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Cobalt in PDB 2xwq: Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product

Enzymatic activity of Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product

All present enzymatic activity of Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product:
4.99.1.3;

Protein crystallography data

The structure of Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product, PDB code: 2xwq was solved by D.Ladakis, A.A.Brindley, E.Deery, M.J.Warren, R.W.Pickersgill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.57 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.010, 99.000, 116.660, 90.00, 90.00, 90.00
R / Rfree (%) 21.656 / 28.234

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product (pdb code 2xwq). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product, PDB code: 2xwq:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 2xwq

Go back to Cobalt Binding Sites List in 2xwq
Cobalt binding site 1 out of 4 in the Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1126

b:46.8
occ:0.50
CO B:SIR1126 0.0 46.8 0.5
CO B:SIR1126 0.1 25.2 0.5
NB B:SIR1126 1.8 21.7 0.5
NB B:SIR1126 1.9 43.7 0.5
NA B:SIR1126 1.9 44.0 0.5
NC B:SIR1126 1.9 17.4 0.5
ND B:SIR1126 1.9 41.8 0.5
NC B:SIR1126 2.0 42.3 0.5
NA B:SIR1126 2.0 19.2 0.5
ND B:SIR1126 2.0 17.3 0.5
O4B B:SIR1126 2.8 23.3 0.5
C1B B:SIR1126 2.8 22.6 0.5
C4B B:SIR1126 2.8 21.9 0.5
C4A B:SIR1126 2.9 44.4 0.5
C1B B:SIR1126 2.9 44.3 0.5
C4B B:SIR1126 2.9 44.0 0.5
C1A B:SIR1126 2.9 43.1 0.5
C1C B:SIR1126 2.9 13.7 0.5
C4A B:SIR1126 3.0 21.9 0.5
C4C B:SIR1126 3.0 15.5 0.5
C1C B:SIR1126 3.0 40.9 0.5
C4D B:SIR1126 3.0 39.8 0.5
C1D B:SIR1126 3.0 40.9 0.5
C1A B:SIR1126 3.0 19.6 0.5
C4D B:SIR1126 3.0 13.8 0.5
C4C B:SIR1126 3.0 40.8 0.5
C1D B:SIR1126 3.1 15.1 0.5
CHB B:SIR1126 3.2 44.0 0.5
CHB B:SIR1126 3.3 20.9 0.5
CHC B:SIR1126 3.3 15.8 0.5
CHC B:SIR1126 3.3 43.4 0.5
CHA B:SIR1126 3.4 40.6 0.5
CHA B:SIR1126 3.4 17.5 0.5
CHD B:SIR1126 3.4 40.0 0.5
CHD B:SIR1126 3.4 13.0 0.5
O2A B:SIR1126 3.6 54.6 0.5
CE1 B:HIS10 3.6 20.3 1.0
O A:HOH2028 3.7 33.4 1.0
CE1 A:HIS10 3.7 17.9 1.0
CEB B:SIR1126 3.8 27.1 0.5
C2B B:SIR1126 4.0 24.9 0.5
C3B B:SIR1126 4.1 24.5 0.5
C2C B:SIR1126 4.2 11.6 0.5
C3A B:SIR1126 4.2 44.8 0.5
C3C B:SIR1126 4.2 13.4 0.5
NE2 B:HIS10 4.2 25.6 1.0
C2B B:SIR1126 4.2 45.0 0.5
C2D B:SIR1126 4.2 39.9 0.5
C3D B:SIR1126 4.2 38.2 0.5
C2C B:SIR1126 4.2 38.4 0.5
C3B B:SIR1126 4.2 45.1 0.5
NE2 A:HIS10 4.2 21.0 1.0
C2A B:SIR1126 4.2 43.5 0.5
C3D B:SIR1126 4.2 12.1 0.5
C3C B:SIR1126 4.3 40.1 0.5
C2D B:SIR1126 4.3 14.1 0.5
CE1 B:HIS74 4.3 17.2 1.0
CDB B:SIR1126 4.3 26.5 0.5
C3A B:SIR1126 4.3 22.6 0.5
C2A B:SIR1126 4.4 20.5 0.5
CE1 A:HIS74 4.4 18.9 1.0
CCA B:SIR1126 4.5 53.4 0.5
ND1 A:HIS10 4.5 20.2 1.0
ND1 B:HIS10 4.5 24.9 1.0
O2B B:SIR1126 4.6 48.0 0.5
O3B B:SIR1126 4.7 27.0 0.5
O3A B:SIR1126 4.7 21.7 0.5
CAA B:SIR1126 4.7 47.4 0.5
CBB B:SIR1126 4.8 29.6 0.5
NE2 B:HIS74 4.9 15.7 1.0
CDA B:SIR1126 4.9 44.8 0.5
CBA B:SIR1126 5.0 50.6 0.5
CAB B:SIR1126 5.0 46.3 0.5

