Atomistry » Cobalt » PDB 1nyi-1rr2 » 1ovv
Atomistry »
  Cobalt »
    PDB 1nyi-1rr2 »
      1ovv »

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

Go back to 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

Go back to 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

Go back to 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

Go back to 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

Go back to 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

Go back to 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: Sun Jul 13 17:41:14 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy