Platinum in PDB 1rli: The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Protein crystallography data
The structure of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis, PDB code: 1rli
was solved by
Y.Kim,
P.Quartey,
A.Joachimiak,
Midwest Center For Structuralgenomics (Mcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.79 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.993,
90.666,
63.446,
90.00,
97.02,
90.00
|
R / Rfree (%)
|
19.6 /
23
|
Platinum Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Platinum atom in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
(pdb code 1rli). This binding sites where shown within
5.0 Angstroms radius around Platinum atom.
In total 11 binding sites of Platinum where determined in the
The Structure of Trp Repressor Binding Protein From Bacillus Subtilis, PDB code: 1rli:
Jump to Platinum binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Platinum binding site 1 out
of 11 in 1rli
Go back to
Platinum Binding Sites List in 1rli
Platinum binding site 1 out
of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 1 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pt601
b:53.6
occ:0.73
|
O
|
A:HOH607
|
2.1
|
15.3
|
1.0
|
O
|
A:HOH690
|
2.3
|
34.2
|
1.0
|
O
|
A:HOH689
|
2.5
|
35.9
|
1.0
|
O
|
A:HOH646
|
2.5
|
30.6
|
1.0
|
CG
|
A:MET83
|
2.8
|
24.5
|
1.0
|
CE
|
A:MET83
|
3.2
|
28.7
|
1.0
|
SD
|
A:MET83
|
3.5
|
30.3
|
1.0
|
O
|
A:HOH613
|
3.5
|
24.5
|
1.0
|
N
|
A:MET83
|
3.7
|
16.2
|
1.0
|
O
|
D:HOH624
|
3.8
|
23.2
|
1.0
|
CB
|
A:MET83
|
4.0
|
19.6
|
1.0
|
OE1
|
A:GLN135
|
4.0
|
26.5
|
1.0
|
CD
|
A:LYS88
|
4.1
|
21.0
|
1.0
|
CA
|
A:MET83
|
4.5
|
16.8
|
1.0
|
CD1
|
A:LEU132
|
4.6
|
19.2
|
1.0
|
CB
|
A:LYS88
|
4.6
|
17.8
|
1.0
|
CA
|
A:GLY82
|
4.7
|
16.0
|
1.0
|
C
|
A:GLY82
|
4.7
|
16.0
|
1.0
|
CE
|
A:LYS88
|
4.7
|
20.0
|
1.0
|
NE2
|
D:GLN135
|
4.8
|
25.5
|
1.0
|
CG
|
A:LYS88
|
4.8
|
18.3
|
1.0
|
CD
|
A:GLN135
|
4.8
|
25.9
|
1.0
|
CE
|
D:LYS88
|
4.9
|
17.7
|
1.0
|
NZ
|
A:LYS88
|
5.0
|
21.9
|
1.0
|
|
Platinum binding site 2 out
of 11 in 1rli
Go back to
Platinum Binding Sites List in 1rli
Platinum binding site 2 out
of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 2 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pt605
b:57.9
occ:0.76
|
O
|
A:HOH705
|
2.4
|
45.2
|
1.0
|
NE2
|
A:HIS70
|
2.4
|
40.1
|
1.0
|
O
|
A:HOH707
|
2.9
|
49.7
|
1.0
|
NZ
|
A:LYS2
|
3.2
|
51.0
|
1.0
|
CD2
|
A:HIS70
|
3.3
|
38.2
|
1.0
|
CE
|
A:LYS2
|
3.4
|
50.3
|
1.0
|
CE1
|
A:HIS70
|
3.5
|
38.5
|
1.0
|
CD
|
A:LYS2
|
3.5
|
48.7
|
1.0
|
CB
|
A:LYS2
|
3.8
|
42.9
|
1.0
|
O
|
A:HOH706
|
4.1
|
49.2
|
1.0
|
CG
|
A:LYS2
|
4.3
|
47.5
|
1.0
|
CG
|
A:HIS70
|
4.5
