Potassium in PDB 1m40: Ultra High Resolution Crystal Structure of Tem-1
Enzymatic activity of Ultra High Resolution Crystal Structure of Tem-1
All present enzymatic activity of Ultra High Resolution Crystal Structure of Tem-1:
3.5.2.6;
Protein crystallography data
The structure of Ultra High Resolution Crystal Structure of Tem-1, PDB code: 1m40
was solved by
G.Minasov,
X.Wang,
B.K.Shoichet,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
10.00 /
0.85
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.313,
61.641,
89.252,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
9.1 /
11.2
|
Potassium Binding Sites:
The binding sites of Potassium atom in the Ultra High Resolution Crystal Structure of Tem-1
(pdb code 1m40). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the
Ultra High Resolution Crystal Structure of Tem-1, PDB code: 1m40:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
Potassium binding site 1 out
of 6 in 1m40
Go back to
Potassium Binding Sites List in 1m40
Potassium binding site 1 out
of 6 in the Ultra High Resolution Crystal Structure of Tem-1
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Ultra High Resolution Crystal Structure of Tem-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1000
b:14.7
occ:0.65
|
K
|
A:K1000
|
0.0
|
14.7
|
0.7
|
|
K
|
A:K1000
|
2.3
|
16.1
|
0.3
|
|
O
|
A:LEU57
|
2.8
|
8.2
|
0.4
|
|
OE1
|
A:GLU58
|
2.8
|
11.1
|
0.6
|
|
OE1
|
A:GLU58
|
3.0
|
9.3
|
0.4
|
|
O
|
A:LEU57
|
3.1
|
8.7
|
0.6
|
|
HA
|
A:GLU58
|
3.4
|
8.2
|
0.6
|
|
HA
|
A:GLU58
|
3.5
|
10.7
|
0.4
|
|
O
|
A:HOH1088
|
3.5
|
17.3
|
1.0
|
|
CD
|
A:GLU58
|
3.6
|
7.8
|
0.4
|
|
O
|
A:HOH1033
|
3.7
|
11.6
|
1.0
|
|
CD
|
A:GLU58
|
3.7
|
10.3
|
0.6
|
|
O
|
A:HOH1161
|
3.7
|
18.8
|
0.6
|
|
C
|
A:LEU57
|
3.9
|
7.3
|
0.4
|
|
OE2
|
A:GLU58
|
3.9
|
9.2
|
0.4
|
|
OE2
|
A:GLU58
|
4.0
|
10.4
|
0.6
|
|
C
|
A:LEU57
|
4.0
|
8.8
|
0.6
|
|
CA
|
A:GLU58
|
4.3
|
6.8
|
0.6
|
|
O
|
A:HOH1016
|
4.3
|
11.3
|
1.0
|
|
CA
|
A:GLU58
|
4.3
|
8.9
|
0.4
|
|
N
|
A:GLU58
|
4.5
|
7.3
|
0.6
|
|
N
|
A:GLU58
|
4.6
|
8.2
|
0.4
|
|
CG
|
A:GLU58
|
4.7
|
7.5
|
0.4
|
|
HA
|
A:LEU57
|
4.7
|
9.6
|
0.4
|
|
CG
|
A:GLU58
|
4.7
|
9.4
|
0.6
|
|
HG2
|
A:GLU58
|
4.8
|
9.1
|
0.4
|
|
O
|
A:HOH1183
|
4.9
|
16.4
|
0.5
|
|
HB2
|
A:GLU58
|
4.9
|
10.2
|
0.6
|
|
CB
|
A:GLU58
|
4.9
|
8.5
|
0.6
|
|
HA
|
A:LEU57
|
4.9
|
10.1
