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Sodium 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:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 13 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in 6jkx

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Sodium binding site 1 out of 13 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 Sodium with other atoms in the Na 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:Na214

b:17.3
occ:1.00
H A:TYR68 2.3 11.3 1.0
HD3 A:PRO13 2.5 12.9 1.0
O A:GLY11 2.7 10.0 1.0
O A:PRO65 2.8 11.2 1.0
H A:THR67 2.8 11.1 1.0
N A:TYR68 2.9 11.0 1.0
HA A:MET66 3.0 12.4 1.0
HA A:ASN12 3.0 12.9 1.0
HA A:TYR68 3.0 10.9 1.0
N A:THR67 3.3 11.1 1.0
CA A:TYR68 3.3 12.4 1.0
CD A:PRO13 3.4 13.0 1.0
C A:TYR68 3.5 11.0 1.0
C A:PRO65 3.5 9.5 1.0
HZ A:PHE26 3.5 9.9 1.0
HB2 A:PRO65 3.6 9.8 1.0
CA A:MET66 3.6 12.6 1.0
C A:MET66 3.6 12.2 1.0
NA A:NA215 3.7 14.7 0.9
C A:GLY11 3.7 9.0 1.0
N A:MET66 3.8 10.3 1.0
CA A:ASN12 3.8 10.2 1.0
OG1 A:THR67 3.8 11.8 1.0
O A:TYR68 3.8 11.2 1.0
HD2 A:PRO13 3.9 12.9 1.0
C A:THR67 3.9 11.4 1.0
N A:MET69 3.9 10.9 1.0
N A:PRO13 4.0 11.9 1.0
CA A:THR67 4.1 11.5 1.0
HA A:MET69 4.1 10.5 1.0
N A:ASN12 4.2 9.8 1.0
C A:ASN12 4.2 11.1 1.0
HG3 A:PRO13 4.2 14.5 1.0
H A:MET69 4.3 10.9 1.0
CZ A:PHE26 4.3 10.6 1.0
CB A:PRO65 4.4 9.7 1.0
CG A:PRO13 4.4 15.0 1.0
H A:GLY11 4.4 9.1 1.0
HG1 A:THR67 4.5 12.8 1.0
O A:MET66 4.5 15.9 1.0
HB3 A:PRO13 4.5 15.2 1.0
CA A:PRO65 4.5 9.1 1.0
CA A:MET69 4.6 10.4 1.0
H A:MET66 4.6 13.5 1.0
CB A:THR67 4.6 12.0 1.0
OD1 A:ASN12 4.7 11.7 1.0
HE1 A:PHE26 4.7 9.9 1.0
HB3 A:PRO65 4.8 9.8 1.0
CB A:TYR68 4.8 14.5 1.0
CB A:PRO13 4.9 15.4 1.0
HA A:THR67 4.9 11.4 1.0
CE1 A:PHE26 5.0 9.1 1.0
CA A:GLY11 5.0 7.8 1.0
CB A:MET66 5.0 14.3 1.0

Sodium binding site 2 out of 13 in 6jkx

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Sodium binding site 2 out of 13 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 Sodium with other atoms in the Na 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:Na215

