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Cobalt in PDB 4ur3: Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form

Enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form

All present enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form:
1.97.1.8;

Protein crystallography data

The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form, PDB code: 4ur3 was solved by M.Bommer, C.Kunze, J.Fesseler, T.Schubert, G.Diekert, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.763 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.315, 110.601, 178.792, 90.00, 95.91, 90.00
R / Rfree (%) 17.93 / 21.77

Other elements in 4ur3:

The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form also contains other interesting chemical elements:

Iron (Fe) 48 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form (pdb code 4ur3). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form, PDB code: 4ur3:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 4ur3

Go back to Cobalt Binding Sites List in 4ur3
Cobalt binding site 1 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co503

b:34.1
occ:1.00
CO A:BVQ503 0.0 34.1 1.0
N21 A:BVQ503 1.9 30.0 1.0
N24 A:BVQ503 1.9 33.0 1.0
N22 A:BVQ503 1.9 33.4 1.0
N23 A:BVQ503 1.9 36.7 1.0
O A:HOH2132 2.2 39.8 1.0
C19 A:BVQ503 2.8 27.7 1.0
C9 A:BVQ503 2.8 36.1 1.0
C4 A:BVQ503 2.9 29.7 1.0
C1 A:BVQ503 2.9 30.4 1.0
C11 A:BVQ503 2.9 37.7 1.0
C6 A:BVQ503 3.0 31.8 1.0
C16 A:BVQ503 3.0 26.2 1.0
C14 A:BVQ503 3.0 30.9 1.0
C10 A:BVQ503 3.2 32.5 1.0
C5 A:BVQ503 3.3 32.0 1.0
C15 A:BVQ503 3.4 28.8 1.0
C20 A:BVQ503 3.5 26.5 1.0
O A:HOH2191 3.7 33.3 1.0
C18 A:BVQ503 4.1 28.4 1.0
C2 A:BVQ503 4.1 28.8 1.0
C3 A:BVQ503 4.2 23.9 1.0
C8 A:BVQ503 4.2 37.2 1.0
C7 A:BVQ503 4.2 33.3 1.0
C17 A:BVQ503 4.3 31.4 1.0
C12 A:BVQ503 4.3 34.1 1.0
C13 A:BVQ503 4.3 35.0 1.0
C26 A:BVQ503 4.6 25.6 1.0
C37 A:BVQ503 4.7 29.6 1.0
C35 A:BVQ503 4.8 31.5 1.0
C41 A:BVQ503 4.8 27.9 1.0
CE2 A:PHE38 4.9 30.0 1.0
C53 A:BVQ503 4.9 30.3 1.0

Cobalt binding site 2 out of 6 in 4ur3

Go back to Cobalt Binding Sites List in 4ur3
Cobalt binding site 2 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co503

b:26.4
occ:1.00
CO B:BVQ503 0.0 26.4 1.0
N21 B:BVQ503 1.9 25.5 1.0
N24 B:BVQ503 1.9 19.7 1.0
N22 B:BVQ503 1.9 18.8 1.0
N23 B:BVQ503 1.9 22.9 1.0
O B:HOH2135 2.3 22.9 1.0
C19 B:BVQ503 2.8 19.7 1.0
C9 B:BVQ503 2.8 23.3 1.0
C1 B:BVQ503 2.9 20.9 1.0
C4 B:BVQ503 2.9 19.4 1.0
C11 B:BVQ503 2.9 18.3 1.0
C6 B:BVQ503 3.0 22.0 1.0
C16 B:BVQ503 3.0 22.1 1.0
C14 B:BVQ503 3.0 21.2 1.0
C10 B:BVQ503 3.2 23.4 1.0
C5 B:BVQ503 3.3 20.9 1.0
C15 B:BVQ503 3.4 24.4 1.0
C20 B:BVQ503 3.5 18.1 1.0
O B:HOH2196 3.7 19.4 1.0
C18 B:BVQ503 4.1 18.5 1.0
C2 B:BVQ503 4.1 19.3 1.0
C8 B:BVQ503 4.2 22.7 1.0
C3 B:BVQ503 4.2 21.1 1.0
C7 B:BVQ503 4.2 22.8 1.0
C17 B:BVQ503 4.3 24.5 1.0
C12 B:BVQ503 4.3 29.6 1.0
C13 B:BVQ503 4.3 23.6 1.0
C42 B:BVQ503 4.5 29.6 1.0
C26 B:BVQ503 4.6 20.4 1.0
C37 B:BVQ503 4.7 24.3 1.0
C35 B:BVQ503 4.8 18.3 1.0
C53 B:BVQ503 4.9 23.9 1.0
C41 B:BVQ503 5.0 22.3 1.0
C54 B:BVQ503 5.0 17.4 1.0

