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Cobalt in PDB 4c1n: Corrinoid Protein Reactivation Complex with Activator

Protein crystallography data

The structure of Corrinoid Protein Reactivation Complex with Activator, PDB code: 4c1n was solved by S.E.Hennig, S.Goetzl, J.H.Jeoung, M.Bommer, F.Lendzian, P.Hildebrandt, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.631 / 2.53
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 67.134, 128.175, 163.366, 77.61, 82.25, 88.76
R / Rfree (%) 19.08 / 24.29

Other elements in 4c1n:

The structure of Corrinoid Protein Reactivation Complex with Activator also contains other interesting chemical elements:

Iron (Fe) 16 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Corrinoid Protein Reactivation Complex with Activator (pdb code 4c1n). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Corrinoid Protein Reactivation Complex with Activator, PDB code: 4c1n:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 4c1n

Go back to Cobalt Binding Sites List in 4c1n
Cobalt binding site 1 out of 4 in the Corrinoid Protein Reactivation Complex with Activator


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Corrinoid Protein Reactivation Complex with Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1444

b:25.7
occ:1.00
CO C:B121444 0.0 25.7 1.0
N21 C:B121444 1.9 27.2 1.0
N24 C:B121444 1.9 29.8 1.0
N23 C:B121444 1.9 27.3 1.0
N22 C:B121444 1.9 32.4 1.0
OG J:SER398 2.4 34.9 0.9
C19 C:B121444 2.8 28.8 1.0
C9 C:B121444 2.8 29.5 1.0
C1 C:B121444 2.9 26.6 1.0
C11 C:B121444 2.9 29.9 1.0
C4 C:B121444 2.9 27.3 1.0
C6 C:B121444 2.9 28.2 1.0
C14 C:B121444 3.0 29.0 1.0
C16 C:B121444 3.0 31.4 1.0
CB J:SER398 3.2 29.7 0.9
C10 C:B121444 3.2 34.1 1.0
C5 C:B121444 3.3 28.9 1.0
C15 C:B121444 3.4 27.1 1.0
C20 C:B121444 3.4 21.8 1.0
OG1 C:THR374 3.8 27.5 1.0
C18 C:B121444 4.1 26.4 1.0
C2 C:B121444 4.1 25.9 1.0
O J:SER398 4.2 34.0 0.9
C7 C:B121444 4.2 32.3 1.0
C8 C:B121444 4.2 30.8 1.0
C3 C:B121444 4.2 24.4 1.0
C12 C:B121444 4.2 28.3 1.0
C13 C:B121444 4.2 29.4 1.0
C17 C:B121444 4.3 30.5 1.0
CG2 C:THR374 4.3 25.6 1.0
CA J:SER398 4.6 30.3 0.9
CB C:THR374 4.6 25.8 1.0
C26 C:B121444 4.6 24.3 1.0
C37 C:B121444 4.6 33.0 1.0
C35 C:B121444 4.7 30.8 1.0
C48 C:B121444 4.8 25.6 1.0
O39 C:B121444 4.8 35.2 1.0
C46 C:B121444 4.8 25.3 1.0
C J:SER398 4.8 29.6 0.9
C53 C:B121444 4.9 28.2 1.0
C41 C:B121444 4.9 28.1 1.0
CA C:THR374 5.0 28.5 1.0
C30 C:B121444 5.0 23.1 1.0

Cobalt binding site 2 out of 4 in 4c1n

Go back to Cobalt Binding Sites List in 4c1n
Cobalt binding site 2 out of 4 in the Corrinoid Protein Reactivation Complex with Activator


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Corrinoid Protein Reactivation Complex with Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Co1631

b:20.7
occ:1.00
CO I:B121631 0.0 20.7 1.0
N21 I:B121631 1.9 24.1 1.0
N24 I:B121631 1.9 18.5 1.0
N23 I:B121631 1.9 20.4 1.0
N22 I:B121631 1.9 23.8 1.0
OG I:SER398 2.4 29.9 1.0
C19 I:B121631 2.8 19.9 1.0
C9 I:B121631 2.8 21.7 1.0
C4 I:B121631 2.8 23.6 1.0
C11 I:B121631 2.9 22.0 1.0
C1 I:B121631 2.9 26.1 1.0
C6 I:B121631 2.9 23.5 1.0
C14 I:B121631 3.0 17.4 1.0
C16 I:B121631 3.0 24.8 1.0
C10 I:B121631 3.2 21.8 1.0
CB I:SER398 3.2 25.0 1.0
C5 I:B121631 3.3 21.1 1.0
C15 I:B121631 3.4 18.4 1.0
C20 I:B121631 3.5 20.2 1.0
OG1 A:THR374 3.7 26.9 1.0
O I:SER398 4.1 33.0 1.0
C18 I:B121631 4.1 22.2 1.0
C2 I:B121631 4.1 22.9 1.0
C7 I:B121631 4.1 24.3 1.0
C3 I:B121631 4.2 22.2 1.0
C8 I:B121631 4.2 20.8 1.0
C12 I:B121631 4.2 21.7 1.0
C13 I:B121631 4.2 20.6 1.0
C17 I:B121631 4.3 25.9 1.0
CG2 A:THR374 4.4 22.9 1.0
C26 I:B121631 4.6 24.8 1.0
C37 I:B121631 4.6 26.1 1.0
CA I:SER398 4.6 28.5 1.0
CB A:THR374 4.6 23.3 1.0
C35 I:B121631 4.7 22.4 1.0
O39 I:B121631 4.7 27.1 1.0
C I:SER398 4.8 28.6 1.0
C46 I:B121631 4.8 18.5 1.0
C48 I:B121631 4.8 20.4 1.0
C53 I:B121631 4.9 18.2 1.0
C41 I:B121631 4.9 24.9 1.0
C30 I:B121631 5.0 20.3 1.0