b:14.7
occ:0.95
H A:GLY11 2.1 9.1 1.0
HA A:LEU10 2.6 9.1 1.0
HB2 A:PRO65 2.7 9.8 1.0
OG A:SER72 2.8 10.1 1.0
O A:GLY11 3.0 10.0 1.0
HD2 A:PRO65 3.0 9.7 1.0
N A:GLY11 3.0 7.6 1.0
HD21 A:LEU10 3.0 9.1 1.0
HG2 A:PRO65 3.1 9.5 1.0
HG A:SER72 3.1 9.3 1.0
HD23 A:LEU10 3.4 9.1 1.0
CA A:LEU10 3.4 7.9 1.0
HA A:MET69 3.4 10.5 1.0
CB A:PRO65 3.5 9.7 1.0
HE1 A:PHE26 3.5 9.9 1.0
HB3 A:LEU10 3.5 8.5 1.0
CG A:PRO65 3.6 9.5 1.0
CD2 A:LEU10 3.6 8.9 1.0
CD A:PRO65 3.7 9.2 1.0
C A:LEU10 3.7 7.7 1.0
NA A:NA214 3.7 17.3 1.0
HB3 A:SER72 3.8 9.3 1.0
CB A:SER72 3.8 9.1 1.0
CB A:LEU10 3.9 8.3 1.0
C A:GLY11 3.9 9.0 1.0
O A:PRO65 3.9 11.2 1.0
SD A:MET69 4.0 10.0 1.0
CA A:GLY11 4.0 7.8 1.0
HB3 A:PRO65 4.1 9.8 1.0
HA A:SER72 4.2 12.8 1.0
O A:GLY9 4.2 8.5 1.0
CE1 A:PHE26 4.3 9.1 1.0
CG A:LEU10 4.3 8.7 1.0
CA A:PRO65 4.4 9.1 1.0
N A:PRO65 4.4 8.3 1.0
CA A:MET69 4.4 10.4 1.0
HD3 A:PRO65 4.4 9.7 1.0
HD22 A:LEU10 4.4 9.1 1.0
HZ A:PHE26 4.5 9.9 1.0
C A:PRO65 4.5 9.5 1.0
HG3 A:PRO65 4.5 9.5 1.0
HB2 A:SER72 4.6 9.3 1.0
CA A:SER72 4.6 9.4 1.0
N A:LEU10 4.6 7.3 1.0
HA3 A:GLY11 4.6 8.1 1.0
HA2 A:GLY11 4.7 8.1 1.0
HE1 A:MET69 4.8 11.1 1.0
CZ A:PHE26 4.8 10.6 1.0
HB2 A:LEU10 4.8 8.5 1.0
OG1 A:THR67 4.8 11.8 1.0
HG1 A:THR67 4.8 12.8 1.0
HD13 A:LEU10 4.9 9.3 1.0
C A:GLY9 4.9 7.2 1.0
O A:TYR68 4.9 11.2 1.0
O A:MET69 4.9 10.2 1.0
CE A:MET69 4.9 11.2 1.0
N A:MET69 4.9 10.9 1.0
O A:LEU10 5.0 8.2 1.0
HE2 A:MET69 5.0 11.1 1.0

Sodium binding site 3 out of 13 in 6jkx

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Sodium binding site 3 out of 13 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 Sodium with other atoms in the Na 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:Na216

b:27.8
occ:1.00
H A:GLU56 2.0 12.9 1.0
N A:GLU56 2.9 12.7 1.0
HE1 A:TYR36 2.9 11.4 1.0
HA A:GLU56 3.0 14.0 1.0
HD1 A:TYR36 3.0 11.4 1.0
CA A:GLU56 3.5 13.8 1.0
HA A:ILE55 3.5 12.9 1.0
CE1 A:TYR36 3.6 13.0 1.0
CD1 A:TYR36 3.6 11.6 1.0
HG2 A:GLU56 3.9 14.9 1.0
CD A:GLU56 3.9 18.8 1.0
H A:GLY57 3.9 12.8 1.0
C A:ILE55 4.0 11.9 1.0
OE1 A:GLU56 4.1 20.4 1.0
O A:ASN54 4.2 15.7 1.0
CA A:ILE55 4.2 12.1 1.0
CG A:GLU56 4.2 16.5 1.0
OE2 A:GLU56 4.3 18.5 1.0
OD1 A:ASN54 4.4 17.4 1.0
CB A:GLU56 4.5 15.9 1.0
C A:GLU56 4.6 13.6 1.0
N A:GLY57 4.6 12.5 1.0
C A:ASN54 4.7 12.0 1.0
HG23 A:ILE55 4.8 14.4 1.0
CZ A:TYR36 4.8 12.9 1.0
N A:ILE55 4.8 10.9 1.0
CG A:TYR36 4.9 10.8 1.0