|
36.4
|
1.0
|
ND1
|
A:HIS70
|
4.6
|
39.1
|
1.0
|
CG2
|
A:ILE3
|
4.7
|
32.7
|
1.0
|
|
Platinum binding site 3 out
of 11 in 1rli
Go back to
Platinum Binding Sites List in 1rli
Platinum binding site 3 out
of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 3 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pt606
b:0.6
occ:0.51
|
O
|
A:HOH710
|
2.2
|
43.5
|
1.0
|
O
|
A:HOH709
|
2.7
|
42.9
|
1.0
|
O
|
A:HOH672
|
2.9
|
39.8
|
1.0
|
OG1
|
A:THR16
|
3.3
|
28.3
|
1.0
|
N
|
A:THR16
|
3.3
|
24.0
|
1.0
|
O
|
A:HOH649
|
3.6
|
43.0
|
1.0
|
N
|
A:ASN15
|
3.7
|
27.4
|
1.0
|
CB
|
A:ASN15
|
3.8
|
22.1
|
1.0
|
O
|
A:HOH713
|
3.8
|
48.4
|
1.0
|
O
|
A:HOH674
|
3.9
|
39.6
|
1.0
|
CB
|
A:THR16
|
3.9
|
28.9
|
1.0
|
CA
|
A:ASN15
|
4.0
|
24.7
|
1.0
|
C
|
A:ASN15
|
4.1
|
23.2
|
1.0
|
CB
|
A:PRO77
|
4.2
|
20.6
|
1.0
|
CA
|
A:THR16
|
4.2
|
25.3
|
1.0
|
C
|
A:GLY14
|
4.5
|
29.8
|
1.0
|
O
|
A:HOH628
|
4.7
|
39.6
|
1.0
|
ND2
|
A:ASN15
|
4.7
|
22.8
|
1.0
|
CG
|
A:ASN15
|
4.7
|
23.6
|
1.0
|
CA
|
A:PRO77
|
4.8
|
17.6
|
1.0
|
CG1
|
A:VAL120
|
4.9
|
19.6
|
1.0
|
CA
|
A:GLY14
|
4.9
|
32.3
|
1.0
|
CB
|
A:VAL120
|
4.9
|
18.3
|
1.0
|
O
|
A:VAL120
|
5.0
|
17.9
|
1.0
|
|
Platinum binding site 4 out
of 11 in 1rli
Go back to
Platinum Binding Sites List in 1rli
Platinum binding site 4 out
of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 4 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Pt603
b:44.3
occ:0.86
|
O
|
C:HOH613
|
2.3
|
13.9
|
1.0
|
O
|
B:HOH701
|
2.3
|
21.3
|
1.0
|
O
|
B:HOH702
|
2.4
|
22.5
|
1.0
|
O
|
C:HOH653
|
2.4
|
21.6
|
1.0
|
NE2
|
B:GLN135
|
2.7
|
26.4
|
0.5
|
CG
|
B:MET83
|
2.8
|
17.1
|
0.5
|
SD
|
B:MET83
|
3.4
|
28.0
|
0.7
|
CE
|
B:MET83
|
3.6
|
23.2
|
0.4
|
O
|
B:HOH642
|
3.7
|
26.1
|
1.0
|
SD
|
B:MET83
|
3.8
|
34.3
|
0.3
|
CB
|
B:MET83
|
3.8
|
22.8
|
0.5
|
CD
|
B:GLN135
|
3.8
|
24.6
|
0.4
|
N
|
B:MET83
|
3.9
|
17.1
|
0.5
|
CE
|
B:MET83
|
3.9
|
32.6
|
0.6
|
N
|
B:MET83
|
3.9
|
15.7
|
0.5
|
CB
|
B:MET83
|
4.0
|
18.0
|
0.5
|
O
|
C:HOH621
|
4.1
|
23.1
|
1.0
|
OE1
|
B:GLN135
|
4.1
|
16.0
|
0.5
|
CG
|
B:MET83
|
4.1
|
25.5
|
0.5
|
CD
|
B:LYS88
|
4.2
|
20.4
|
1.0
|
OE1
|
B:GLN135
|
4.2
|
25.5
|
0.5
|
CA
|
B:MET83
|
4.4
|
18.4
|
0.5
|
CB
|
B:LYS88
|
4.5
|
15.6
|
1.0
|
CA
|
B:MET83
|
4.5
|
15.9
|
0.5
|
CE
|
C:LYS88
|
4.7
|
15.4
|
1.0
|
CD1
|
B:LEU132
|
4.7
|
21.6
|
1.0
|
CG
|
B:LYS88
|
4.7
|
18.7
|
1.0
|
CE
|
B:LYS88
|
4.7
|
22.8
|
1.0
|
NE2
|
C:GLN135
|
4.9
|
24.4
|
1.0
|
C
|
B:GLY82
|
4.9
|
15.3
|
1.0
|
CA
|
B:GLY82
|
4.9
|
16.5
|
1.0
|
CD
|
B:GLN135
|
4.9
|
16.7
|
0.6
|
|
Platinum binding site 5 out
of 11 in 1rli
Go back to
Platinum Binding Sites List in 1rli
Platinum binding site 5 out