Cobalt binding site 3 out of 4 in 4c1n

Go back to Cobalt Binding Sites List in 4c1n
Cobalt binding site 3 out of 4 in the Corrinoid Protein Reactivation Complex with Activator


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Corrinoid Protein Reactivation Complex with Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Co1631

b:25.6
occ:1.00
CO K:B121631 0.0 25.6 1.0
N21 K:B121631 1.9 34.4 1.0
N24 K:B121631 1.9 32.8 1.0
N23 K:B121631 1.9 32.7 1.0
N22 K:B121631 1.9 31.4 1.0
OG K:SER398 2.4 34.5 1.0
C19 K:B121631 2.8 33.9 1.0
C9 K:B121631 2.8 32.8 1.0
C1 K:B121631 2.9 30.6 1.0
C11 K:B121631 2.9 32.4 1.0
C4 K:B121631 2.9 28.3 1.0
C6 K:B121631 2.9 25.8 1.0
C14 K:B121631 3.0 31.2 1.0
C16 K:B121631 3.0 36.5 1.0
CB K:SER398 3.1 34.4 1.0
C10 K:B121631 3.2 35.2 1.0
C5 K:B121631 3.3 26.8 1.0
C15 K:B121631 3.4 31.8 1.0
C20 K:B121631 3.4 26.7 1.0
OG1 G:THR374 3.7 32.5 1.0
O K:SER398 4.0 34.7 1.0
C18 K:B121631 4.1 34.3 1.0
C2 K:B121631 4.1 30.4 1.0
C7 K:B121631 4.2 31.5 1.0
C8 K:B121631 4.2 31.5 1.0
C3 K:B121631 4.2 29.2 1.0
C12 K:B121631 4.2 33.0 1.0
C17 K:B121631 4.3 36.4 1.0
C13 K:B121631 4.3 31.2 1.0
CG2 G:THR374 4.3 33.4 1.0
CA K:SER398 4.5 35.8 1.0
C49 K:B121631 4.5 35.9 1.0
CB G:THR374 4.5 31.2 1.0
C26 K:B121631 4.6 31.5 1.0
C37 K:B121631 4.7 31.5 1.0
C K:SER398 4.7 31.4 1.0
C35 K:B121631 4.8 27.9 1.0
O39 K:B121631 4.8 36.3 1.0
C46 K:B121631 4.9 30.6 1.0
C53 K:B121631 4.9 35.5 1.0
C41 K:B121631 4.9 30.1 1.0
CA G:THR374 4.9 30.6 1.0
C30 K:B121631 5.0 26.3 1.0

Cobalt binding site 4 out of 4 in 4c1n

Go back to Cobalt Binding Sites List in 4c1n
Cobalt binding site 4 out of 4 in the Corrinoid Protein Reactivation Complex with Activator


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Corrinoid Protein Reactivation Complex with Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Co1631

b:22.4
occ:1.00
CO X:B121631 0.0 22.4 1.0
N21 X:B121631 1.9 22.2 1.0
N24 X:B121631 1.9 25.1 1.0
N23 X:B121631 1.9 22.6 1.0
N22 X:B121631 1.9 23.9 1.0
OG X:SER398 2.6 28.4 1.0
CB X:SER398 2.8 26.2 1.0
C19 X:B121631 2.8 24.8 1.0
C9 X:B121631 2.8 25.7 1.0
C1 X:B121631 2.9 24.2 1.0
C4 X:B121631 2.9 25.2 1.0
C11 X:B121631 2.9 22.2 1.0
C6 X:B121631 2.9 21.5 1.0
C14 X:B121631 3.0 21.8 1.0
C16 X:B121631 3.0 24.8 1.0
C10 X:B121631 3.2 22.2 1.0
C5 X:B121631 3.3 22.5 1.0
C15 X:B121631 3.4 28.8 1.0
C20 X:B121631 3.4 20.6 1.0
OG1 E:THR374 3.8 25.2 1.0
C2 X:B121631 4.1 22.9 1.0
C18 X:B121631 4.1 22.4 1.0
C7 X:B121631 4.2 26.0 1.0
C3 X:B121631 4.2 24.4 1.0
C8 X:B121631 4.2 26.3 1.0
C12 X:B121631 4.2 28.2 1.0
CG2 E:THR374 4.2 22.0 1.0
C13 X:B121631 4.2 23.2 1.0
CA X:SER398 4.2 25.7 1.0
C17 X:B121631 4.3 23.5 1.0
O X:SER398 4.4 30.4 1.0
CB E:THR374 4.6 28.0 1.0
C26 X:B121631 4.6 25.3 1.0
N40 X:B121631 4.7 25.1 1.0
C37 X:B121631 4.7 25.1 1.0
C48 X:B121631 4.7 22.6 1.0
C35 X:B121631 4.7 22.2 1.0
C46 X:B121631 4.8 26.4 1.0
C X:SER398 4.8 29.1 1.0
C53 X:B121631 4.9 28.5 1.0
C41 X:B121631 4.9 25.5 1.0
C30 X:B121631 5.0 24.7 1.0

Reference:

S.E.Hennig, S.Goetzl, J.H.Jeoung, M.Bommer, F.Lendzian, P.Hildebrandt, H.Dobbek. Atp-Induced Electron Transfer By Redox-Selective Partner Recognition Nat.Commun. V. 5 4626 2014.
ISSN: ISSN 2041-1723
PubMed: 25109607
DOI: 10.1038/NCOMMS5626
Page generated: Tue Jul 30 16:58:03 2024

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