Platinum in PDB 1qvr: Crystal Structure Analysis of Clpb
Protein crystallography data
The structure of Crystal Structure Analysis of Clpb, PDB code: 1qvr
was solved by
S.Lee,
M.E.Sowa,
Y.Watanabe,
P.B.Sigler,
W.Chiu,
M.Yoshida,
F.T.F.Tsai,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.04 /
3.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
107.747,
138.482,
212.215,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26.3 /
30.7
|
Platinum Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
23;
Binding sites:
The binding sites of Platinum atom in the Crystal Structure Analysis of Clpb
(pdb code 1qvr). This binding sites where shown within
5.0 Angstroms radius around Platinum atom.
In total 23 binding sites of Platinum where determined in the
Crystal Structure Analysis of Clpb, PDB code: 1qvr:
Jump to Platinum binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Platinum binding site 1 out
of 23 in 1qvr
Go back to
Platinum Binding Sites List in 1qvr
Platinum binding site 1 out
of 23 in the Crystal Structure Analysis of Clpb
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 1 of Crystal Structure Analysis of Clpb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Pt855
b:54.5
occ:0.15
|
SD
|
B:MET24
|
2.3
|
50.2
|
1.0
|
CG
|
B:MET24
|
2.4
|
58.0
|
1.0
|
CE
|
B:MET24
|
3.3
|
32.2
|
1.0
|
CD1
|
B:LEU20
|
3.8
|
41.8
|
1.0
|
CB
|
B:MET24
|
3.9
|
70.3
|
1.0
|
CA
|
B:MET24
|
4.9
|
73.4
|
1.0
|
CG
|
B:LEU20
|
4.9
|
43.7
|
1.0
|
|
Platinum binding site 2 out
of 23 in 1qvr
Go back to
Platinum Binding Sites List in 1qvr
Platinum binding site 2 out
of 23 in the Crystal Structure Analysis of Clpb
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 2 of Crystal Structure Analysis of Clpb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Pt856
b:39.9
occ:0.18
|
CE
|
B:MET619
|
2.1
|
49.0
|
1.0
|
SD
|
B:MET619
|
2.4
|
61.1
|
1.0
|
CG
|
B:MET619
|
3.5
|
41.8
|
1.0
|
CB
|
B:MET619
|
3.5
|
57.6
|
1.0
|
CG
|
B:LYS606
|
3.6
|
67.2
|
1.0
|
CD
|
B:LYS606
|
4.2
|
73.0
|
1.0
|
O
|
B:GLU616
|
4.3
|
55.7
|
1.0
|
NH2
|
C:ARG747
|
4.6
|
0.2
|
1.0
|
CB
|
B:LYS606
|
4.8
|
69.4
|
1.0
|
CA
|
B:MET619
|
5.0
|
56.6
|
1.0
|
|
Platinum binding site 3 out
of 23 in 1qvr
Go back to
Platinum Binding Sites List in 1qvr
Platinum binding site 3 out
of 23 in the Crystal Structure Analysis of Clpb
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 3 of Crystal Structure Analysis of Clpb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Pt855
b:46.3
occ:0.18
|
CE
|
C:MET619
|
2.2
|
77.4
|
1.0
|
SD
|
C:MET619
|
2.5
|
70.5
|
1.0
|
CG
|
C:MET619
|
3.5
|
59.2
|
1.0
|
CB
|
C:MET619
|
3.5
|
65.8
|
1.0
|
CG
|
C:LYS606
|
3.7
|
58.3
|
1.0
|
O
|
C:GLU616
|
4.1
|
86.8
|
1.0
|
CD
|
C:LYS606
|
4.4
|
70.3
|
1.0
|
CB
|
C:LYS606
|
4.8
|
35.7
|
1.0
|
CA
|
C:MET619
|
4.9
|
69.0
|
1.0
|
|
Platinum binding site 4 out
of 23 in 1qvr
Go back to
Platinum Binding Sites List in 1qvr
