Cadmium in PDB 4h3u: Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928
Protein crystallography data
The structure of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928, PDB code: 4h3u
was solved by
E.V.Filippova,
G.Minasov,
L.Shuvalova,
O.Kiryukhina,
R.Jedrzejczak,
A.Joachimiak,
W.F.Anderson,
Midwest Center For Structural Genomics(Mcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.94 /
1.15
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.578,
61.578,
144.576,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
12.8 /
14.3
|
Other elements in 4h3u:
The structure of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928
(pdb code 4h3u). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the
Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928, PDB code: 4h3u:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
Cadmium binding site 1 out
of 7 in 4h3u
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Cadmium Binding Sites List in 4h3u
Cadmium binding site 1 out
of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd201
b:13.5
occ:1.00
|
OE1
|
A:GLU45
|
2.3
|
12.4
|
1.0
|
O
|
A:HOH333
|
2.4
|
46.3
|
1.0
|
CD
|
A:GLU45
|
3.0
|
9.9
|
1.0
|
OE2
|
A:GLU45
|
3.0
|
17.2
|
1.0
|
O
|
A:HOH371
|
4.3
|
19.4
|
1.0
|
CG
|
A:GLU45
|
4.4
|
7.9
|
1.0
|
|
Cadmium binding site 2 out
of 7 in 4h3u
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Cadmium Binding Sites List in 4h3u
Cadmium binding site 2 out
of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd202
b:9.3
occ:0.90
|
CL
|
B:CL204
|
2.4
|
11.0
|
1.0
|
CL
|
A:CL205
|
2.4
|
11.1
|
1.0
|
O
|
B:TYR114
|
2.4
|
7.4
|
1.0
|
O
|
A:TYR114
|
2.4
|
7.3
|
1.0
|
CL
|
A:CL206
|
2.5
|
12.1
|
1.0
|
C
|
A:TYR114
|
3.3
|
7.1
|
1.0
|
C
|
B:TYR114
|
3.3
|
7.3
|
1.0
|
N
|
A:TYR114
|
3.9
|
7.9
|
1.0
|
N
|
B:TYR114
|
3.9
|
7.7
|
1.0
|
N
|
B:SER115
|
4.0
|
8.0
|
1.0
|
N
|
A:SER115
|
4.0
|
7.6
|
1.0
|
CA
|
B:SER115
|
4.0
|
8.4
|
1.0
|
CA
|
A:SER115
|
4.0
|
7.8
|
1.0
|
CA
|
A:TYR114
|
4.2
|
7.6
|
1.0
|
CA
|
B:TYR114
|
4.2
|
7.8
|
1.0
|
N
|
A:LEU116
|
4.6
|
8.1
|
1.0
|
N
|
B:LEU116
|
4.6
|
8.2
|
1.0
|
CB
|
A:ALA36
|
4.7
|
10.6
|
1.0
|
CB
|
B:ALA36
|
4.7
|
10.9
|
1.0
|
O
|
B:HOH325
|
4.8
|
16.0
|
1.0
|
O
|
A:HOH328
|
4.8
|
16.8
|
1.0
|
CA
|
A:ALA36
|
4.8
|
9.9
|
1.0
|
CA
|
B:ALA36
|
4.8
|
10.2
|
1.0