Sodium binding site 4 out of 13 in 6jkx

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Sodium binding site 4 out of 13 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 Sodium with other atoms in the Na binding site number 4 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:Na217

b:25.4
occ:1.00
O A:HOH512 2.5 26.9 1.0
OG1 A:THR39 2.9 14.7 1.0
HA A:THR39 3.0 12.2 1.0
HG23 A:THR39 3.1 14.5 1.0
O A:HOH423 3.3 20.3 1.0
HG1 A:THR39 3.5 13.2 1.0
CB A:THR39 3.6 13.5 1.0
CA A:THR39 3.7 12.5 1.0
CG2 A:THR39 3.7 14.6 1.0
HG22 A:THR39 4.0 14.5 1.0
H A:LEU40 4.3 12.2 1.0
N A:THR39 4.4 12.4 1.0
O A:HOH368 4.5 21.9 1.0
HB A:THR39 4.5 12.7 1.0
HG21 A:THR39 4.5 14.5 1.0
C A:THR39 4.9 10.9 1.0
H A:THR39 4.9 12.7 1.0
O A:ILE38 4.9 13.0 1.0
N A:LEU40 4.9 11.6 1.0
C A:ILE38 4.9 10.9 1.0

Sodium binding site 5 out of 13 in 6jkx

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Sodium binding site 5 out of 13 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 Sodium with other atoms in the Na binding site number 5 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:Na218

b:24.8
occ:0.90
H A:HIS0 1.9 16.4 1.0
HB2 A:SER-1 2.7 16.4 1.0
O A:HOH347 2.7 28.8 1.0
HB3 A:SER5 2.8 15.0 1.0
O A:ASN3 2.8 18.5 1.0
N A:HIS0 2.9 20.7 1.0
HA A:SER-1 3.0 20.6 1.0
HB2 A:ASN3 3.0 13.4 1.0
OG A:SER5 3.0 15.4 1.0
HB1 A:ALA89 3.1 10.1 1.0
HG A:SER5 3.3 15.0 1.0
O A:HIS0 3.3 19.0 1.0
CB A:SER5 3.4 13.9 1.0
CB A:SER-1 3.4 19.1 1.0
CA A:SER-1 3.5 19.5 1.0
HB2 A:ALA89 3.5 10.1 1.0
C A:SER-1 3.6 19.8 1.0
HB3 A:HIS0 3.7 28.3 1.0
H1 A:MOH206 3.7 17.6 0.8
C A:ASN3 3.7 11.8 1.0
HB3 A:SER-1 3.8 16.4 1.0
CA A:HIS0 3.8 23.1 1.0
HO A:MOH206 3.8 17.6 0.8
CB A:ASN3 3.8 13.3 1.0
HB3 A:ASN3 3.8 13.4 1.0
CB A:ALA89 3.8 10.2 1.0
C A:HIS0 3.8 24.5 1.0
HB2 A:SER5 4.0 15.0 1.0
H A:SER5 4.1 9.2 1.0
N A:SER5 4.1 9.3 1.0
CB A:HIS0 4.2 30.2 1.0
CA A:ASN3 4.3 11.6 1.0
HB3 A:ALA89 4.3 10.1 1.0
CA A:SER5 4.3 9.4 1.0
H A:ASN3 4.5 13.4 1.0
C A:ILE4 4.5 9.6 1.0
C A:MOH206 4.5 19.0 0.8
O A:MOH206 4.5 17.0 0.8
HB2 A:HIS0 4.5 28.3 1.0
HG A:SER-1 4.6 14.1 1.0
N A:ASN3 4.6 16.0 1.0
OG A:SER-1 4.6 14.4 1.0
HA A:HIS0 4.6 23.3 1.0
O A:HOH332 4.6 13.1 1.0
O A:HOH409 4.6 33.2 1.0
HD22 A:ASN3 4.7 26.2 1.0
N A:ILE4 4.7 9.9 1.0
HA A:ILE4 4.7 9.2 0.5
O A:MET1 4.7 24.9 1.0
HA A:ILE4 4.8 9.2 0.5
HA A:SER5 4.8 9.7 1.0
N A:MET1 4.8 23.7 1.0
HA A:ALA89 4.8 9.4 1.0
H3 A:MOH206 4.8 17.6 0.8
O A:SER-1 4.9 23.3 1.0
N A:SER-1 4.9 20.5 1.0
CA A:ILE4 4.9 9.5 0.5
CA A:ALA89 5.0 9.3 1.0
CA A:ILE4 5.0 9.0 0.5
O A:ILE4 5.0 10.8 1.0
O A:HOH353 5.0 22.0 1.0