|
0.6
|
|
HG3
|
A:GLU58
|
4.9
|
11.2
|
0.6
|
|
CA
|
A:LEU57
|
4.9
|
8.0
|
0.4
|
|
H
|
A:SER59
|
4.9
|
11.1
|
0.4
|
|
O
|
A:ILE56
|
5.0
|
11.2
|
0.6
|
|
Potassium binding site 2 out
of 6 in 1m40
Go back to
Potassium Binding Sites List in 1m40
Potassium binding site 2 out
of 6 in the Ultra High Resolution Crystal Structure of Tem-1
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Ultra High Resolution Crystal Structure of Tem-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1000
b:16.1
occ:0.35
|
K
|
A:K1000
|
0.0
|
16.1
|
0.3
|
|
O
|
A:HOH1161
|
1.6
|
18.8
|
0.6
|
|
K
|
A:K1000
|
2.3
|
14.7
|
0.7
|
|
O
|
A:HOH1088
|
2.6
|
17.3
|
1.0
|
|
O
|
A:LEU57
|
2.6
|
8.2
|
0.4
|
|
O
|
A:LEU57
|
2.7
|
8.7
|
0.6
|
|
O
|
A:HOH1183
|
3.1
|
16.4
|
0.5
|
|
OE2
|
A:GLU58
|
3.6
|
9.2
|
0.4
|
|
C
|
A:LEU57
|
3.7
|
7.3
|
0.4
|
|
HA
|
A:LEU57
|
3.8
|
9.6
|
0.4
|
|
C
|
A:LEU57
|
3.8
|
8.8
|
0.6
|
|
CD
|
A:GLU58
|
3.9
|
7.8
|
0.4
|
|
HA
|
A:LEU57
|
3.9
|
10.1
|
0.6
|
|
OE1
|
A:GLU58
|
4.0
|
9.3
|
0.4
|
|
OE2
|
A:GLU58
|
4.0
|
10.4
|
0.6
|
|
OE1
|
A:GLU58
|
4.1
|
11.1
|
0.6
|
|
CA
|
A:LEU57
|
4.3
|
8.0
|
0.4
|
|
CD
|
A:GLU58
|
4.3
|
10.3
|
0.6
|
|
O
|
A:HOH1183
|
4.4
|
12.1
|
0.5
|
|
O
|
A:HOH1293
|
4.4
|
18.7
|
0.5
|
|
CA
|
A:LEU57
|
4.5
|
8.4
|
0.6
|
|
HA
|
A:GLU58
|
4.6
|
8.2
|
0.6
|
|
HG2
|
A:GLU58
|
4.6
|
9.1
|
0.4
|
|
HA
|
A:GLU58
|
4.6
|
10.7
|
0.4
|
|
HB3
|
A:LEU57
|
4.6
|
9.9
|
0.4
|
|
HD23
|
A:LEU57
|
4.7
|
14.5
|
0.4
|
|
HB3
|
A:LEU57
|
4.8
|
10.3
|
0.6
|
|
N
|
A:GLU58
|
4.8
|
8.2
|
0.4
|
|
CG
|
A:GLU58
|
4.9
|
7.5
|
0.4
|
|
O
|
A:ILE56
|
4.9
|
11.2
|
0.6
|
|
N
|
A:GLU58
|
4.9
|
7.3
|
0.6
|
|
H3
|
A:HIS26
|
4.9
|
13.8
|
0.4
|
|
HB2
|
A:GLU58
|
5.0
|
10.2
|
0.6
|
|
Potassium binding site 3 out
of 6 in 1m40
Go back to
Potassium Binding Sites List in 1m40
Potassium binding site 3 out
of 6 in the Ultra High Resolution Crystal Structure of Tem-1
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Ultra High Resolution Crystal Structure of Tem-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1001
b:9.6
occ:0.50
|
O
|
A:HOH1203
|
1.6
|
22.1
|
0.5
|
|
O
|
A:TYR97
|
2.5
|
20.4
|
0.5
|
|
O
|
A:TYR97
|
2.6
|
9.0
|
0.5
|
|
O
|
A:LEU113
|
2.7
|
9.8
|
1.0
|
|
O
|
A:HOH1098
|
2.8
|
16.2
|
1.0
|
|
O
|
A:HOH1192
|
3.0
|
20.6
|
0.5
|
|
O
|
A:HOH1203
|
3.0
|
14.9
|
0.5
|
|
O
|
A:HOH1086
|
3.3
|
10.9