Cobalt binding site 2 out of 4 in 2xwq

Go back to Cobalt Binding Sites List in 2xwq
Cobalt binding site 2 out of 4 in the Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1126

b:25.2
occ:0.50
CO B:SIR1126 0.0 25.2 0.5
CO B:SIR1126 0.1 46.8 0.5
NB B:SIR1126 1.8 43.7 0.5
NB B:SIR1126 1.9 21.7 0.5
NA B:SIR1126 1.9 19.2 0.5
NA B:SIR1126 1.9 44.0 0.5
NC B:SIR1126 1.9 42.3 0.5
ND B:SIR1126 2.0 17.3 0.5
NC B:SIR1126 2.0 17.4 0.5
ND B:SIR1126 2.0 41.8 0.5
C1B B:SIR1126 2.8 44.3 0.5
O4B B:SIR1126 2.8 23.3 0.5
C4B B:SIR1126 2.8 44.0 0.5
C1B B:SIR1126 2.8 22.6 0.5
C4A B:SIR1126 2.9 44.4 0.5
C4B B:SIR1126 2.9 21.9 0.5
C4A B:SIR1126 2.9 21.9 0.5
C1C B:SIR1126 2.9 40.9 0.5
C1A B:SIR1126 2.9 19.6 0.5
C4D B:SIR1126 3.0 13.8 0.5
C1A B:SIR1126 3.0 43.1 0.5
C1C B:SIR1126 3.0 13.7 0.5
C4C B:SIR1126 3.0 40.8 0.5
C4C B:SIR1126 3.0 15.5 0.5
C1D B:SIR1126 3.1 15.1 0.5
C1D B:SIR1126 3.1 40.9 0.5
C4D B:SIR1126 3.1 39.8 0.5
CHB B:SIR1126 3.2 44.0 0.5
CHB B:SIR1126 3.2 20.9 0.5
CHC B:SIR1126 3.3 43.4 0.5
CHA B:SIR1126 3.3 17.5 0.5
CHC B:SIR1126 3.4 15.8 0.5
CHA B:SIR1126 3.4 40.6 0.5
CHD B:SIR1126 3.5 40.0 0.5
CHD B:SIR1126 3.5 13.0 0.5
O2A B:SIR1126 3.6 54.6 0.5
CE1 B:HIS10 3.6 20.3 1.0
O A:HOH2028 3.6 33.4 1.0
CE1 A:HIS10 3.7 17.9 1.0
CEB B:SIR1126 3.8 27.1 0.5
C2B B:SIR1126 4.0 24.9 0.5
C2B B:SIR1126 4.1 45.0 0.5
C3B B:SIR1126 4.1 24.5 0.5
C3B B:SIR1126 4.1 45.1 0.5
C2C B:SIR1126 4.2 38.4 0.5
NE2 B:HIS10 4.2 25.6 1.0
C3D B:SIR1126 4.2 12.1 0.5
C3A B:SIR1126 4.2 44.8 0.5
C3C B:SIR1126 4.2 40.1 0.5
C3C B:SIR1126 4.2 13.4 0.5
C2C B:SIR1126 4.2 11.6 0.5
C2D B:SIR1126 4.3 14.1 0.5
NE2 A:HIS10 4.3 21.0 1.0
C3A B:SIR1126 4.3 22.6 0.5
C2A B:SIR1126 4.3 20.5 0.5
C2A B:SIR1126 4.3 43.5 0.5
C2D B:SIR1126 4.3 39.9 0.5
C3D B:SIR1126 4.3 38.2 0.5
CDB B:SIR1126 4.4 26.5 0.5
CE1 A:HIS74 4.4 18.9 1.0
CE1 B:HIS74 4.4 17.2 1.0
CCA B:SIR1126 4.5 53.4 0.5
ND1 A:HIS10 4.5 20.2 1.0
ND1 B:HIS10 4.5 24.9 1.0
O2B B:SIR1126 4.6 48.0 0.5
O3A B:SIR1126 4.7 21.7 0.5
O3B B:SIR1126 4.7 27.0 0.5
CAA B:SIR1126 4.8 47.4 0.5
CBB B:SIR1126 4.9 29.6 0.5
CAB B:SIR1126 4.9 46.3 0.5
CDB B:SIR1126 4.9 43.7 0.5
NE2 B:HIS74 5.0 15.7 1.0
CDA B:SIR1126 5.0 44.8 0.5
CBA B:SIR1126 5.0 50.6 0.5

Cobalt binding site 3 out of 4 in 2xwq

Go back to Cobalt Binding Sites List in 2xwq
Cobalt binding site 3 out of 4 in the Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1126

b:0.1
occ:0.50
CO D:SIR1126 0.0 0.1 0.5
CO D:SIR1126 0.1 34.7 0.5
NB D:SIR1126 1.8 0.6 0.5
NA D:SIR1126 1.9 0.5 0.5
NA D:SIR1126 1.9 31.1 0.5
NB D:SIR1126 1.9 33.0 0.5
ND D:SIR1126 1.9 0.3 0.5
NC D:SIR1126 1.9 0.4 0.5
NC D:SIR1126 2.0 30.2 0.5
ND D:SIR1126 2.0 27.7 0.5
C1B D:SIR1126 2.8 0.4 0.5
C4B D:SIR1126 2.8 0.5 0.5
C4A D:SIR1126 2.9 0.3 0.5
C1A D:SIR1126 2.9 0.3 0.5
C4A D:SIR1126 2.9 31.9 0.5
C1B D:SIR1126 2.9 33.4 0.5
C1A D:SIR1126 2.9 30.8 0.5
C4B D:SIR1126 2.9 33.4 0.5
C4D D:SIR1126 3.0 0.0 0.5
C1C D:SIR1126 3.0 0.2 0.5
C1D D:SIR1126 3.0 0.9 0.5
C1C D:SIR1126 3.0 29.3 0.5
C4C D:SIR1126 3.0 0.9 0.5
C4D D:SIR1126 3.0 27.8 0.5
C4C D:SIR1126 3.1 27.8 0.5
C1D D:SIR1126 3.1 26.8 0.5
CHB D:SIR1126 3.2 0.3 0.5
CE1 C:HIS10 3.3 39.8 1.0
CHB D:SIR1126 3.3 32.6 0.5
CHC D:SIR1126 3.3 0.4 0.5
CHA D:SIR1126 3.3 0.1 0.5
CHA D:SIR1126 3.3 28.1 0.5
CHC D:SIR1126 3.4 32.3 0.5
CHD D:SIR1126 3.4 0.8 0.5
CHD D:SIR1126 3.5 26.6 0.5
O4B D:SIR1126 3.7 37.9 0.5
NE2 D:HIS10 3.8 43.5 1.0
NE2 C:HIS10 3.8 40.5 1.0
C3B D:SIR1126 4.0 0.4 0.5
C2B D:SIR1126 4.1 0.2 0.5
C2A D:SIR1126 4.2 0.2 0.5
C3A D:SIR1126 4.2 0.2 0.5
C3D D:SIR1126 4.2 0.7 0.5
C2D D:SIR1126 4.2 0.7 0.5
C2C D:SIR1126 4.2 0.7 0.5
C3C D:SIR1126 4.2 0.4 0.5
C2C D:SIR1126 4.2 27.2 0.5
C3A D:SIR1126 4.3 31.4 0.5
C2B D:SIR1126 4.3 35.0 0.5
C3B D:SIR1126 4.3 35.1 0.5
C3D D:SIR1126 4.3 21.7 0.5
C2A D:SIR1126 4.3 30.1 0.5
C3C D:SIR1126 4.3 27.7 0.5
ND1 C:HIS10 4.3 42.1 1.0
C2D D:SIR1126 4.3 22.6 0.5
CE1 D:HIS10 4.4 44.0 1.0
CE1 C:HIS74 4.5 39.6 1.0
CE1 D:HIS74 4.6 31.7 1.0
CD2 D:HIS10 4.6 41.1 1.0
CEB D:SIR1126 4.6 35.8 0.5
CDA D:SIR1126 4.7 0.1 0.5
CDB D:SIR1126 4.7 1.0 0.5
NH1 D:ARG44 4.8 62.3 1.0
O3A D:SIR1126 4.8 23.2 0.5
CBA D:SIR1126 4.9 0.9 0.5
CD2 C:HIS10 5.0 38.9 1.0
CBB D:SIR1126 5.0 35.0 0.5