Sodium binding site 6 out of 13 in 6jkx

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Sodium binding site 6 out of 13 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 Sodium with other atoms in the Na binding site number 6 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:Na219

b:15.8
occ:1.00
H A:ALA153 1.9 10.3 1.0
O A:GLN19 2.8 12.8 1.0
HH2 A:TRP27 2.8 10.4 1.0
N A:ALA153 2.9 10.0 1.0
OE1 A:GLN158 2.9 11.7 1.0
HA A:LYS152 2.9 10.3 1.0
HB3 A:ALA153 3.0 10.5 1.0
HB2 A:ALA153 3.1 10.5 1.0
HZ2 A:TRP27 3.3 10.4 1.0
HG3 A:ARG21 3.3 10.6 1.0
HE1 A:MET161 3.4 12.9 1.0
CB A:ALA153 3.4 9.8 1.0
HG2 A:ARG21 3.5 10.6 1.0
HA A:ARG21 3.6 9.3 1.0
CH2 A:TRP27 3.6 11.8 1.0
HA A:THR20 3.7 10.6 1.0
N A:ARG21 3.7 9.3 1.0
CA A:LYS152 3.7 10.7 1.0
CA A:ALA153 3.7 10.0 1.0
HG3 A:LYS152 3.7 16.5 1.0
CZ2 A:TRP27 3.8 11.4 1.0
C A:LYS152 3.8 10.3 1.0
H A:ARG21 3.8 10.6 1.0
CG A:ARG21 3.8 10.8 1.0
C A:THR20 3.9 9.2 1.0
O A:HOH448 3.9 39.4 1.0
O A:HOH374 3.9 13.3 1.0
C A:GLN19 3.9 10.9 1.0
O A:GLY151 4.0 12.1 1.0
CD A:GLN158 4.1 10.3 1.0
CA A:ARG21 4.1 9.1 1.0
CE A:MET161 4.2 13.0 1.0
HE3 A:MET161 4.2 12.9 1.0
CA A:THR20 4.2 10.6 1.0
HB1 A:ALA153 4.3 10.5 1.0
HE21 A:GLN158 4.3 11.4 1.0
HA A:ALA153 4.4 11.0 1.0
HG2 A:LYS152 4.4 16.5 1.0
CG A:LYS152 4.4 12.7 1.0
O A:THR20 4.4 9.4 1.0
N A:THR20 4.5 10.7 1.0
CB A:ARG21 4.6 10.0 1.0
CB A:LYS152 4.6 11.2 1.0
HE2 A:MET161 4.6 12.9 1.0
NE2 A:GLN158 4.6 11.7 1.0
O A:ALA153 4.7 10.1 1.0
N A:LYS152 4.7 10.6 1.0
C A:ALA153 4.7 10.5 1.0
CZ3 A:TRP27 4.7 10.3 1.0
HB3 A:GLN19 4.8 14.7 1.0
C A:GLY151 4.8 11.4 1.0
HB2 A:GLN158 4.8 10.3 1.0
HB2 A:LYS152 4.9 11.8 1.0
HZ1 A:LYS152 4.9 21.5 1.0
HZ3 A:TRP27 4.9 10.4 1.0
O A:LYS152 5.0 10.9 1.0