|
C
|
B:SER115
|
4.8
|
8.2
|
1.0
|
C
|
A:SER115
|
4.8
|
7.8
|
1.0
|
C
|
A:TYR113
|
4.9
|
7.7
|
1.0
|
C
|
B:TYR113
|
4.9
|
8.0
|
1.0
|
|
Cadmium binding site 3 out
of 7 in 4h3u
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Cadmium Binding Sites List in 4h3u
Cadmium binding site 3 out
of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd203
b:22.4
occ:1.00
|
O
|
A:HOH414
|
2.2
|
33.2
|
1.0
|
NE2
|
A:HIS62
|
2.3
|
15.3
|
1.0
|
OXT
|
A:ACT212
|
2.3
|
38.2
|
1.0
|
O
|
A:HOH435
|
2.3
|
30.3
|
1.0
|
O
|
A:HOH401
|
2.3
|
25.6
|
1.0
|
O
|
A:ACT212
|
2.4
|
26.1
|
1.0
|
C
|
A:ACT212
|
2.7
|
28.4
|
1.0
|
CD2
|
A:HIS62
|
3.2
|
14.7
|
1.0
|
CE1
|
A:HIS62
|
3.3
|
13.8
|
1.0
|
CH3
|
A:ACT212
|
4.2
|
35.7
|
1.0
|
O
|
A:HOH363
|
4.2
|
21.0
|
1.0
|
O
|
A:HOH436
|
4.3
|
39.4
|
1.0
|
O
|
A:HOH458
|
4.3
|
24.0
|
1.0
|
CG
|
A:HIS62
|
4.4
|
12.9
|
1.0
|
ND1
|
A:HIS62
|
4.4
|
12.6
|
1.0
|
O
|
A:HOH472
|
4.4
|
31.0
|
1.0
|
O
|
A:HOH329
|
4.6
|
17.4
|
1.0
|
O
|
A:HOH505
|
4.7
|
40.7
|
1.0
|
CB
|
A:ALA93
|
4.9
|
9.7
|
1.0
|
|
Cadmium binding site 4 out
of 7 in 4h3u
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Cadmium Binding Sites List in 4h3u
Cadmium binding site 4 out
of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd204
b:37.6
occ:1.00
|
O
|
A:ACT210
|
2.2
|
43.2
|
1.0
|
NE2
|
A:HIS74
|
2.2
|
23.1
|
1.0
|
O
|
A:HOH471
|
2.3
|
31.6
|
1.0
|
O
|
A:ACT211
|
2.4
|
51.1
|
1.0
|
OXT
|
A:ACT211
|
2.6
|
61.5
|
1.0
|
CL
|
A:CL209
|
2.7
|
33.0
|
0.5
|
OXT
|
A:ACT210
|
2.7
|
38.0
|
1.0
|
C
|
A:ACT210
|
2.8
|
38.3
|
1.0
|
C
|
A:ACT211
|
2.8
|
53.1
|
1.0
|
CL
|
B:CL205
|
3.1
|
43.5
|
1.0
|
CD2
|
A:HIS74
|
3.1
|
20.3
|
1.0
|
CE1
|
A:HIS74
|
3.3
|
21.3
|
1.0
|
CL
|
A:CL209
|
3.3
|
21.3
|
0.5
|
CG
|
A:HIS74
|
4.3
|
15.1
|
1.0
|
CH3
|
A:ACT210
|
4.3
|
36.2
|
1.0
|
ND1
|
A:HIS74
|
4.3
|
17.5
|
1.0
|
CH3
|
A:ACT211
|
4.4
|
54.1
|
1.0
|
O
|
A:HOH484
|
4.7
|
44.9
|
1.0
|
|
Cadmium binding site 5 out
of 7 in 4h3u
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Cadmium Binding Sites List in 4h3u
Cadmium binding site 5 out
of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd201
b:18.4
occ:0.70
|
O
|
B:HOH453
|
2.2
|
29.3
|
1.0
|
O
|
B:ACT206
|
2.2
|
29.4
|
0.5
|
O
|
B:HOH377
|
2.2
|
25.4
|
1.0
|
NE2
|
B:HIS62
|
2.3
|
13.9
|
1.0
|
O
|
B:HOH454
|
2.3
|
33.9
|
1.0
|
