Copper in PDB 7tep: Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant
Protein crystallography data
The structure of Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant, PDB code: 7tep
was solved by
A.Kakkis,
E.Golub,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.30 /
2.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.08,
80.57,
49.44,
90,
102.33,
90
|
R / Rfree (%)
|
25.3 /
33.9
|
Other elements in 7tep:
The structure of Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant
(pdb code 7tep). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the
Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant, PDB code: 7tep:
Jump to Copper binding site number:
1;
2;
3;
4;
Copper binding site 1 out
of 4 in 7tep
Go back to
Copper Binding Sites List in 7tep
Copper binding site 1 out
of 4 in the Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu202
b:21.6
occ:1.00
|
NE2
|
A:HIS77
|
1.8
|
20.3
|
1.0
|
OE2
|
A:GLU81
|
2.0
|
21.8
|
1.0
|
NE2
|
B:HIS63
|
2.2
|
21.0
|
1.0
|
O
|
C:HOH307
|
2.3
|
23.7
|
1.0
|
HE1
|
A:HIS77
|
2.4
|
25.2
|
1.0
|
CE1
|
A:HIS77
|
2.4
|
21.0
|
1.0
|
HE1
|
B:HIS63
|
2.6
|
28.7
|
1.0
|
CE1
|
B:HIS63
|
2.7
|
23.9
|
1.0
|
HB2
|
C:CYS96
|
3.0
|
29.9
|
1.0
|
CD2
|
A:HIS77
|
3.1
|
20.9
|
1.0
|
CD
|
A:GLU81
|
3.2
|
21.5
|
1.0
|
CD2
|
B:HIS63
|
3.5
|
21.6
|
1.0
|
HD2
|
A:HIS77
|
3.5
|
25.1
|
1.0
|
ND1
|
A:HIS77
|
3.6
|
21.1
|
1.0
|
HE22
|
C:GLN71
|
3.7
|
33.3
|
1.0
|
O
|
C:CYS96
|
3.8
|
25.1
|
1.0
|
OE1
|
A:GLU81
|
3.8
|
21.6
|
1.0
|
HD2
|
B:HIS63
|
3.9
|
25.9
|
1.0
|
CB
|
C:CYS96
|
3.9
|
25.0
|
1.0
|
CG
|
A:HIS77
|
4.0
|
20.6
|
1.0
|
HD2
|
B:HIS59
|
4.0
|
28.5
|
1.0
|
ND1
|
B:HIS63
|
4.0
|
22.9
|
1.0
|
O
|
B:HOH301
|
4.1
|
19.7
|
1.0
|
HB3
|
B:HIS59
|
4.1
|
27.2
|
1.0
|
OG1
|
C:THR97
|
4.1
|
27.7
|
1.0
|
C
|
C:CYS96
|
4.1
|
26.2
|
1.0
|
HB3
|
C:CYS96
|
4.1
|
29.9
|
1.0
|
HG1
|
C:THR97
|
4.2
|
33.3
|
1.0
|
HD1
|
A:HIS77
|
4.3
|
25.2
|
1.0
|
HG3
|
A:GLU81
|
4.3
|
23.0
|
1.0
|
CG
|
B:HIS63
|
4.4
|
21.2
|
1.0
|
CG
|
A:GLU81
|
4.4
|
19.1
|
1.0
|
NE2
|
C:GLN71
|
4.5
|
27.7
|
1.0
|
CA
|
C:CYS96
|
4.6
|
26.7
|
1.0
|
HD1
|
B:HIS63
|
4.7
|
27.4
|
1.0
|
HD23
|
A:LEU78
|
4.7
|
23.0
|
1.0
|
HG
|
C:CYS96
|
4.8
|
39.0
|
1.0
|
N
|
C:THR97
|
4.8
|
26.2
|
1.0
|
H
|
C:CYS96
|
4.8
|
31.6
|
1.0
|
CD2
|
B:HIS59
|
4.8
|
23.8
|
1.0
|
HG2
|
A:GLU81
|
4.8
|
23.0
|
1.0
|
OE1
|
C:GLN71
|
4.9
|
25.2
|
1.0
|
CB
|
B:HIS59
|
5.0
|
22.6
|
1.0
|
|
Copper binding site 2 out
of 4 in 7tep
Go back to
Copper Binding Sites List in 7tep
Copper binding site 2 out
of 4 in the Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu203
b:39.8
occ:1.00
|
SG
|
A:CYS96
|
1.7
|
25.1
|
1.0
|
NE2
|
C:HIS77
|
1.8
|
27.8
|
1.0
|
OE2
|
C:GLU81
|
2.0
|
27.0
|
1.0
|
CE1
|
C:HIS77
|
2.5
|
26.8
|
1.0
|
NE2
|
D:HIS63
|
2.6
|
28.0
|
1.0
|
HE1
|
C:HIS77
|
2.6
|
32.2
|
1.0
|
CD2
|
C:HIS77
|
2.9
|
27.6
|
1.0
|
HB2
|
A:CYS96
|
3.0
|
27.8
|
1.0
|
CD
|
C:GLU81
|
3.0
|
27.1
|
1.0
|
CB
|
A:CYS96
|
3.1
|
23.2
|
1.0
|
HD2
|
C:HIS77
|
3.3
|
33.1
|
1.0
|
CE1
|
D:HIS63
|
3.4
|
28.1
|
1.0
|
HE1
|
D:HIS63
|
3.4
|
33.7
|
1.0
|
OE1
|
C:GLU81
|
3.4
|
27.9
|
1.0
|
HB3
|
A:CYS96
|
3.5
|
27.8
|
1.0
|
HG1
|
A:THR97
|
3.6
|
28.0
|
1.0
|
CD2
|
D:HIS63
|
3.6
|
28.3
|
1.0
|
ND1
|
C:HIS77
|
3.7
|
26.6
|
1.0
|
HE22
|
A:GLN71
|
3.8
|
27.1
|
1.0
|
HD2
|
D:HIS63
|
3.8
|
34.0
|
1.0
|
CG
|
C:HIS77
|
3.9
|
27.6
|
1.0
|
HE21
|
A:GLN71
|
3.9
|
27.1
|
1.0
|
HB3
|
D:HIS59
|
4.0
|
32.6
|
1.0
|
NE2
|
A:GLN71
|
4.2
|
22.5
|
1.0
|
OG1
|
A:THR97
|
4.3
|
23.3
|
1.0
|
CG
|
C:GLU81
|
4.3
|
26.4
|
1.0
|
H
|
A:THR97
|
4.4
|
27.4
|
1.0
|
CA
|
A:CYS96
|
4.4
|
22.8
|
1.0
|
HD23
|
C:LEU78
|
4.4
|
34.4
|
1.0
|
HD1
|
C:HIS77
|
4.4
|
32.0
|
1.0
|
HG3
|
C:GLU81
|
4.4
|
31.7
|
1.0
|
N
|
A:THR97
|
4.5
|
22.8
|
1.0
|
ND1
|
D:HIS63
|
4.5
|
28.0
|
1.0
|
HZ1
|
C:LYS83
|
4.6
|
27.3
|
1.0
|
HG2
|
C:GLU81
|
4.6
|
31.7
|
1.0
|
C
|
A:CYS96
|
4.6
|
23.6
|
1.0
|
HD21
|
C:LEU78
|
4.7
|
34.4
|
1.0
|
CG
|
D:HIS63
|
4.7
|
27.2
|
1.0
|
O
|
A:GLN93
|
4.8
|
24.5
|
1.0
|
HZ2
|
C:LYS83
|
4.8
|
27.3
|
1.0