Cobalt binding site 3 out of 6 in 4ur3

Go back to Cobalt Binding Sites List in 4ur3
Cobalt binding site 3 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co503

b:28.5
occ:1.00
CO C:BVQ503 0.0 28.5 1.0
N21 C:BVQ503 1.9 21.6 1.0
N24 C:BVQ503 1.9 22.9 1.0
N22 C:BVQ503 1.9 24.6 1.0
N23 C:BVQ503 1.9 27.0 1.0
C19 C:BVQ503 2.8 14.7 1.0
C9 C:BVQ503 2.8 23.6 1.0
C1 C:BVQ503 2.9 20.0 1.0
C4 C:BVQ503 2.9 22.0 1.0
C11 C:BVQ503 2.9 22.3 1.0
C6 C:BVQ503 3.0 23.0 1.0
C16 C:BVQ503 3.0 22.1 1.0
C14 C:BVQ503 3.0 20.1 1.0
O C:HOH2176 3.1 24.9 1.0
C10 C:BVQ503 3.2 17.7 1.0
C5 C:BVQ503 3.3 22.8 1.0
C15 C:BVQ503 3.4 21.5 1.0
O C:HOH2252 3.5 23.8 1.0
C20 C:BVQ503 3.5 15.6 1.0
C18 C:BVQ503 4.1 20.9 1.0
C2 C:BVQ503 4.1 15.3 1.0
C3 C:BVQ503 4.2 16.9 1.0
C8 C:BVQ503 4.2 21.1 1.0
C7 C:BVQ503 4.2 20.1 1.0
C17 C:BVQ503 4.3 23.8 1.0
C12 C:BVQ503 4.3 23.3 1.0
C13 C:BVQ503 4.3 24.7 1.0
C42 C:BVQ503 4.5 32.9 1.0
C26 C:BVQ503 4.6 14.7 1.0
C37 C:BVQ503 4.7 23.6 1.0
C35 C:BVQ503 4.8 18.4 1.0
C53 C:BVQ503 4.9 24.1 1.0
CE2 C:PHE38 4.9 24.4 1.0
C41 C:BVQ503 4.9 23.5 1.0

Cobalt binding site 4 out of 6 in 4ur3

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Cobalt binding site 4 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co503

b:26.1
occ:1.00
CO D:BVQ503 0.0 26.1 1.0
N21 D:BVQ503 1.9 20.7 1.0
N24 D:BVQ503 1.9 20.1 1.0
N22 D:BVQ503 1.9 20.0 1.0
N23 D:BVQ503 1.9 23.8 1.0
O D:HOH2134 2.2 27.8 1.0
C19 D:BVQ503 2.8 20.2 1.0
C9 D:BVQ503 2.8 20.6 1.0
C1 D:BVQ503 2.9 22.3 1.0
C4 D:BVQ503 2.9 17.1 1.0
C11 D:BVQ503 2.9 20.1 1.0
C6 D:BVQ503 3.0 20.4 1.0
C16 D:BVQ503 3.0 21.5 1.0
C14 D:BVQ503 3.0 22.9 1.0
C10 D:BVQ503 3.2 23.0 1.0
C5 D:BVQ503 3.3 19.0 1.0
C15 D:BVQ503 3.4 19.1 1.0
C20 D:BVQ503 3.5 18.8 1.0
O D:HOH2197 3.7 19.4 1.0
C18 D:BVQ503 4.1 18.2 1.0
C2 D:BVQ503 4.1 18.9 1.0
C8 D:BVQ503 4.2 25.8 1.0
C3 D:BVQ503 4.2 18.8 1.0
C7 D:BVQ503 4.2 21.8 1.0
C17 D:BVQ503 4.3 20.0 1.0
C12 D:BVQ503 4.3 22.4 1.0
C13 D:BVQ503 4.3 21.7 1.0
C26 D:BVQ503 4.6 19.0 1.0
C37 D:BVQ503 4.6 19.4 1.0
CE2 D:PHE38 4.8 24.5 1.0
C35 D:BVQ503 4.8 17.3 1.0
C41 D:BVQ503 4.8 21.5 1.0
C53 D:BVQ503 4.9 19.2 1.0