Sodium binding site 7 out of 13 in 6jkx

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Sodium binding site 7 out of 13 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 Sodium with other atoms in the Na binding site number 7 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:Na220

b:20.4
occ:1.00
HD2 A:PRO181 2.7 12.5 1.0
NA A:NA222 2.8 18.1 1.0
HG2 A:PRO181 3.0 15.5 1.0
CD A:PRO181 3.5 12.6 1.0
O A:HOH526 3.5 52.8 1.0
HA A:GLN179 3.5 11.3 1.0
CG A:PRO181 3.6 15.2 1.0
HB2 A:PRO181 3.7 15.7 1.0
HD3 A:PRO181 3.9 12.5 1.0
CB A:PRO181 4.2 15.3 1.0
HG2 A:GLN179 4.3 12.3 1.0
H A:GLN182 4.4 11.9 1.0
HG3 A:PRO181 4.4 15.5 1.0
H A:VAL180 4.4 17.5 1.0
CA A:GLN179 4.5 11.1 1.0
O A:GLY178 4.5 12.7 1.0
N A:PRO181 4.6 12.5 1.0
N A:VAL180 4.8 12.1 1.0
C A:GLN179 4.9 11.0 1.0
HB3 A:PRO181 4.9 15.7 1.0
HB3 A:GLN179 4.9 10.8 1.0

Sodium binding site 8 out of 13 in 6jkx

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Sodium binding site 8 out of 13 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 Sodium with other atoms in the Na binding site number 8 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:Na221

b:21.9
occ:1.00
HH12 A:ARG21 2.2 13.2 1.0
NH1 A:ARG21 2.9 14.0 1.0
HA A:HIS148 3.0 19.5 1.0
HA3 A:GLY151 3.0 12.9 1.0
HH11 A:ARG21 3.2 13.2 1.0
O A:HOH302 3.3 36.6 1.0
O A:GLY147 3.5 31.3 1.0
O A:HOH327 3.7 28.2 1.0
HH22 A:ARG21 3.8 13.2 1.0
CA A:HIS148 4.0 20.2 1.0
CA A:GLY151 4.0 13.7 1.0
CZ A:ARG21 4.1 12.1 1.0
O A:HIS148 4.1 16.5 1.0
NH2 A:ARG21 4.3 14.0 1.0
O A:HOH494 4.3 42.0 1.0
C A:GLY147 4.4 33.4 1.0
O A:HOH484 4.4 32.6 1.0
HA2 A:GLY151 4.4 12.9 1.0
ND1 A:HIS148 4.5 21.5 1.0
H A:GLY151 4.5 13.4 1.0
C A:HIS148 4.5 16.2 1.0
N A:HIS148 4.6 24.8 1.0
N A:GLY151 4.7 13.4 1.0
C A:GLY151 4.8 11.4 1.0
CB A:HIS148 4.9 21.9 1.0
H A:LYS152 5.0 12.4 1.0

Sodium binding site 9 out of 13 in 6jkx

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Sodium binding site 9 out of 13 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 Sodium with other atoms in the Na binding site number 9 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:Na222