|
H
|
A:CYS96
|
4.8
|
25.1
|
1.0
|
CD2
|
C:LEU78
|
4.9
|
28.6
|
1.0
|
HD22
|
C:LEU78
|
4.9
|
34.4
|
1.0
|
CB
|
D:HIS59
|
5.0
|
27.2
|
1.0
|
|
Copper binding site 3 out
of 4 in 7tep
Go back to
Copper Binding Sites List in 7tep
Copper binding site 3 out
of 4 in the Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu202
b:35.0
occ:1.00
|
OE1
|
B:GLU81
|
1.5
|
28.4
|
1.0
|
NE2
|
B:HIS77
|
1.6
|
28.2
|
1.0
|
NE2
|
A:HIS63
|
1.9
|
28.6
|
0.7
|
O
|
D:HOH312
|
2.2
|
29.4
|
1.0
|
CD
|
B:GLU81
|
2.5
|
28.2
|
1.0
|
CD2
|
B:HIS77
|
2.7
|
27.8
|
1.0
|
CE1
|
B:HIS77
|
2.7
|
27.7
|
1.0
|
CE1
|
A:HIS63
|
2.7
|
28.7
|
0.7
|
HE1
|
A:HIS63
|
2.8
|
34.5
|
0.7
|
OE2
|
B:GLU81
|
2.9
|
27.2
|
1.0
|
HD2
|
B:HIS77
|
2.9
|
33.3
|
1.0
|
HE1
|
B:HIS77
|
2.9
|
33.2
|
1.0
|
CD2
|
A:HIS63
|
3.0
|
27.9
|
0.7
|
HD2
|
A:HIS63
|
3.3
|
33.5
|
0.7
|
HB3
|
D:CYS96
|
3.3
|
39.0
|
1.0
|
HB2
|
D:CYS96
|
3.7
|
39.0
|
1.0
|
ND1
|
B:HIS77
|
3.8
|
27.4
|
1.0
|
CG
|
B:HIS77
|
3.8
|
27.2
|
1.0
|
ND1
|
A:HIS63
|
3.8
|
27.2
|
0.7
|
CB
|
D:CYS96
|
4.0
|
32.5
|
1.0
|
CG
|
B:GLU81
|
4.0
|
29.4
|
1.0
|
CG
|
A:HIS63
|
4.0
|
26.9
|
0.7
|
HE21
|
D:GLN71
|
4.0
|
32.7
|
0.7
|
OG1
|
D:THR97
|
4.2
|
29.2
|
1.0
|
HG2
|
B:GLU81
|
4.3
|
35.2
|
1.0
|
HB3
|
A:HIS59
|
4.3
|
36.3
|
1.0
|
O
|
B:HIS77
|
4.4
|
25.0
|
1.0
|
HG1
|
D:THR97
|
4.5
|
35.1
|
1.0
|
HD1
|
B:HIS77
|
4.6
|
32.9
|
1.0
|
HG3
|
B:GLU81
|
4.6
|
35.2
|
1.0
|
HD1
|
A:HIS63
|
4.6
|
32.7
|
0.7
|
C
|
D:CYS96
|
4.6
|
31.5
|
1.0
|
HB2
|
B:GLU81
|
4.7
|
37.5
|
1.0
|
HD23
|
B:LEU78
|
4.8
|
34.7
|
1.0
|
O
|
D:CYS96
|
4.8
|
33.0
|
1.0
|
NE2
|
D:GLN71
|
4.8
|
27.3
|
0.7
|
HE21
|
D:GLN71
|
4.8
|
32.9
|
0.3
|
N
|
D:THR97
|
4.9
|
29.7
|
1.0
|
CB
|
B:GLU81
|
4.9
|
31.2
|
1.0
|
OE1
|
D:GLN71
|
4.9
|
27.6
|
0.3
|
CA
|
D:CYS96
|
4.9
|
31.3
|
1.0
|
HB2
|
A:HIS63
|
4.9
|
32.8
|
0.3
|
HE22
|
D:GLN71
|
4.9
|
32.7
|
0.7
|
O
|
D:GLN93
|
5.0
|
30.1
|
1.0
|
HB3
|
B:GLU81
|
5.0
|
37.5
|
1.0
|
H
|
D:THR97
|
5.0
|
35.7
|
1.0
|
|
Copper binding site 4 out
of 4 in 7tep
Go back to
