Chlorine in PDB 6jkx: Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution.

Enzymatic activity of Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution.

All present enzymatic activity of Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution.:
3.1.1.29;

Protein crystallography data

The structure of Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution., PDB code: 6jkx was solved by V.Viswanathan, P.Sharma, A.Bhushan, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.03 / 1.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.151, 66.264, 76.299, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 17.8

Other elements in 6jkx:

The structure of Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution. also contains other interesting chemical elements:

Sodium (Na) 13 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution. (pdb code 6jkx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution., PDB code: 6jkx:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6jkx

Go back to Chlorine Binding Sites List in 6jkx
Chlorine binding site 1 out of 3 in the Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:21.0
occ:0.90
 HH11 A:ARG133 2.4 18.6 1.0
HD2 A:ARG105 3.0 33.6 1.0
NH1 A:ARG133 3.1 30.2 1.0
O A:HOH310 3.1 27.9 1.0
HD3 A:ARG133 3.2 16.1 1.0
HB3 A:ARG105 3.2 12.1 1.0
HH12 A:ARG133 3.3 18.6 1.0
HD3 A:ARG105 3.5 33.5 1.0
HB2 A:ARG105 3.6 12.1 1.0
CD A:ARG105 3.7 26.6 1.0
CB A:LYS107 3.8 13.7 0.5
CB A:ARG105 3.8 12.2 1.0
HD2 A:ARG133 3.9 16.1 1.0
CD A:LYS107 3.9 18.1 0.5
HH11 A:ARG105 3.9 41.7 1.0
CD A:ARG133 4.0 13.9 1.0
CD A:LYS107 4.1 16.2 0.5
CB A:LYS107 4.1 11.9 0.5
CG A:LYS107 4.2 15.7 0.5
CZ A:ARG133 4.2 23.4 1.0
CG A:ARG105 4.4 17.9 1.0
CG A:LYS107 4.5 13.5 0.5
NE A:ARG133 4.5 16.7 1.0
O A:HOH303 4.6 35.3 1.0
HD21 A:ASN188 4.6 16.5 1.0
O A:LEU106 4.6 13.5 1.0
CA A:LYS107 4.6 11.1 0.5
CA A:LYS107 4.6 11.1 0.5
NH1 A:ARG105 4.7 53.8 1.0
C A:LEU106 4.8 9.6 1.0
HO A:MOH210 4.8 25.5 0.9
NE A:ARG105 4.8 47.0 1.0
N A:LYS107 4.9 9.6 1.0
HG3 A:ARG105 4.9 17.1 1.0
CE A:LYS107 4.9 22.1 0.5
O A:HOH430 4.9 37.7 1.0

Chlorine binding site 2 out of 3 in 6jkx

Go back to Chlorine Binding Sites List in 6jkx
Chlorine binding site 2 out of 3 in the Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:25.0
occ:0.80
 HD1 A:HIS124 2.1 12.1 1.0
HA A:HIS124 2.9 12.3 1.0
ND1 A:HIS124 2.9 12.0 1.0
O A:HOH441 3.0 33.5 1.0
HB3 A:HIS124 3.3 11.8 1.0
CA A:HIS124 3.7 12.3 1.0
CB A:HIS124 3.7 12.9 1.0
CG A:HIS124 3.7 11.0 1.0
CE1 A:HIS124 4.0 12.4 1.0
O A:HIS124 4.1 17.9 1.0
HE1 A:HIS124 4.2 12.1 1.0
HZ3 A:LYS81 4.3 36.2 1.0
HG12 A:VAL77 4.4 14.1 1.0
C A:HIS124 4.4 14.2 1.0
HZ2 A:LYS81 4.5 36.4 1.0
HB2 A:HIS124 4.7 11.7 1.0
O A:PRO123 4.8 14.1 1.0
N A:HIS124 4.8 11.4 1.0
NZ A:LYS81 4.8 84.6 1.0
CD2 A:HIS124 5.0 12.3 1.0

Chlorine binding site 3 out of 3 in 6jkx

Go back to Chlorine Binding Sites List in 6jkx
Chlorine binding site 3 out of 3 in the Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:13.9
occ:0.85
 HD21 A:ASN12 2.5 12.0 1.0
HD2 A:HIS22 2.8 13.2 1.0
HB3 A:MET69 2.9 10.8 1.0
O A:HOH432 3.1 31.3 1.0
HD22 A:LEU150 3.2 16.4 1.0
O A:HOH391 3.2 18.1 1.0
O A:HOH507 3.3 41.9 1.0
OD1 A:ASN116 3.4 18.9 1.0
ND2 A:ASN12 3.4 12.4 1.0
CD2 A:HIS22 3.5 11.2 1.0
HD21 A:ASN116 3.5 11.9 1.0
HB2 A:MET69 3.7 10.8 1.0
CB A:MET69 3.7 10.6 1.0
NE2 A:HIS22 3.7 12.3 1.0
HD22 A:ASN12 3.8 12.0 1.0
HG2 A:MET69 3.9 11.3 1.0
HD12 A:LEU150 4.0 18.6 1.0
ND2 A:ASN116 4.1 12.3 1.0
OD1 A:ASN12 4.2 11.7 1.0
CD2 A:LEU150 4.2 16.8 1.0
CG A:ASN116 4.2 13.3 1.0
CG A:ASN12 4.2 11.6 1.0
H A:MET69 4.3 10.9 1.0
CG A:MET69 4.4 10.6 1.0
H A:ASN70 4.5 11.6 1.0
HD23 A:LEU150 4.6 16.4 1.0
HD21 A:LEU150 4.6 16.4 1.0
CG A:HIS22 4.7 10.4 1.0
HG3 A:MET69 4.8 11.3 1.0
CD1 A:LEU150 4.8 19.7 1.0
HG A:LEU150 4.9 16.1 1.0
HG23 A:VAL149 4.9 15.6 1.0
CA A:MET69 4.9 10.4 1.0
HB3 A:ASN70 4.9 17.9 1.0
O A:HOH483 4.9 35.9 1.0
N A:MET69 5.0 10.9 1.0
CG A:LEU150 5.0 16.7 1.0
HD22 A:ASN116 5.0 11.9 1.0

Reference:

V.Viswanathan, P.Sharma, A.Bhushan, S.Sharma, T.P.Singh. Crystal Structure of Peptidyl-Trna Hydrolase with Multiple Sodium and Chloride Ions at 1.08 A Resolution. To Be Published.
Page generated: Sat Dec 12 13:11:37 2020

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