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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 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 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 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 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 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 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

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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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