Cobalt in PDB 1ovv: Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form II)
Protein crystallography data
The structure of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form II), PDB code: 1ovv
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)
|
15.00 /
2.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
36.920,
80.050,
96.620,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26.7 /
32
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form II)
(pdb code 1ovv). 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 II), PDB code: 1ovv:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
Cobalt binding site 1 out
of 7 in 1ovv
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Cobalt Binding Sites List in 1ovv
Cobalt binding site 1 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form II)
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 II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co101
b:52.0
occ:1.00
|
ND1
|
A:HIS39
|
1.8
|
17.4
|
1.0
|
OE2
|
A:GLU10
|
1.8
|
53.0
|
1.0
|
OE1
|
A:GLU36
|
1.8
|
48.3
|
1.0
|
OE2
|
B:GLU36
|
2.0
|
55.3
|
1.0
|
OE1
|
A:GLU10
|
2.0
|
39.9
|
1.0
|
CD
|
A:GLU10
|
2.2
|
38.7
|
1.0
|
CE1
|
A:HIS39
|
2.5
|
24.6
|
1.0
|
CD
|
A:GLU36
|
2.9
|
48.9
|
1.0
|
CG
|
A:HIS39
|
3.0
|
27.0
|
1.0
|
CD
|
B:GLU36
|
3.1
|
55.5
|
1.0
|
CB
|
A:HIS39
|
3.6
|
42.7
|
1.0
|
OE2
|
A:GLU36
|
3.6
|
52.6
|
1.0
|
CG
|
A:GLU10
|
3.7
|
37.0
|
1.0
|
NE2
|
A:HIS39
|
3.8
|
21.8
|
1.0
|
OE1
|
B:GLU36
|
3.8
|
45.0
|
1.0
|
CB
|
A:GLU36
|
3.9
|
40.2
|
1.0
|
CA
|
A:GLU36
|
3.9
|
44.2
|
1.0
|
CG
|
A:GLU36
|
3.9
|
38.2
|
1.0
|
CD2
|
A:HIS39
|
4.0
|
20.6
|
1.0
|
CO
|
B:CO102
|
4.1
|
61.5
|
1.0
|
CG
|
B:GLU36
|
4.3
|
60.3
|
1.0
|
O
|
A:ASP35
|
4.3
|
39.8
|
1.0
|
OH
|
B:TYR17
|
4.4
|
48.9
|
1.0
|
CG2
|
B:ILE32
|
4.4
|
53.9
|
1.0
|
CB
|
A:GLU10
|
4.6
|
43.6
|
1.0
|
N
|
A:GLU36
|
4.7
|
40.9
|
1.0
|
C
|
A:ASP35
|
4.8
|
43.7
|
1.0
|
CE1
|
B:TYR17
|
4.8
|
49.7
|
1.0
|
CE1
|
B:HIS39
|
4.8
|
20.7
|
1.0
|
C
|
A:GLU36
|
5.0
|
49.1
|
1.0
|
OE1
|
B:GLU10
|
5.0
|
54.3
|
1.0
|
|
Cobalt binding site 2 out
of 7 in 1ovv
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Cobalt Binding Sites List in 1ovv
Cobalt binding site 2 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form II)
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 II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co102
b:61.5
