Cobalt in PDB 1ovu: Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)
Protein crystallography data
The structure of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I), PDB code: 1ovu
was solved by
L.Di Costanzo,
S.Geremia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
3.10
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.780,
147.720,
37.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
24.7 /
30.4
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)
(pdb code 1ovu). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the
Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I), PDB code: 1ovu:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
Cobalt binding site 1 out
of 7 in 1ovu
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Cobalt Binding Sites List in 1ovu
Cobalt binding site 1 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co101
b:49.0
occ:1.00
|
OE1
|
A:GLU36
|
1.9
|
55.3
|
1.0
|
ND1
|
A:HIS39
|
1.9
|
51.7
|
1.0
|
OE2
|
A:GLU10
|
2.0
|
51.7
|
1.0
|
OE1
|
A:GLU10
|
2.1
|
58.8
|
1.0
|
CD
|
A:GLU10
|
2.3
|
63.2
|
1.0
|
CE1
|
A:HIS39
|
2.6
|
51.2
|
1.0
|
CD
|
A:GLU36
|
2.8
|
53.4
|
1.0
|
CG
|
A:HIS39
|
3.2
|
52.7
|
1.0
|
OE2
|
A:GLU36
|
3.3
|
51.4
|
1.0
|
NE2
|
A:HIS39
|
3.8
|
57.5
|
1.0
|
CB
|
A:HIS39
|
3.8
|
50.4
|
1.0
|
CG
|
A:GLU10
|
3.9
|
64.4
|
1.0
|
CG
|
A:GLU36
|
4.0
|
42.8
|
1.0
|
CD2
|
A:HIS39
|
4.1
|
50.2
|
1.0
|
CB
|
A:GLU36
|
4.1
|
42.1
|
1.0
|
CA
|
A:GLU36
|
4.1
|
43.6
|
1.0
|
CB
|
A:GLU10
|
4.8
|
59.0
|
1.0
|
N
|
A:GLU36
|
4.9
|
43.6
|
1.0
|
O
|
A:ASP35
|
4.9
|
42.6
|
1.0
|
|
Cobalt binding site 2 out
of 7 in 1ovu
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Cobalt Binding Sites List in 1ovu
Cobalt binding site 2 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co105
b:86.6
occ:1.00
|
OE1
|
A:GLU19
|
2.1
|
57.4
|
1.0
|
O
|
A:HOH108
|
2.4
|
54.1
|
1.0
|
CD
|
A:GLU19
|
3.1
|
62.8
|
1.0
|
OE2
|
A:GLU19
|
3.6
|
76.5
|
1.0
|
O
|
A:HOH106
|
4.2
|
60.3
|
1.0
|
CG
|
A:GLU19
|
4.3
|
52.6
|
1.0
|
O
|
A:HOH107
|
4.5
|
22.8
|
1.0
|
|
Cobalt binding site 3 out
of 7 in 1ovu
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Cobalt Binding Sites List in 1ovu
Cobalt binding site 3 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co102