Platinum binding site 4 out
of 23 in the Crystal Structure Analysis of Clpb
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 4 of Crystal Structure Analysis of Clpb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pt855
b:52.6
occ:0.18
|
CE
|
A:MET619
|
2.0
|
57.2
|
1.0
|
SD
|
A:MET619
|
2.4
|
74.8
|
1.0
|
CG
|
A:MET619
|
3.4
|
50.0
|
1.0
|
CB
|
A:MET619
|
3.4
|
58.2
|
1.0
|
CG
|
A:LYS606
|
3.6
|
73.5
|
1.0
|
O
|
A:GLU616
|
4.1
|
89.2
|
1.0
|
CD
|
A:LYS606
|
4.4
|
89.3
|
1.0
|
NH2
|
B:ARG747
|
4.8
|
0.0
|
1.0
|
CB
|
A:LYS606
|
4.8
|
51.5
|
1.0
|
CA
|
A:MET619
|
4.8
|
65.9
|
1.0
|
|
Platinum binding site 5 out
of 23 in 1qvr
Go back to
Platinum Binding Sites List in 1qvr
Platinum binding site 5 out
of 23 in the Crystal Structure Analysis of Clpb
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 5 of Crystal Structure Analysis of Clpb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Pt857
b:16.6
occ:0.10
|
CE
|
B:MET394
|
2.1
|
34.9
|
1.0
|
SD
|
B:MET394
|
2.6
|
78.7
|
1.0
|
NH1
|
C:ARG180
|
3.0
|
0.9
|
1.0
|
NH2
|
C:ARG180
|
3.4
|
0.2
|
1.0
|
CZ
|
C:ARG180
|
3.6
|
0.4
|
1.0
|
CG
|
C:PRO221
|
3.6
|
0.2
|
1.0
|
CD
|
C:PRO221
|
3.9
|
0.4
|
1.0
|
CG
|
B:MET394
|
4.2
|
68.1
|
1.0
|
PT
|
B:PT858
|
4.5
|
31.8
|
0.1
|
O
|
C:ASP219
|
4.7
|
0.2
|
1.0
|
CB
|
B:SER398
|
4.7
|
0.0
|
1.0
|
NE
|
C:ARG180
|
4.8
|
1.0
|
1.0
|
CB
|
B:MET394
|
4.8
|
69.8
|
1.0
|
|
Platinum binding site 6 out
of 23 in 1qvr
Go back to
Platinum Binding Sites List in 1qvr
Platinum binding site 6 out
of 23 in the Crystal Structure Analysis of Clpb
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 6 of Crystal Structure Analysis of Clpb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Pt856
b:19.4
occ:0.10
|
CB
|
C:TYR627
|
2.1
|
1.0
|
1.0
|
SD
|
C:MET624
|
2.4
|
77.2
|
1.0
|
CE
|
C:MET624
|
2.5
|
80.3
|
1.0
|
CG
|
C:TYR627
|
2.6
|
0.1
|
1.0
|
CD1
|
C:TYR627
|
2.8
|
0.3
|
1.0
|
CA
|
C:MET624
|
3.1
|
0.4
|
1.0
|
CA
|
C:TYR627
|
3.1
|
0.4
|
1.0
|
O
|
C:MET624
|
3.2
|
0.5
|
1.0
|
O
|
C:TYR627
|
3.2
|
0.6
|
1.0
|
N
|
C:TYR627
|
3.4
|
1.0
|
1.0
|
C
|
C:MET624
|
3.6
|
0.0
|
1.0
|
C
|
C:TYR627
|
3.6
|
0.5
|
1.0
|
CG
|
C:MET624
|
3.7
|
88.2
|
1.0
|
CD2
|
C:TYR627
|
3.7
|
0.1
|
1.0
|
CB
|
C:MET624
|
3.8
|
0.1
|
1.0
|
CE1
|
C:TYR627
|
4.0
|
0.1
|
1.0
|
N
|
C:MET624
|
4.0
|
0.3
|
1.0
|
CG2
|
C:ILE622
|
4.2
|
76.9
|
1.0
|
O
|
C:ASP623
|
4.4
|
91.3
|
1.0
|
C
|
C:ASP623
|
4.5
|
97.0
|
1.0
|
C
|
C:GLU626
|
4.7
|
0.2
|
1.0
|
CE2
|
C:TYR627
|
4.7
|
0.4
|
1.0
|
CZ
|
C:TYR627
|
4.8
|
0.6
|
1.0
|
N
|
C:THR625
|
4.9
|
0.3
|
1.0
|
N
|
C:MET628
|
4.9
|
0.4
|
1.0
|
CB
|
C:HIS631
|
4.9
|
0.3
|
1.0
|
N
|
C:GLU626
|
5.0
|
0.5
|
1.0
|
|
Platinum binding site 7 out
of 23 in 1qvr
Go back to
Platinum Binding Sites List in 1qvr
Platinum binding site 7 out
of 23 in the Crystal Structure Analysis of Clpb