occ:1.00
|
OE1
|
B:GLU36
|
1.7
|
45.0
|
1.0
|
OE2
|
B:GLU10
|
1.8
|
55.0
|
1.0
|
OE2
|
A:GLU36
|
2.1
|
52.6
|
1.0
|
ND1
|
B:HIS39
|
2.1
|
28.4
|
1.0
|
OE1
|
B:GLU10
|
2.1
|
54.3
|
1.0
|
CD
|
B:GLU10
|
2.2
|
49.0
|
1.0
|
CD
|
B:GLU36
|
2.8
|
55.5
|
1.0
|
CE1
|
B:HIS39
|
2.9
|
20.7
|
1.0
|
CD
|
A:GLU36
|
3.0
|
48.9
|
1.0
|
OE1
|
A:GLU36
|
3.2
|
48.3
|
1.0
|
CG
|
B:HIS39
|
3.2
|
32.0
|
1.0
|
OE2
|
B:GLU36
|
3.2
|
55.3
|
1.0
|
CB
|
B:HIS39
|
3.7
|
37.3
|
1.0
|
CG
|
B:GLU10
|
3.7
|
46.4
|
1.0
|
CG2
|
A:ILE32
|
3.9
|
45.2
|
1.0
|
OH
|
A:TYR17
|
4.0
|
37.7
|
1.0
|
CA
|
B:GLU36
|
4.0
|
61.5
|
1.0
|
NE2
|
B:HIS39
|
4.0
|
28.2
|
1.0
|
CG
|
B:GLU36
|
4.1
|
60.3
|
1.0
|
CO
|
A:CO101
|
4.1
|
52.0
|
1.0
|
CB
|
B:GLU36
|
4.2
|
63.3
|
1.0
|
CD2
|
B:HIS39
|
4.2
|
28.0
|
1.0
|
CG
|
A:GLU36
|
4.4
|
38.2
|
1.0
|
CE1
|
A:TYR17
|
4.5
|
38.6
|
1.0
|
CB
|
B:GLU10
|
4.5
|
48.1
|
1.0
|
CZ
|
A:TYR17
|
4.7
|
37.4
|
1.0
|
N
|
B:GLU36
|
4.8
|
62.1
|
1.0
|
CE1
|
A:HIS39
|
4.8
|
24.6
|
1.0
|
|
Cobalt binding site 3 out
of 7 in 1ovv
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Cobalt Binding Sites List in 1ovv
Cobalt binding site 3 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form II)
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 II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co103
b:61.7
occ:1.00
|
OE2
|
D:GLU36
|
1.8
|
34.6
|
1.0
|
ND1
|
C:HIS39
|
1.9
|
51.5
|
1.0
|
OE1
|
C:GLU36
|
2.0
|
52.3
|
1.0
|
OE1
|
C:GLU10
|
2.0
|
52.1
|
1.0
|
OE2
|
C:GLU10
|
2.1
|
32.0
|
1.0
|
CD
|
C:GLU10
|
2.3
|
46.2
|
1.0
|
CE1
|
C:HIS39
|
2.6
|
50.8
|
1.0
|
CD
|
C:GLU36
|
2.7
|
52.7
|
1.0
|
OE2
|
C:GLU36
|
2.9
|
47.0
|
1.0
|
CD
|
D:GLU36
|
3.1
|
50.6
|
1.0
|
CG
|
C:HIS39
|
3.1
|
53.5
|
1.0
|
CO
|
D:CO104
|
3.6
|
62.5
|
1.0
|
CB
|
C:HIS39
|
3.7
|
50.5
|
1.0
|
CG
|
C:GLU10
|
3.8
|
58.2
|
1.0
|
NE2
|
C:HIS39
|
3.8
|
45.9
|
1.0
|
OE1
|
D:GLU36
|
3.9
|
59.2
|
1.0
|
CD2
|
C:HIS39
|
4.1
|
51.1
|
1.0
|
CG
|
D:GLU36
|
4.1
|
48.8
|
1.0
|
CG
|
C:GLU36
|
4.1
|
39.4
|
1.0
|
CE1
|
D:TYR17
|
4.2
|
42.9
|
1.0
|
OH
|
D:TYR17
|
4.5
|
40.1
|
1.0
|
CB
|
C:GLU10
|
4.6
|
68.8
|
1.0
|
CB
|
C:GLU36
|
4.6
|
42.9
|
1.0
|
CZ
|
D:TYR17
|
4.7
|
39.8
|
1.0
|
CE1
|
D:HIS39
|
4.7
|
63.5
|
1.0
|
CA
|
C:GLU36
|
4.7
|
44.0
|
1.0
|
ND1
|
D:HIS39
|
4.8
|
64.6
|
1.0
|
CA
|
C:GLU10
|
4.8
|
69.4
|
1.0
|
CG2
|
D:ILE32
|
4.9
|
47.4
|
1.0
|
O
|
C:ASP35
|
5.0
|
39.5
|
1.0
|