of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 5 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Pt608
b:0.2
occ:0.69
|
O4
|
B:PO4614
|
2.1
|
35.0
|
0.9
|
ND1
|
B:HIS70
|
2.4
|
42.5
|
1.0
|
O
|
B:HOH726
|
2.6
|
47.7
|
1.0
|
CE1
|
B:HIS70
|
3.3
|
44.4
|
1.0
|
CG
|
B:HIS70
|
3.3
|
38.3
|
1.0
|
O
|
B:HOH745
|
3.4
|
54.8
|
1.0
|
P
|
B:PO4614
|
3.4
|
36.0
|
0.9
|
CB
|
B:HIS70
|
3.6
|
31.9
|
1.0
|
O2
|
B:PO4614
|
3.7
|
42.4
|
0.7
|
O3
|
B:PO4614
|
4.3
|
41.8
|
0.9
|
NE2
|
B:HIS70
|
4.4
|
43.8
|
1.0
|
O1
|
B:PO4614
|
4.4
|
41.4
|
0.9
|
CD2
|
B:HIS70
|
4.4
|
41.0
|
1.0
|
CD1
|
B:ILE71
|
4.8
|
30.1
|
1.0
|
CG1
|
B:ILE71
|
4.8
|
27.4
|
1.0
|
|
Platinum binding site 6 out
of 11 in 1rli
Go back to
Platinum Binding Sites List in 1rli
Platinum binding site 6 out
of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 6 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Pt604
b:47.0
occ:0.74
|
O
|
B:HOH703
|
2.2
|
27.6
|
1.0
|
O
|
C:HOH614
|
2.2
|
15.8
|
1.0
|
O
|
C:HOH636
|
2.5
|
25.9
|
1.0
|
O
|
C:HOH623
|
2.5
|
25.4
|
1.0
|
O
|
B:HOH643
|
3.3
|
30.6
|
1.0
|
O
|
C:HOH703
|
3.3
|
41.5
|
1.0
|
CD
|
C:LYS36
|
4.0
|
36.0
|
1.0
|
NZ
|
C:LYS36
|
4.0
|
38.7
|
1.0
|
CB
|
C:PHE52
|
4.3
|
40.1
|
1.0
|
N
|
C:GLY85
|
4.5
|
16.9
|
1.0
|
O
|
C:PHE52
|
4.6
|
41.2
|
1.0
|
CE2
|
C:TYR79
|
4.6
|
33.6
|
1.0
|
N
|
C:GLY50
|
4.6
|
43.4
|
1.0
|
CE
|
C:LYS36
|
4.6
|
36.7
|
1.0
|
CA
|
C:GLY85
|
4.6
|
17.4
|
1.0
|
CD1
|
C:PHE52
|
4.7
|
40.0
|
1.0
|
O
|
C:HOH658
|
4.7
|
32.5
|
1.0
|
C
|
C:PHE52
|
4.8
|
41.2
|
1.0
|
N
|
C:THR86
|
4.8
|
17.1
|
1.0
|
N
|
C:PHE52
|
4.8
|
40.8
|
1.0
|
CA
|
C:PHE52
|
4.9
|
40.7
|
1.0
|
CG2
|
C:THR86
|
4.9
|
19.0
|
1.0
|
CA
|
C:GLY50
|
4.9
|
43.4
|
1.0
|
CG
|
C:PHE52
|
5.0
|
40.7
|
1.0
|
|
Platinum binding site 7 out
of 11 in 1rli
Go back to
Platinum Binding Sites List in 1rli
Platinum binding site 7 out
of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 7 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Pt609
b:72.5
occ:0.80
|
O
|
C:HOH699
|
2.0
|
31.4
|
1.0
|
O
|
C:HOH697
|
2.6
|
26.6
|
1.0
|
O
|
C:HOH700
|
2.6
|
38.4
|
1.0
|
O
|
C:HOH715
|
3.1
|
49.7
|
1.0
|
O
|
C:HOH711
|
3.6
|
62.2
|
1.0
|
N
|
C:ASN15
|
3.7
|
33.8
|
1.0
|
CA
|
C:GLY14
|
4.1
|
37.4
|
1.0
|
N
|
C:THR16
|
4.2
|
31.4
|
1.0
|
OG1
|
C:THR16
|
4.2
|
35.2
|
1.0
|
C
|
C:GLY14
|
4.3
|
34.8
|
1.0
|
CB
|
C:ASN15
|
4.4
|
31.0
|
1.0
|
O
|
C:HOH693
|
4.5
|
48.5
|
1.0
|
CA
|
C:ASN15
|
4.5
|
32.3
|
1.0
|
ND2
|
C:ASN15
|
4.5
|
33.0
|
1.0
|
CB
|
C:PRO77
|
4.7
|
22.3
|
1.0
|
CB
|
C:THR16
|
4.8
|
34.0
|
1.0
|
CG
|
C:ASN15
|
4.8
|
32.1
|
1.0
|
C
|
C:ASN15
|
4.9
|
30.6
|
1.0
|
O
|
C:THR10
|
4.9
|
54.4
|
1.0
|
|
Platinum binding site 8 out