Copper Binding Sites List in 7tep
Copper binding site 4 out
of 4 in the Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Crystal Structure of A Cu-Bound Cytochrome CB562 Variant in the Presence of Reductant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu202
b:46.5
occ:1.00
|
NE2
|
C:HIS63
|
1.7
|
32.5
|
1.0
|
SG
|
B:CYS96
|
1.8
|
27.9
|
1.0
|
NE2
|
D:HIS77
|
2.0
|
32.1
|
1.0
|
OE2
|
D:GLU81
|
2.5
|
35.8
|
1.0
|
CE1
|
C:HIS63
|
2.6
|
29.9
|
1.0
|
CD2
|
C:HIS63
|
2.8
|
29.5
|
1.0
|
HE1
|
C:HIS63
|
2.9
|
35.9
|
1.0
|
CE1
|
D:HIS77
|
3.0
|
32.2
|
1.0
|
CD2
|
D:HIS77
|
3.0
|
32.1
|
1.0
|
HD2
|
C:HIS63
|
3.1
|
35.4
|
1.0
|
HE1
|
D:HIS77
|
3.2
|
38.6
|
1.0
|
HD2
|
D:HIS77
|
3.2
|
38.5
|
1.0
|
HB2
|
B:CYS96
|
3.2
|
36.4
|
1.0
|
CD
|
D:GLU81
|
3.3
|
36.2
|
1.0
|
CB
|
B:CYS96
|
3.3
|
30.3
|
1.0
|
OE1
|
D:GLU81
|
3.3
|
38.6
|
1.0
|
HZ3
|
C:TRP66
|
3.7
|
37.0
|
1.0
|
HB3
|
B:CYS96
|
3.7
|
36.4
|
1.0
|
ND1
|
C:HIS63
|
3.8
|
28.8
|
1.0
|
CG
|
C:HIS63
|
3.8
|
29.7
|
1.0
|
ND1
|
D:HIS77
|
4.1
|
30.7
|
1.0
|
CG
|
D:HIS77
|
4.1
|
32.9
|
1.0
|
CZ3
|
C:TRP66
|
4.2
|
30.8
|
1.0
|
HE21
|
B:GLN71
|
4.3
|
32.6
|
1.0
|
HE22
|
B:GLN71
|
4.4
|
32.6
|
1.0
|
HE3
|
C:TRP66
|
4.5
|
36.9
|
1.0
|
CA
|
B:CYS96
|
4.5
|
30.0
|
1.0
|
HB3
|
C:HIS59
|
4.5
|
37.0
|
1.0
|
HD1
|
C:HIS63
|
4.6
|
34.5
|
1.0
|
C
|
B:CYS96
|
4.6
|
29.1
|
1.0
|
CE3
|
C:TRP66
|
4.6
|
30.8
|
1.0
|
ND1
|
C:HIS59
|
4.6
|
33.1
|
1.0
|
O
|
D:HIS77
|
4.7
|
34.9
|
1.0
|
NE2
|
B:GLN71
|
4.7
|
27.2
|
1.0
|
CG
|
D:GLU81
|
4.7
|
36.3
|
1.0
|
HG1
|
B:THR97
|
4.8
|
32.2
|
1.0
|
O
|
B:CYS96
|
4.8
|
27.8
|
1.0
|
O
|
C:HIS59
|
4.9
|
28.5
|
1.0
|
HG2
|
D:GLU81
|
4.9
|
43.5
|
1.0
|
HD1
|
D:HIS77
|
4.9
|
36.8
|
1.0
|
HA
|
C:HIS59
|
4.9
|
37.4
|
1.0
|
N
|
B:THR97
|
4.9
|
28.3
|
1.0
|
CH2
|
C:TRP66
|
4.9
|
30.3
|
1.0
|
OG1
|
B:THR97
|
5.0
|
26.9
|
1.0
|
|
Reference:
A.Kakkis,
E.Golub.
Crystal Structure of A Co-Bound Cytochrome CB562 Variant in the Presence of Reductant To Be Published.
Page generated: Wed Jul 31 09:15:04 2024
|