|
Cobalt binding site 4 out
of 7 in 1ovv
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Cobalt Binding Sites List in 1ovv
Cobalt binding site 4 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form II)
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 II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co107
b:84.1
occ:1.00
|
OE1
|
C:GLU19
|
2.2
|
75.3
|
1.0
|
CD
|
C:GLU19
|
2.4
|
80.7
|
1.0
|
CG
|
C:GLU19
|
2.7
|
79.4
|
1.0
|
OE2
|
C:GLU19
|
3.3
|
85.2
|
1.0
|
CB
|
C:GLU19
|
3.5
|
76.6
|
1.0
|
OE2
|
C:GLU22
|
4.0
|
0.2
|
1.0
|
CA
|
C:GLU19
|
4.5
|
77.0
|
1.0
|
C
|
C:GLU19
|
4.8
|
78.8
|
1.0
|
|
Cobalt binding site 5 out
of 7 in 1ovv
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Cobalt Binding Sites List in 1ovv
Cobalt binding site 5 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form II)
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 II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co104
b:62.5
occ:1.00
|
OE2
|
C:GLU36
|
1.9
|
47.0
|
1.0
|
OE1
|
D:GLU10
|
1.9
|
51.7
|
1.0
|
OE1
|
D:GLU36
|
1.9
|
59.2
|
1.0
|
ND1
|
D:HIS39
|
2.1
|
64.6
|
1.0
|
OE2
|
D:GLU10
|
2.3
|
51.2
|
1.0
|
CD
|
D:GLU10
|
2.4
|
51.8
|
1.0
|
CD
|
D:GLU36
|
2.6
|
50.6
|
1.0
|
OE2
|
D:GLU36
|
2.7
|
34.6
|
1.0
|
CE1
|
D:HIS39
|
3.0
|
63.5
|
1.0
|
CD
|
C:GLU36
|
3.1
|
52.7
|
1.0
|
CG
|
D:HIS39
|
3.2
|
56.7
|
1.0
|
CB
|
D:HIS39
|
3.6
|
55.6
|
1.0
|
CO
|
C:CO103
|
3.6
|
61.7
|
1.0
|
OE1
|
C:GLU36
|
3.9
|
52.3
|
1.0
|
CG
|
D:GLU10
|
3.9
|
57.7
|
1.0
|
CG
|
D:GLU36
|
4.1
|
48.8
|
1.0
|
CG
|
C:GLU36
|
4.2
|
39.4
|
1.0
|
NE2
|
D:HIS39
|
4.2
|
59.2
|
1.0
|
CD2
|
D:HIS39
|
4.3
|
47.3
|
1.0
|
CE1
|
C:HIS39
|
4.4
|
50.8
|
1.0
|
CA
|
D:GLU36
|
4.5
|
46.0
|
1.0
|
CG2
|
C:ILE32
|
4.6
|
52.6
|
1.0
|
CB
|
D:GLU36
|
4.6
|
48.0
|
1.0
|
CB
|
D:GLU10
|
4.7
|
62.9
|
1.0
|
OH
|
C:TYR17
|
4.7
|
37.4
|
1.0
|
OE1
|
C:GLU10
|
4.8
|
52.1
|
1.0
|
ND1
|
C:HIS39
|
4.8
|
51.5
|
1.0
|
O
|
D:ASP35
|
4.9
|
47.7
|
1.0
|
|
Cobalt binding site 6 out
of 7 in 1ovv
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Cobalt Binding Sites List in 1ovv
Cobalt binding site 6 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form II)
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 II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Co105
b:51.4
occ:1.00
|
OE1
|
E:GLU36
|
1.7
|
56.1
|
1.0
|
OE1
|
E:GLU10
|
1.8
|
49.9
|
1.0
|
ND1
|
E:HIS39