|
0.4
|
|
HA
|
A:SER98
|
3.5
|
10.4
|
0.5
|
|
HA
|
A:SER98
|
3.6
|
10.9
|
0.5
|
|
C
|
A:TYR97
|
3.7
|
9.0
|
1.0
|
|
HG
|
A:SER98
|
3.7
|
13.6
|
0.5
|
|
O
|
A:HOH1086
|
3.8
|
11.7
|
0.6
|
|
C
|
A:LEU113
|
3.8
|
8.8
|
1.0
|
|
HA
|
A:THR114
|
4.0
|
11.7
|
1.0
|
|
H
|
A:TYR97
|
4.0
|
10.8
|
1.0
|
|
O
|
A:HOH1205
|
4.1
|
16.6
|
0.7
|
|
CB
|
A:SER98
|
4.2
|
8.9
|
0.5
|
|
HB3
|
A:LEU113
|
4.2
|
11.2
|
1.0
|
|
CA
|
A:SER98
|
4.2
|
9.1
|
0.5
|
|
HB3
|
A:HIS96
|
4.3
|
13.7
|
1.0
|
|
OG
|
A:SER98
|
4.3
|
9.1
|
0.5
|
|
O
|
A:THR114
|
4.3
|
12.3
|
0.4
|
|
CA
|
A:SER98
|
4.3
|
8.7
|
0.5
|
|
N
|
A:TYR97
|
4.4
|
9.0
|
1.0
|
|
O
|
A:THR114
|
4.4
|
9.8
|
0.6
|
|
N
|
A:SER98
|
4.4
|
7.6
|
0.5
|
|
N
|
A:SER98
|
4.5
|
9.6
|
0.5
|
|
HA
|
A:LEU113
|
4.5
|
10.4
|
1.0
|
|
O
|
A:HOH1205
|
4.5
|
18.0
|
0.3
|
|
CA
|
A:THR114
|
4.6
|
9.7
|
1.0
|
|
CA
|
A:LEU113
|
4.7
|
8.6
|
1.0
|
|
C
|
A:THR114
|
4.7
|
9.5
|
1.0
|
|
CA
|
A:TYR97
|
4.7
|
9.0
|
1.0
|
|
O
|
A:HOH1108
|
4.7
|
18.7
|
1.0
|
|
N
|
A:THR114
|
4.7
|
9.3
|
1.0
|
|
CB
|
A:SER98
|
4.9
|
8.6
|
0.5
|
|
CB
|
A:LEU113
|
4.9
|
9.3
|
1.0
|
|
HD23
|
A:LEU113
|
4.9
|
16.6
|
1.0
|
|
Potassium binding site 4 out
of 6 in 1m40
Go back to
Potassium Binding Sites List in 1m40
Potassium binding site 4 out
of 6 in the Ultra High Resolution Crystal Structure of Tem-1
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Ultra High Resolution Crystal Structure of Tem-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1002
b:13.8
occ:0.10
|
K
|
A:K1002
|
0.0
|
13.8
|
0.1
|
|
K
|
A:K1002
|
1.2
|
10.2
|
0.4
|
|
O
|
A:HOH1241
|
1.8
|
27.1
|
0.8
|
|
O
|
A:HOH1554
|
2.7
|
13.0
|
0.2
|
|
O
|
A:HOH1075
|
2.7
|
14.4
|
1.0
|
|
O
|
A:HOH1054
|
2.8
|
14.6
|
1.0
|
|
O
|
A:HOH1554
|
3.4
|
12.3
|
0.2
|
|
O
|
A:HOH1068
|
3.6
|
19.0
|
1.0
|
|
O
|
A:HOH1554
|
3.8
|
22.7
|
0.4
|
|
O
|
A:LYS111
|
3.9
|
13.6
|
0.4
|
|
O
|
A:LYS111
|
3.9
|
9.6
|
0.6
|
|
O
|
A:HOH1035
|
4.1
|
13.6
|
1.0
|
|
HB
|
A:THR114
|
4.2
|
13.4
|
1.0
|
|
O
|
A:HOH1298
|
4.4
|
18.2
|
0.5
|
|
O
|
A:HOH1298
|
4.6
|
18.4
|
0.5
|
|
OG1
|
A:THR114
|
4.7
|
13.9
|
1.0
|
|
O
|
A:HOH1015
|
4.8
|
11.9
|
1.0
|
|
H
|
A:THR114
|
4.8
|
11.1
|
1.0
|
|
HA
|
A:HIS112
|
4.8
|
11.2
|
1.0
|
|
CB
|
A:THR114
|
4.9
|
11.1
|
1.0
|
|
C
|
A:LYS111
|
5.0
|
9.8
|
0.4
|
|
Potassium binding site 5 out
of 6 in 1m40
Go back to
Potassium Binding Sites List in 1m40
