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:
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
Go back to
Sodium Binding Sites List in 6jkx
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
Go back to
Sodium Binding Sites List in 6jkx
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
Go back to
Sodium Binding Sites List in 6jkx
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
Go back to
Sodium Binding Sites List in 6jkx
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
Go back to
Sodium Binding Sites List in 6jkx
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
Go back to
Sodium Binding Sites List in 6jkx
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
Go back to
Sodium Binding Sites List in 6jkx
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
Go back to
Sodium Binding Sites List in 6jkx
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 Sites List in 6jkx
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 Dec 15 12:25:32 2020
|