|
1.8
|
42.2
|
1.0
|
OE2
|
F:GLU36
|
1.9
|
44.8
|
1.0
|
OE2
|
E:GLU10
|
2.2
|
52.5
|
1.0
|
CD
|
E:GLU10
|
2.2
|
46.0
|
1.0
|
CD
|
E:GLU36
|
2.6
|
53.6
|
1.0
|
CE1
|
E:HIS39
|
2.6
|
51.4
|
1.0
|
OE2
|
E:GLU36
|
2.9
|
44.9
|
1.0
|
CG
|
E:HIS39
|
2.9
|
54.6
|
1.0
|
CD
|
F:GLU36
|
3.1
|
53.8
|
1.0
|
CB
|
E:HIS39
|
3.4
|
58.4
|
1.0
|
CG
|
E:GLU10
|
3.7
|
52.2
|
1.0
|
NE2
|
E:HIS39
|
3.8
|
50.2
|
1.0
|
OE1
|
F:GLU36
|
3.9
|
63.2
|
1.0
|
CD2
|
E:HIS39
|
4.0
|
49.9
|
1.0
|
CG2
|
F:ILE32
|
4.0
|
53.6
|
1.0
|
CG
|
E:GLU36
|
4.0
|
54.6
|
1.0
|
CO
|
F:CO106
|
4.1
|
54.1
|
1.0
|
CG
|
F:GLU36
|
4.1
|
44.6
|
1.0
|
CA
|
E:GLU36
|
4.2
|
54.2
|
1.0
|
CB
|
E:GLU36
|
4.4
|
54.8
|
1.0
|
CB
|
E:GLU10
|
4.4
|
47.6
|
1.0
|
OH
|
F:TYR17
|
4.4
|
54.8
|
1.0
|
CE1
|
F:HIS39
|
4.6
|
37.8
|
1.0
|
OE1
|
F:GLU10
|
4.9
|
45.2
|
1.0
|
CA
|
E:HIS39
|
4.9
|
55.5
|
1.0
|
O
|
E:ASP35
|
5.0
|
58.2
|
1.0
|
|
Cobalt binding site 7 out
of 7 in 1ovv
Go back to
Cobalt Binding Sites List in 1ovv
Cobalt binding site 7 out
of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form II)
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 II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Co106
b:54.1
occ:1.00
|
OE2
|
F:GLU10
|
1.7
|
53.3
|
1.0
|
OE2
|
E:GLU36
|
1.8
|
44.9
|
1.0
|
OE1
|
F:GLU36
|
1.8
|
63.2
|
1.0
|
ND1
|
F:HIS39
|
1.8
|
41.0
|
1.0
|
OE1
|
F:GLU10
|
1.9
|
45.2
|
1.0
|
CD
|
F:GLU10
|
2.0
|
38.5
|
1.0
|
CE1
|
F:HIS39
|
2.5
|
37.8
|
1.0
|
CD
|
F:GLU36
|
2.6
|
53.8
|
1.0
|
OE2
|
F:GLU36
|
2.9
|
44.8
|
1.0
|
CD
|
E:GLU36
|
3.0
|
53.6
|
1.0
|
CG
|
F:HIS39
|
3.0
|
47.5
|
1.0
|
CG
|
F:GLU10
|
3.4
|
44.7
|
1.0
|
CB
|
F:HIS39
|
3.7
|
53.0
|
1.0
|
NE2
|
F:HIS39
|
3.7
|
35.6
|
1.0
|
OE1
|
E:GLU36
|
3.8
|
56.1
|
1.0
|
CG
|
E:GLU36
|
3.9
|
54.6
|
1.0
|
CD2
|
F:HIS39
|
4.0
|
45.0
|
1.0
|
CG
|
F:GLU36
|
4.0
|
44.6
|
1.0
|
OH
|
E:TYR17
|
4.0
|
45.8
|
1.0
|
CA
|
F:GLU36
|
4.1
|
52.6
|
1.0
|
CO
|
E:CO105
|
4.1
|
51.4
|
1.0
|
CB
|
F:GLU36
|
4.3
|
47.0
|
1.0
|
CB
|
F:GLU10
|
4.4
|
41.1
|
1.0
|
CE1
|
E:TYR17
|
4.4
|
37.3
|
1.0
|
CG2
|
E:ILE32
|
4.5
|
37.3
|
1.0
|
O
|
F:ASP35
|
4.6
|
57.2
|
1.0
|
CZ
|
E:TYR17
|
4.7
|
38.8
|
1.0
|
N
|
F:GLU36
|
4.7
|
53.2
|
1.0
|
CE1
|
E:HIS39
|
4.9
|
51.4
|
1.0
|
C
|
F:ASP35
|
4.9
|
57.4
|
1.0
|
OE1
|
E:GLU10
|
5.0
|
49.9
|
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
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