b:45.6
occ:1.00
|
OE2
|
B:GLU10
|
1.9
|
52.1
|
1.0
|
ND1
|
B:HIS39
|
2.1
|
45.5
|
1.0
|
OE1
|
B:GLU36
|
2.1
|
49.5
|
1.0
|
OE1
|
B:GLU10
|
2.1
|
38.9
|
1.0
|
CD
|
B:GLU10
|
2.3
|
37.4
|
1.0
|
CE1
|
B:HIS39
|
2.7
|
54.9
|
1.0
|
CD
|
B:GLU36
|
3.2
|
52.5
|
1.0
|
CG
|
B:HIS39
|
3.3
|
47.6
|
1.0
|
CG
|
B:GLU10
|
3.7
|
33.9
|
1.0
|
OE2
|
B:GLU36
|
3.7
|
47.6
|
1.0
|
CB
|
B:HIS39
|
3.8
|
47.4
|
1.0
|
NE2
|
B:HIS39
|
4.0
|
59.2
|
1.0
|
CD2
|
B:HIS39
|
4.2
|
46.8
|
1.0
|
CG
|
B:GLU36
|
4.4
|
42.8
|
1.0
|
CB
|
B:GLU36
|
4.4
|
45.2
|
1.0
|
CB
|
B:GLU10
|
4.7
|
44.7
|
1.0
|
CA
|
B:GLU36
|
4.7
|
48.0
|
1.0
|
|
Cobalt binding site 4 out
of 7 in 1ovu
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Cobalt Binding Sites List in 1ovu
Cobalt binding site 4 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co103
b:59.2
occ:1.00
|
OE2
|
D:GLU36
|
1.9
|
65.9
|
1.0
|
OE2
|
C:GLU10
|
2.0
|
63.0
|
1.0
|
OE1
|
C:GLU36
|
2.0
|
63.4
|
1.0
|
OE1
|
C:GLU10
|
2.0
|
66.4
|
1.0
|
ND1
|
C:HIS39
|
2.1
|
49.6
|
1.0
|
CD
|
C:GLU10
|
2.3
|
62.8
|
1.0
|
CE1
|
C:HIS39
|
2.9
|
51.2
|
1.0
|
CD
|
C:GLU36
|
3.1
|
68.8
|
1.0
|
CD
|
D:GLU36
|
3.2
|
71.5
|
1.0
|
CG
|
C:HIS39
|
3.2
|
48.0
|
1.0
|
CB
|
C:HIS39
|
3.7
|
48.9
|
1.0
|
OE2
|
C:GLU36
|
3.7
|
63.4
|
1.0
|
CG
|
C:GLU10
|
3.8
|
60.8
|
1.0
|
OE1
|
D:GLU36
|
4.0
|
68.0
|
1.0
|
CG
|
D:GLU36
|
4.1
|
67.0
|
1.0
|
CO
|
D:CO104
|
4.1
|
52.1
|
1.0
|
NE2
|
C:HIS39
|
4.1
|
41.4
|
1.0
|
CD2
|
C:HIS39
|
4.3
|
49.6
|
1.0
|
CG
|
C:GLU36
|
4.3
|
67.7
|
1.0
|
CB
|
C:GLU36
|
4.4
|
60.5
|
1.0
|
CG2
|
D:ILE32
|
4.4
|
60.0
|
1.0
|
CA
|
C:GLU36
|
4.5
|
60.7
|
1.0
|
CB
|
C:GLU10
|
4.7
|
60.5
|
1.0
|
OH
|
D:TYR17
|
4.7
|
44.9
|
1.0
|
OE1
|
D:GLU10
|
4.7
|
59.5
|
1.0
|
CE1
|
D:TYR17
|
4.9
|
54.3
|
1.0
|
CE1
|
D:HIS39
|
5.0
|
37.9
|
1.0
|
|
Cobalt binding site 5 out
of 7 in 1ovu
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Cobalt Binding Sites List in 1ovu
Cobalt binding site 5 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co104
b:52.1
occ:1.00
|
OE1
|
D:GLU36
|
1.8
|
68.0
|
1.0
|
OE2
|
C:GLU36
|
1.8
|
63.4
|
1.0
|
OE2
|
D:GLU10
|
1.9
|
73.5
|
1.0
|
ND1
|
D:HIS39
|
2.0
|
34.7
|
1.0
|
OE1
|
D:GLU10
|
2.0
|
59.5
|
1.0
|
CD
|
D:GLU10
|
2.2