Potassium binding site 5 out
of 6 in the Ultra High Resolution Crystal Structure of Tem-1
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Ultra High Resolution Crystal Structure of Tem-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1002
b:10.2
occ:0.40
|
K
|
A:K1002
|
0.0
|
10.2
|
0.4
|
|
K
|
A:K1002
|
1.2
|
13.8
|
0.1
|
|
O
|
A:HOH1554
|
1.6
|
13.0
|
0.2
|
|
O
|
A:HOH1554
|
2.2
|
12.3
|
0.2
|
|
O
|
A:HOH1554
|
2.7
|
22.7
|
0.4
|
|
O
|
A:HOH1054
|
2.8
|
14.6
|
1.0
|
|
O
|
A:HOH1075
|
2.9
|
14.4
|
1.0
|
|
O
|
A:HOH1241
|
3.0
|
27.1
|
0.8
|
|
OG1
|
A:THR114
|
4.1
|
13.9
|
1.0
|
|
HB
|
A:THR114
|
4.1
|
13.4
|
1.0
|
|
O
|
A:HOH1160
|
4.1
|
23.4
|
1.0
|
|
O
|
A:LYS111
|
4.4
|
13.6
|
0.4
|
|
O
|
A:HOH1015
|
4.4
|
11.9
|
1.0
|
|
O
|
A:LYS111
|
4.5
|
9.6
|
0.6
|
|
O
|
A:HOH1347
|
4.6
|
24.7
|
0.7
|
|
O
|
A:HOH1068
|
4.7
|
19.0
|
1.0
|
|
CB
|
A:THR114
|
4.7
|
11.1
|
1.0
|
|
H
|
A:THR114
|
4.7
|
11.1
|
1.0
|
|
O
|
A:HOH1035
|
4.7
|
13.6
|
1.0
|
|
Potassium binding site 6 out
of 6 in 1m40
Go back to
Potassium Binding Sites List in 1m40
Potassium binding site 6 out
of 6 in the Ultra High Resolution Crystal Structure of Tem-1
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Ultra High Resolution Crystal Structure of Tem-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1003
b:9.1
occ:0.55
|
HB2
|
A:ASP214
|
0.4
|
9.5
|
0.4
|
|
CB
|
A:ASP214
|
1.3
|
7.9
|
0.4
|
|
HB3
|
A:ASP214
|
1.9
|
9.5
|
0.4
|
|
CG
|
A:ASP214
|
2.1
|
7.5
|
0.4
|
|
CA
|
A:ASP214
|
2.4
|
7.9
|
0.4
|
|
OD2
|
A:ASP214
|
2.5
|
7.8
|
0.4
|
|
O
|
A:ASP233
|
2.5
|
7.2
|
1.0
|
|
O
|
A:MET211
|
2.6
|
8.3
|
0.4
|
|
O
|
A:MET211
|
2.6
|
7.6
|
0.6
|
|
O
|
A:ALA213
|
2.6
|
10.8
|
0.6
|
|
HA
|
A:ASP214
|
2.6
|
9.5
|
0.4
|
|
O
|
A:HOH1421
|
2.7
|
9.4
|
0.6
|
|
OD1
|
A:ASP233
|
2.9
|
9.3
|
1.0
|
|
N
|
A:ASP214
|
2.9
|
7.9
|
0.4
|
|
OD1
|
A:ASP214
|
3.1
|
8.3
|
0.4
|
|
HA
|
A:MET211
|
3.1
|
9.2
|
1.0
|
|
HB2
|
A:ASP214
|
3.1
|
11.3
|
0.6
|
|
HH22
|
A:ARG222
|
3.3
|
10.8
|
0.6
|
|
H
|
A:ASP233
|
3.3
|
8.0
|
1.0
|
|
HG22
|
A:ILE127
|
3.4
|
12.2
|
0.3
|
|
C
|
A:MET211
|
3.5
|
7.3
|
1.0
|
|
C
|
A:ASP233
|
3.5
|
6.5
|
1.0
|
|
HH21
|
A:ARG222
|
3.7
|
8.4
|
0.4
|
|
C
|
A:ASP214
|
3.7
|
8.5
|
0.4
|
|
CA
|
A:MET211
|
3.8
|
7.7
|
1.0
|
|
C
|
A:ALA213
|
3.8
|
8.7
|
0.6
|
|
HA
|
A:LYS234
|
3.9
|
7.6
|
1.0
|
|
HA
|
A:THR128