Cobalt binding site 4 out of 4 in 2xwq

Go back to Cobalt Binding Sites List in 2xwq
Cobalt binding site 4 out of 4 in the Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Anaerobic Cobalt Chelatase From Archeaoglobus Fulgidus ( Cbix) in Complex with Metalated Sirohydrochlorin Product within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1126

b:34.7
occ:0.50
CO D:SIR1126 0.0 34.7 0.5
CO D:SIR1126 0.1 0.1 0.5
NB D:SIR1126 1.8 0.6 0.5
NA D:SIR1126 1.9 0.5 0.5
NA D:SIR1126 1.9 31.1 0.5
NB D:SIR1126 1.9 33.0 0.5
NC D:SIR1126 1.9 0.4 0.5
ND D:SIR1126 1.9 0.3 0.5
NC D:SIR1126 2.0 30.2 0.5
ND D:SIR1126 2.0 27.7 0.5
C4B D:SIR1126 2.8 0.5 0.5
C1B D:SIR1126 2.8 0.4 0.5
C4A D:SIR1126 2.9 31.9 0.5
C4A D:SIR1126 2.9 0.3 0.5
C1A D:SIR1126 2.9 0.3 0.5
C1B D:SIR1126 2.9 33.4 0.5
C1A D:SIR1126 2.9 30.8 0.5
C4B D:SIR1126 2.9 33.4 0.5
C1C D:SIR1126 3.0 0.2 0.5
C4D D:SIR1126 3.0 0.0 0.5
C1D D:SIR1126 3.0 0.9 0.5
C4C D:SIR1126 3.0 0.9 0.5
C1C D:SIR1126 3.0 29.3 0.5
C4D D:SIR1126 3.0 27.8 0.5
C4C D:SIR1126 3.1 27.8 0.5
C1D D:SIR1126 3.1 26.8 0.5
CHB D:SIR1126 3.2 0.3 0.5
CHB D:SIR1126 3.3 32.6 0.5
CHC D:SIR1126 3.3 0.4 0.5
CHA D:SIR1126 3.3 28.1 0.5
CHA D:SIR1126 3.3 0.1 0.5
CHC D:SIR1126 3.4 32.3 0.5
CE1 C:HIS10 3.4 39.8 1.0
CHD D:SIR1126 3.4 0.8 0.5
CHD D:SIR1126 3.5 26.6 0.5
NE2 D:HIS10 3.7 43.5 1.0
O4B D:SIR1126 3.8 37.9 0.5
NE2 C:HIS10 3.9 40.5 1.0
C3B D:SIR1126 4.0 0.4 0.5
C2B D:SIR1126 4.0 0.2 0.5
C2A D:SIR1126 4.1 0.2 0.5
C3A D:SIR1126 4.2 0.2 0.5
C2D D:SIR1126 4.2 0.7 0.5
C3D D:SIR1126 4.2 0.7 0.5
C2C D:SIR1126 4.2 0.7 0.5
C3C D:SIR1126 4.2 0.4 0.5
C3A D:SIR1126 4.2 31.4 0.5
C2B D:SIR1126 4.2 35.0 0.5
C2C D:SIR1126 4.2 27.2 0.5
C2A D:SIR1126 4.2 30.1 0.5
C3B D:SIR1126 4.3 35.1 0.5
CE1 D:HIS10 4.3 44.0 1.0
C3D D:SIR1126 4.3 21.7 0.5
C3C D:SIR1126 4.3 27.7 0.5
C2D D:SIR1126 4.3 22.6 0.5
ND1 C:HIS10 4.4 42.1 1.0
CE1 D:HIS74 4.5 31.7 1.0
CD2 D:HIS10 4.5 41.1 1.0
NH1 D:ARG44 4.6 62.3 1.0
CE1 C:HIS74 4.6 39.6 1.0
CEB D:SIR1126 4.7 35.8 0.5
CDB D:SIR1126 4.7 1.0 0.5
CDA D:SIR1126 4.7 0.1 0.5
O3A D:SIR1126 4.9 23.2 0.5
CBB D:SIR1126 4.9 35.0 0.5
CBA D:SIR1126 5.0 0.9 0.5

Reference:

C.V.Romao, D.Ladakis, S.A.Lobo, M.A.Carrondo, A.A.Brindley, E.Deery, P.M.Matias, R.W.Pickersgill, L.M.Saraiva, M.J.Warren. Evolution in A Family of Chelatases Facilitated By the Introduction of Active Site Asymmetry and Protein Oligomerization. Proc.Natl.Acad.Sci.Usa V. 108 97 2011.
ISSN: ISSN 0027-8424
PubMed: 21173279
DOI: 10.1073/PNAS.1014298108
Page generated: Sun Dec 13 10:39:29 2020

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