b:18.1
occ:1.00
H A:GLN182 2.2 11.9 1.0
NA A:NA220 2.8 20.4 1.0
HB3 A:GLN179 2.8 10.8 1.0
HB2 A:GLN182 2.8 12.5 1.0
HD2 A:PRO181 2.8 12.5 1.0
HA A:GLN179 2.9 11.3 1.0
N A:GLN182 3.1 11.6 1.0
HB2 A:PRO181 3.1 15.7 1.0
HB3 A:GLN182 3.2 12.5 1.0
CB A:GLN182 3.4 12.2 1.0
HG2 A:GLN179 3.4 12.3 1.0
CA A:GLN179 3.4 11.1 1.0
CB A:GLN179 3.4 10.6 1.0
C A:GLN179 3.5 11.0 1.0
CD A:PRO181 3.6 12.6 1.0
HE22 A:GLN182 3.6 13.2 1.0
O A:GLN179 3.7 11.8 1.0
N A:PRO181 3.8 12.5 1.0
CA A:GLN182 3.8 12.1 1.0
CB A:PRO181 3.8 15.3 1.0
CG A:GLN179 3.9 11.9 1.0
C A:PRO181 4.0 11.7 1.0
HG2 A:PRO181 4.0 15.5 1.0
CA A:PRO181 4.1 12.8 1.0
CG A:PRO181 4.1 15.2 1.0
N A:VAL180 4.1 12.1 1.0
HE22 A:GLN179 4.2 13.1 1.0
HB2 A:GLN179 4.3 10.8 1.0
H A:VAL180 4.3 17.5 1.0
H A:ALA183 4.3 11.0 1.0
HA A:GLN182 4.4 12.2 1.0
HD3 A:PRO181 4.4 12.5 1.0
NE2 A:GLN182 4.4 14.3 1.0
C A:VAL180 4.6 11.9 1.0
HG3 A:GLN179 4.6 12.3 1.0
HB3 A:PRO181 4.7 15.7 1.0
NE2 A:GLN179 4.7 13.4 1.0
CG A:GLN182 4.8 13.2 1.0
N A:GLN179 4.8 10.5 1.0
CD A:GLN179 4.8 12.8 1.0
HE21 A:GLN182 5.0 13.2 1.0
C A:GLN182 5.0 11.9 1.0

Sodium binding site 10 out of 13 in 6jkx

Go back to Sodium Binding Sites List in 6jkx
Sodium binding site 10 out of 13 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 Sodium with other atoms in the Na binding site number 10 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:Na223

b:16.7
occ:1.00
HH11 A:ARG131 2.2 11.4 1.0
HG2 A:ARG131 2.6 8.6 1.0
O A:HOH415 2.8 37.7 1.0
NE2 A:HIS94 2.9 9.1 1.0
HD3 A:ARG131 2.9 10.9 1.0
CE A:LYS107 3.0 20.4 0.5
NH1 A:ARG131 3.1 10.8 1.0
HB2 A:ARG131 3.1 9.0 1.0
HG2 A:ARG133 3.2 12.8 1.0
HB3 A:ARG131 3.2 9.0 1.0
CG A:ARG131 3.2 8.5 1.0
HD12 A:LEU118 3.4 12.3 1.0
HD2 A:ARG133 3.4 16.1 1.0
CB A:ARG131 3.4 8.1 1.0
HE1 A:HIS94 3.4 9.1 1.0
HH12 A:ARG131 3.4 11.4 1.0
HD13 A:LEU118 3.5 12.3 1.0
NZ A:LYS107 3.5 23.4 0.5
CD A:ARG131 3.5 9.6 1.0
CE1 A:HIS94 3.5 8.8 1.0
HE A:ARG133 3.8 18.3 1.0
CG A:ARG133 3.8 10.5 1.0
CD1 A:LEU118 3.8 12.4 1.0
CD A:ARG133 3.9 13.9 1.0
NE A:ARG133 3.9 16.7 1.0
HG3 A:ARG133 3.9 12.8 1.0
CZ A:ARG131 4.1 9.6 1.0
CD2 A:HIS94 4.1 8.6 1.0
HG3 A:ARG131 4.1 8.6 1.0
HD11 A:LEU118 4.1 12.3 1.0
NE A:ARG131 4.2 9.1 1.0
HD2 A:ARG131 4.3 10.9 1.0
CD A:LYS107 4.3 16.2 0.5
HD2 A:HIS94 4.4 9.1 1.0
O A:GLY111 4.4 18.0 1.0
CG A:LYS107 4.5 13.5 0.5
OE1 A:GLU96 4.6 13.4 1.0
CB A:LYS107 4.7 11.9 0.5
CZ A:ARG133 4.7 23.4 1.0
ND1 A:HIS94 4.7 8.7 1.0
HD3 A:ARG133 4.8 16.1 1.0
CA A:ARG131 4.9 7.6 1.0
HD22 A:LEU118 5.0 10.7 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: Tue Oct 8 11:27:19 2024

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