Cobalt binding site 5 out of 6 in 4ur3

Go back to Cobalt Binding Sites List in 4ur3
Cobalt binding site 5 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co503

b:46.1
occ:1.00
CO E:BVQ503 0.0 46.1 1.0
N21 E:BVQ503 1.9 42.0 1.0
N24 E:BVQ503 1.9 39.5 1.0
N22 E:BVQ503 1.9 42.2 1.0
N23 E:BVQ503 1.9 43.7 1.0
O E:HOH2098 2.2 40.8 1.0
C19 E:BVQ503 2.8 38.4 1.0
C9 E:BVQ503 2.8 43.4 1.0
C4 E:BVQ503 2.9 38.1 1.0
C1 E:BVQ503 2.9 39.8 1.0
C11 E:BVQ503 2.9 42.3 1.0
C6 E:BVQ503 3.0 41.0 1.0
C16 E:BVQ503 3.0 42.4 1.0
C14 E:BVQ503 3.0 44.7 1.0
C10 E:BVQ503 3.2 40.5 1.0
C5 E:BVQ503 3.3 40.0 1.0
C15 E:BVQ503 3.4 45.7 1.0
C20 E:BVQ503 3.5 37.3 1.0
C18 E:BVQ503 4.1 40.0 1.0
C2 E:BVQ503 4.1 35.4 1.0
C3 E:BVQ503 4.2 39.0 1.0
C7 E:BVQ503 4.2 37.1 1.0
C8 E:BVQ503 4.2 40.8 1.0
C17 E:BVQ503 4.2 40.1 1.0
C12 E:BVQ503 4.2 48.3 1.0
C13 E:BVQ503 4.3 43.7 1.0
C26 E:BVQ503 4.6 35.8 1.0
C37 E:BVQ503 4.6 37.1 1.0
C42 E:BVQ503 4.7 46.7 1.0
C35 E:BVQ503 4.8 39.7 1.0
C53 E:BVQ503 4.9 47.5 1.0

Cobalt binding site 6 out of 6 in 4ur3

Go back to Cobalt Binding Sites List in 4ur3
Cobalt binding site 6 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co503

b:35.0
occ:1.00
CO F:BVQ503 0.0 35.0 1.0
N21 F:BVQ503 1.9 24.5 1.0
N24 F:BVQ503 1.9 24.9 1.0
N22 F:BVQ503 1.9 28.1 1.0
N23 F:BVQ503 1.9 27.2 1.0
C19 F:BVQ503 2.8 22.4 1.0
C9 F:BVQ503 2.8 32.1 1.0
C1 F:BVQ503 2.9 24.4 1.0
C4 F:BVQ503 2.9 23.3 1.0
C11 F:BVQ503 2.9 29.6 1.0
C6 F:BVQ503 3.0 29.1 1.0
C16 F:BVQ503 3.0 26.9 1.0
C14 F:BVQ503 3.0 27.6 1.0
O F:HOH2096 3.1 28.1 1.0
C10 F:BVQ503 3.2 30.2 1.0
C5 F:BVQ503 3.3 26.4 1.0
C15 F:BVQ503 3.4 28.4 1.0
C20 F:BVQ503 3.5 28.1 1.0
O F:HOH2132 3.7 30.1 1.0
C18 F:BVQ503 4.1 26.4 1.0
C2 F:BVQ503 4.1 23.9 1.0
C3 F:BVQ503 4.2 25.7 1.0
C8 F:BVQ503 4.2 28.5 1.0
C7 F:BVQ503 4.2 29.1 1.0
C12 F:BVQ503 4.3 28.7 1.0
C17 F:BVQ503 4.3 28.4 1.0
C13 F:BVQ503 4.3 30.2 1.0
C26 F:BVQ503 4.6 23.4 1.0
C37 F:BVQ503 4.7 29.8 1.0
C42 F:BVQ503 4.7 37.3 1.0
C35 F:BVQ503 4.8 25.4 1.0
C53 F:BVQ503 4.9 32.3 1.0
CE2 F:PHE38 4.9 26.3 1.0

Reference:

M.Bommer, C.Kunze, J.Fesseler, T.Schubert, G.Diekert, H.Dobbek. Structural Basis For Organohalide Respiration. Science V. 346 455 2014.
ISSN: ISSN 0036-8075
PubMed: 25278505
DOI: 10.1126/SCIENCE.1258118
Page generated: Sun Dec 13 10:46:12 2020

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