|
3.9
|
9.8
|
0.7
|
|
O
|
A:ILE127
|
3.9
|
9.0
|
0.3
|
|
CB
|
A:ASP214
|
3.9
|
9.4
|
0.6
|
|
HG23
|
A:ILE127
|
3.9
|
12.5
|
0.7
|
|
NH2
|
A:ARG222
|
4.0
|
9.0
|
0.6
|
|
N
|
A:ASP233
|
4.0
|
6.6
|
1.0
|
|
O
|
A:TRP210
|
4.1
|
8.8
|
1.0
|
|
HG21
|
A:ILE127
|
4.1
|
12.2
|
0.3
|
|
CG
|
A:ASP233
|
4.1
|
8.3
|
1.0
|
|
CG2
|
A:ILE127
|
4.1
|
8.1
|
0.3
|
|
HG21
|
A:ILE127
|
4.1
|
12.5
|
0.7
|
|
HA
|
A:THR128
|
4.2
|
10.4
|
0.3
|
|
NH2
|
A:ARG222
|
4.2
|
7.0
|
0.4
|
|
C
|
A:ALA213
|
4.2
|
7.8
|
0.4
|
|
CA
|
A:ASP214
|
4.2
|
8.2
|
0.6
|
|
HH21
|
A:ARG222
|
4.2
|
10.8
|
0.6
|
|
OD2
|
A:ASP214
|
4.2
|
9.6
|
0.6
|
|
CA
|
A:ASP233
|
4.3
|
6.4
|
1.0
|
|
O
|
A:ASP214
|
4.3
|
8.5
|
0.4
|
|
O
|
A:ILE127
|
4.3
|
9.1
|
0.7
|
|
HG23
|
A:ILE127
|
4.3
|
12.2
|
0.3
|
|
HH22
|
A:ARG222
|
4.4
|
8.4
|
0.4
|
|
HB3
|
A:MET211
|
4.4
|
9.0
|
1.0
|
|
N
|
A:LYS234
|
4.4
|
6.5
|
1.0
|
|
CG
|
A:ASP214
|
4.4
|
9.2
|
0.6
|
|
HD2
|
A:LYS234
|
4.5
|
8.7
|
1.0
|
|
HE
|
A:ARG222
|
4.5
|
9.0
|
0.6
|
|
CG2
|
A:ILE127
|
4.5
|
8.4
|
0.7
|
|
N
|
A:ASP214
|
4.5
|
9.5
|
0.6
|
|
H
|
A:LYS215
|
4.5
|
9.5
|
0.4
|
|
CA
|
A:LYS234
|
4.6
|
6.3
|
1.0
|
|
N
|
A:LYS215
|
4.6
|
7.9
|
0.4
|
|
N
|
A:GLU212
|
4.6
|
8.8
|
0.6
|
|
C
|
A:ILE127
|
4.6
|
7.5
|
0.3
|
|
N
|
A:ALA213
|
4.6
|
8.3
|
0.6
|
|
HB3
|
A:ASP214
|
4.6
|
11.3
|
0.6
|
|
N
|
A:GLU212
|
4.7
|
7.5
|
0.4
|
|
CB
|
A:MET211
|
4.7
|
7.5
|
1.0
|
|
C
|
A:GLU212
|
4.7
|
7.6
|
0.6
|
|
O
|
A:HOH1046
|
4.7
|
10.1
|
1.0
|
|
CB
|
A:ASP233
|
4.8
|
6.9
|
1.0
|
|
N
|
A:ALA213
|
4.8
|
7.9
|
0.4
|
|
C
|
A:GLU212
|
4.8
|
9.3
|
0.4
|
|
HG2
|
A:MET211
|
4.8
|
9.5
|
1.0
|
|
N
|
A:MET211
|
4.8
|
8.0
|
1.0
|
|
HB3
|
A:ALA217
|
4.8
|
8.3
|
0.4
|
|
HG22
|
A:ILE127
|
4.8
|
12.5
|
0.7
|
|
CA
|
A:THR128
|
4.9
|
8.1
|
0.7
|
|
HB2
|
A:LYS234
|
4.9
|
7.8
|
1.0
|
|
HE
|
A:ARG222
|
4.9
|
10.9
|
0.4
|
|
CA
|
A:ALA213
|
4.9
|
8.8
|
0.6
|
|
C
|
A:TRP210
|
4.9
|
7.9
|
1.0
|
|
O
|
A:ALA213
|
4.9
|
9.1
|
0.4
|
|
CZ
|
A:ARG222
|
4.9
|
8.5
|
0.6
|
|
HA
|
A:GLU212
|
4.9
|
11.0
|
0.4
|
|
C
|
A:ILE127
|
5.0
|
7.2
|
0.7
|
|
Reference:
G.Minasov,
X.Wang,
B.K.Shoichet.
An Ultrahigh Resolution Structure of Tem-1 Beta-Lactamase Suggests A Role For GLU166 As the General Base in Acylation. J.Am.Chem.Soc. V. 124 5333 2002.
ISSN: ISSN 0002-7863
PubMed: 11996574
DOI: 10.1021/JA0259640
Page generated: Sun Dec 13 22:50:18 2020
|
