR76 4.3 13.2 1.0
CD A:GLN74 4.3 16.8 1.0
CG A:GLN74 4.5 14.2 1.0
HB3 A:HIS105 4.7 16.9 1.0
HD1 A:HIS105 4.7 19.1 1.0
C A:TYR76 4.8 11.8 1.0
CB A:HIS105 4.8 14.1 1.0
CA A:TYR76 4.9 12.1 1.0
HB2 A:HIS105 5.0 16.9 1.0

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: Fri Jul 26 14:28:38 2024

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