OXT
|
B:ACT206
|
2.4
|
39.7
|
0.5
|
OXT
|
B:ACT206
|
2.4
|
21.3
|
0.5
|
C
|
B:ACT206
|
2.6
|
26.1
|
0.5
|
O
|
B:ACT206
|
2.7
|
50.9
|
0.5
|
C
|
B:ACT206
|
2.9
|
33.0
|
0.5
|
CD2
|
B:HIS62
|
3.2
|
15.4
|
1.0
|
CE1
|
B:HIS62
|
3.3
|
13.4
|
1.0
|
CH3
|
B:ACT206
|
4.1
|
29.4
|
0.5
|
O
|
B:HOH359
|
4.2
|
20.6
|
1.0
|
O
|
B:HOH468
|
4.3
|
25.1
|
1.0
|
O
|
B:HOH476
|
4.4
|
37.1
|
1.0
|
CG
|
B:HIS62
|
4.4
|
13.1
|
1.0
|
ND1
|
B:HIS62
|
4.4
|
12.8
|
1.0
|
O
|
B:HOH392
|
4.4
|
33.2
|
1.0
|
O
|
B:HOH475
|
4.4
|
40.1
|
1.0
|
CH3
|
B:ACT206
|
4.4
|
24.5
|
0.5
|
O
|
B:HOH329
|
4.6
|
17.6
|
1.0
|
O
|
B:HOH455
|
4.8
|
42.2
|
1.0
|
CB
|
B:ALA93
|
4.9
|
10.0
|
1.0
|
|
Cadmium binding site 6 out
of 7 in 4h3u
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Cadmium Binding Sites List in 4h3u
Cadmium binding site 6 out
of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd202
b:13.5
occ:1.00
|
ND1
|
B:HIS84
|
2.2
|
7.7
|
1.0
|
CE1
|
B:HIS84
|
3.1
|
7.2
|
1.0
|
CG
|
B:HIS84
|
3.3
|
7.3
|
1.0
|
CB
|
B:HIS84
|
3.7
|
6.8
|
1.0
|
NE2
|
B:HIS84
|
4.3
|
7.4
|
1.0
|
CD2
|
B:HIS84
|
4.4
|
7.9
|
1.0
|
ND2
|
B:ASN60
|
4.5
|
23.7
|
0.5
|
CB
|
B:PRO91
|
4.6
|
7.5
|
1.0
|
CD
|
B:PRO91
|
4.7
|
7.0
|
1.0
|
CG
|
B:PRO91
|
4.7
|
8.1
|
1.0
|
O
|
B:HOH336
|
5.0
|
18.9
|
1.0
|
|
Cadmium binding site 7 out
of 7 in 4h3u
Go back to
Cadmium Binding Sites List in 4h3u
Cadmium binding site 7 out
of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd203
b:36.6
occ:1.00
|
O
|
B:HOH430
|
2.3
|
34.8
|
1.0
|
NE2
|
B:HIS74
|
2.3
|
23.5
|
1.0
|
O
|
B:HOH480
|
2.4
|
23.8
|
1.0
|
O
|
A:HOH426
|
2.4
|
37.0
|
0.5
|
O
|
A:HOH426
|
2.7
|
25.5
|
0.5
|
CL
|
A:CL207
|
2.7
|
33.4
|
0.5
|
CL
|
A:CL208
|
3.0
|
44.8
|
1.0
|
CL
|
A:CL207
|
3.3
|
21.1
|
0.5
|
CD2
|
B:HIS74
|
3.3
|
20.6
|
1.0
|
CE1
|
B:HIS74
|
3.3
|
24.7
|
1.0
|
O
|
B:HOH481
|
3.7
|
36.3
|
1.0
|
ND1
|
B:HIS74
|
4.4
|
18.8
|
1.0
|
CG
|
B:HIS74
|
4.4
|
15.9
|
1.0
|
|
Reference:
E.V.Filippova,
C.H.Luan,
S.F.Dunne,
O.Kiryukhina,
G.Minasov,
L.Shuvalova,
W.F.Anderson.
Structural Characterization of A Hypothetical Protein: A Potential Agent Involved in Trimethylamine Metabolism in Catenulispora Acidiphila. J.Struct.Funct.Genom. V. 15 33 2014.
ISSN: ISSN 1345-711X
PubMed: 24562475
DOI: 10.1007/S10969-014-9176-Z
Page generated: Fri Jul 19 17:25:10 2024
|