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 7 of Crystal Structure Analysis of Clpb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pt856
b:69.7
occ:0.15
|
SD
|
A:MET24
|
2.0
|
82.8
|
1.0
|
CE
|
A:MET24
|
2.5
|
63.4
|
1.0
|
NZ
|
A:LYS73
|
3.1
|
0.7
|
1.0
|
CG
|
A:MET24
|
3.5
|
75.7
|
1.0
|
CB
|
A:MET24
|
3.8
|
89.8
|
1.0
|
CE
|
A:LYS73
|
4.3
|
0.1
|
1.0
|
CA
|
A:MET24
|
4.3
|
100.0
|
1.0
|
O
|
A:MET24
|
4.6
|
0.8
|
1.0
|
C
|
A:MET24
|
4.9
|
1.0
|
1.0
|
|
Platinum binding site 8 out
of 23 in 1qvr
Go back to
Platinum Binding Sites List in 1qvr
Platinum binding site 8 out
of 23 in the Crystal Structure Analysis of Clpb
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 8 of Crystal Structure Analysis of Clpb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pt857
b:44.7
occ:0.14
|
CD2
|
A:LEU83
|
4.7
|
76.9
|
1.0
|
NH2
|
A:ARG5
|
4.8
|
95.9
|
1.0
|
|
Platinum binding site 9 out
of 23 in 1qvr
Go back to
Platinum Binding Sites List in 1qvr
Platinum binding site 9 out
of 23 in the Crystal Structure Analysis of Clpb
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 9 of Crystal Structure Analysis of Clpb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Pt858
b:31.8
occ:0.10
|
SD
|
B:MET394
|
2.4
|
78.7
|
1.0
|
CG
|
B:MET394
|
2.5
|
68.1
|
1.0
|
NH2
|
C:ARG180
|
2.6
|
0.2
|
1.0
|
CE
|
B:MET394
|
3.4
|
34.9
|
1.0
|
CZ
|
C:ARG180
|
3.6
|
0.4
|
1.0
|
CB
|
B:MET394
|
3.9
|
69.8
|
1.0
|
NE
|
C:ARG180
|
4.0
|
1.0
|
1.0
|
O
|
B:ARG391
|
4.2
|
75.1
|
1.0
|
PT
|
B:PT857
|
4.5
|
16.6
|
0.1
|
CG
|
B:ARG391
|
4.5
|
86.1
|
1.0
|
NH1
|
C:ARG180
|
4.6
|
0.9
|
1.0
|
N
|
B:ALA395
|
4.6
|
79.9
|
1.0
|
C
|
B:ARG391
|
4.8
|
67.1
|
1.0
|
CA
|
B:ARG391
|
4.9
|
66.7
|
1.0
|
|
Platinum binding site 10 out
of 23 in 1qvr
Go back to
Platinum Binding Sites List in 1qvr
Platinum binding site 10 out
of 23 in the Crystal Structure Analysis of Clpb
Mono view
Stereo pair view
|
A full contact list of Platinum with other atoms in the Pt binding
site number 10 of Crystal Structure Analysis of Clpb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Pt859
b:50.2
occ:0.13
|
OG1
|
B:THR625
|
2.4
|
0.6
|
1.0
|
O
|
B:THR625
|
2.6
|
0.8
|
1.0
|
SD
|
B:MET628
|
2.9
|
97.2
|
1.0
|
C
|
B:THR625
|
3.3
|
1.0
|
1.0
|
CA
|
B:THR625
|
3.3
|
1.0
|
1.0
|
CB
|
B:THR625
|
3.4
|
0.1
|
1.0
|
CE
|
B:MET628
|
3.9
|
79.2
|
1.0
|
CG
|
B:MET628
|
4.0
|
0.9
|
1.0
|
CG
|
B:LYS671
|
4.2
|
89.8
|
1.0
|
CB
|
B:LYS671
|
4.4
|
85.8
|
1.0
|
CD
|
B:LYS671
|
4.4
|
97.7
|
1.0
|
CG2
|
B:THR625
|
4.6
|
0.7
|
1.0
|
N
|
B:GLU626
|
4.6
|
0.9
|
1.0
|
N
|
B:THR625
|
4.7
|
0.6
|
1.0
|
CE
|
B:LYS671
|
5.0
|
0.8
|
1.0
|
|
Reference:
S.Lee,
M.E.Sowa,
Y.Watanabe,
P.B.Sigler,
W.Chiu,
M.Yoshida,
F.T.F.Tsai.
The Structure of Clpb: A Molecular Chaperone That Rescues Proteins From An Aggregated State Cell(Cambridge,Mass.) V. 115 229 2003.
ISSN: ISSN 0092-8674
PubMed: 14567920
DOI: 10.1016/S0092-8674(03)00807-9
Page generated: Thu Oct 10 10:36:54 2024
|