|
68.6
|
1.0
|
CD
|
D:GLU36
|
2.5
|
71.5
|
1.0
|
CE1
|
D:HIS39
|
2.8
|
37.9
|
1.0
|
OE2
|
D:GLU36
|
2.9
|
65.9
|
1.0
|
CD
|
C:GLU36
|
2.9
|
68.8
|
1.0
|
CG
|
D:HIS39
|
3.2
|
43.3
|
1.0
|
OE1
|
C:GLU36
|
3.4
|
63.4
|
1.0
|
CB
|
D:HIS39
|
3.7
|
49.8
|
1.0
|
CG
|
D:GLU36
|
3.8
|
67.0
|
1.0
|
CG
|
D:GLU10
|
3.8
|
59.0
|
1.0
|
NE2
|
D:HIS39
|
3.9
|
51.2
|
1.0
|
CG2
|
C:ILE32
|
4.1
|
52.1
|
1.0
|
CO
|
C:CO103
|
4.1
|
59.2
|
1.0
|
CB
|
D:GLU36
|
4.1
|
61.0
|
1.0
|
CD2
|
D:HIS39
|
4.2
|
42.4
|
1.0
|
CG
|
C:GLU36
|
4.2
|
67.7
|
1.0
|
CA
|
D:GLU36
|
4.3
|
62.4
|
1.0
|
CE1
|
C:TYR17
|
4.4
|
44.5
|
1.0
|
OH
|
C:TYR17
|
4.5
|
45.4
|
1.0
|
CB
|
D:GLU10
|
4.7
|
56.2
|
1.0
|
CZ
|
C:TYR17
|
4.8
|
49.1
|
1.0
|
CE1
|
C:HIS39
|
4.9
|
51.2
|
1.0
|
O
|
D:ASP35
|
5.0
|
62.4
|
1.0
|
|
Cobalt binding site 6 out
of 7 in 1ovu
Go back to
Cobalt Binding Sites List in 1ovu
Cobalt binding site 6 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co106
b:76.7
occ:1.00
|
OE1
|
D:GLU19
|
2.3
|
51.7
|
1.0
|
OE1
|
D:GLN16
|
2.8
|
85.2
|
1.0
|
CD
|
D:GLU19
|
3.2
|
57.1
|
1.0
|
OE2
|
D:GLU19
|
3.5
|
65.3
|
1.0
|
CD
|
D:GLN16
|
3.5
|
86.2
|
1.0
|
NE2
|
D:GLN16
|
3.5
|
90.3
|
1.0
|
CG
|
D:GLU19
|
4.6
|
59.4
|
1.0
|
OE1
|
C:GLU5
|
4.7
|
77.2
|
1.0
|
OE2
|
C:GLU5
|
4.7
|
76.0
|
1.0
|
CB
|
D:GLU19
|
4.8
|
63.1
|
1.0
|
CG
|
D:GLN16
|
5.0
|
70.4
|
1.0
|
|
Cobalt binding site 7 out
of 7 in 1ovu
Go back to
Cobalt Binding Sites List in 1ovu
Cobalt binding site 7 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 7 of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co107
b:89.1
occ:1.00
|
O
|
D:HOH110
|
2.9
|
36.9
|
1.0
|
O
|
D:HOH109
|
2.9
|
51.2
|
1.0
|
O
|
D:HOH108
|
3.1
|
49.9
|
1.0
|
OE1
|
D:GLU44
|
3.2
|
63.8
|
1.0
|
OE2
|
D:GLU44
|
3.5
|
65.7
|
1.0
|
CD
|
D:GLU44
|
3.6
|
64.4
|
1.0
|
CG
|
D:GLU44
|
4.8
|
59.1
|
1.0
|
|
Reference:
S.Geremia,
L.Di Costanzo,
L.Randaccio,
D.E.Engel,
A.Lombardi,
F.Nastri,
W.F.Degrado.
Response of A Designed Metalloprotein to Changes in Metal Ion Coordination, Exogenous Ligands, and Active Site Volume Determined By X-Ray Crystallography. J.Am.Chem.Soc. V. 127 17266 2005.
ISSN: ISSN 0002-7863
PubMed: 16332076
DOI: 10.1021/JA054199X
Page generated: Tue Jul 30 14:29:35 2024
|