of 11 in 1rli
Go back to
Platinum Binding Sites List in 1rli
Platinum binding site 8 out
of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 8 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Pt610
b:83.3
occ:0.79
|
O
|
C:HOH695
|
2.3
|
54.9
|
1.0
|
O
|
C:HOH694
|
2.4
|
46.0
|
1.0
|
ND1
|
C:HIS70
|
2.4
|
47.6
|
1.0
|
NZ
|
C:LYS2
|
2.9
|
57.5
|
1.0
|
CG
|
C:HIS70
|
3.2
|
45.4
|
1.0
|
CB
|
C:HIS70
|
3.4
|
41.6
|
1.0
|
CE1
|
C:HIS70
|
3.4
|
48.6
|
1.0
|
CE
|
C:LYS2
|
3.8
|
58.0
|
1.0
|
CD2
|
C:HIS70
|
4.4
|
47.7
|
1.0
|
NE2
|
C:HIS70
|
4.5
|
48.9
|
1.0
|
CG
|
C:LYS2
|
4.6
|
53.4
|
1.0
|
O
|
C:HOH696
|
4.7
|
48.3
|
1.0
|
CD
|
C:LYS2
|
4.8
|
56.6
|
1.0
|
CA
|
C:HIS70
|
4.9
|
38.2
|
1.0
|
|
Platinum binding site 9 out
of 11 in 1rli
Go back to
Platinum Binding Sites List in 1rli
Platinum binding site 9 out
of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 9 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Pt602
b:52.1
occ:0.78
|
O
|
A:HOH691
|
2.2
|
24.6
|
1.0
|
O
|
D:HOH711
|
2.3
|
30.1
|
1.0
|
O
|
D:HOH615
|
2.4
|
16.4
|
1.0
|
O
|
D:HOH636
|
2.4
|
28.3
|
1.0
|
O
|
D:HOH692
|
3.0
|
40.7
|
1.0
|
O
|
A:HOH636
|
3.4
|
30.3
|
1.0
|
CD
|
D:LYS36
|
4.2
|
27.9
|
1.0
|
CB
|
D:PHE52
|
4.2
|
31.6
|
1.0
|
CE2
|
D:TYR79
|
4.3
|
29.8
|
1.0
|
N
|
D:GLY50
|
4.4
|
41.1
|
1.0
|
NZ
|
D:LYS36
|
4.4
|
36.2
|
1.0
|
O
|
D:HOH626
|
4.4
|
27.6
|
1.0
|
O
|
D:PHE52
|
4.5
|
32.5
|
1.0
|
N
|
D:GLY85
|
4.5
|
16.0
|
1.0
|
CA
|
D:GLY85
|
4.7
|
17.5
|
1.0
|
C
|
D:PHE52
|
4.7
|
32.8
|
1.0
|
CA
|
D:GLY50
|
4.7
|
42.1
|
1.0
|
N
|
D:PHE52
|
4.8
|
34.6
|
1.0
|
CD1
|
D:PHE52
|
4.8
|
31.3
|
1.0
|
N
|
D:THR86
|
4.8
|
14.4
|
1.0
|
CE
|
D:LYS36
|
4.8
|
31.2
|
1.0
|
CA
|
D:PHE52
|
4.8
|
32.0
|
1.0
|
CD2
|
D:TYR79
|
4.9
|
26.6
|
1.0
|
CG2
|
D:THR86
|
4.9
|
16.0
|
1.0
|
CG
|
D:PHE52
|
5.0
|
31.0
|
1.0
|
|
Platinum binding site 10 out
of 11 in 1rli
Go back to
Platinum Binding Sites List in 1rli
Platinum binding site 10 out
of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 10 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Pt607
b:74.6
occ:0.75
|
O
|
D:HOH736
|
2.6
|
36.0
|
1.0
|
NZ
|
D:LYS2
|
2.7
|
43.4
|
1.0
|
ND1
|
D:HIS70
|
2.8
|
35.7
|
1.0
|
CE
|
D:LYS2
|
3.1
|
43.7
|
1.0
|
CG
|
D:HIS70
|
3.4
|
31.4
|
1.0
|
CE1
|
D:HIS70
|
3.6
|
36.0
|
1.0
|
CB
|
D:HIS70
|
3.6
|
28.9
|
1.0
|
CD2
|
D:HIS70
|
4.3
|
34.6
|
1.0
|
O
|
D:HOH764
|
4.3
|
44.1
|
1.0
|
CD
|
D:LYS2
|
4.3
|
42.8
|
1.0
|
NE2
|
D:HIS70
|
4.3
|
36.5
|
1.0
|
|
Reference:
Y.Kim,
P.Quartey,
A.Joachimiak.
Crystal Structure Analysis of Trp Repressor Binding Protein From Bacillus Subtilis To Be Published.
Page generated: Thu Oct 10 10:37:29 2024
|