Cobalt in PDB 3c86: Opda From Agrobacterium Radiobacter with Bound Product Diethyl Thiophosphate From Crystal Soaking with Tetraethyl Dithiopyrophosphate- 1.8 A

Enzymatic activity of Opda From Agrobacterium Radiobacter with Bound Product Diethyl Thiophosphate From Crystal Soaking with Tetraethyl Dithiopyrophosphate- 1.8 A

All present enzymatic activity of Opda From Agrobacterium Radiobacter with Bound Product Diethyl Thiophosphate From Crystal Soaking with Tetraethyl Dithiopyrophosphate- 1.8 A:
3.1.8.1;

Protein crystallography data

The structure of Opda From Agrobacterium Radiobacter with Bound Product Diethyl Thiophosphate From Crystal Soaking with Tetraethyl Dithiopyrophosphate- 1.8 A, PDB code: 3c86 was solved by D.L.Ollis, C.J.Jackson, J.L.Foo, H.K.Kim, P.D.Carr, J.W.Liu, G.Salem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.00 / 1.80
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	108.918, 108.918, 62.648, 90.00, 90.00, 120.00
*R / R_free (%)*	16.2 / 18.7

Other elements in 3c86:

The structure of Opda From Agrobacterium Radiobacter with Bound Product Diethyl Thiophosphate From Crystal Soaking with Tetraethyl Dithiopyrophosphate- 1.8 A also contains other interesting chemical elements:

Iron

(Fe)

1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Opda From Agrobacterium Radiobacter with Bound Product Diethyl Thiophosphate From Crystal Soaking with Tetraethyl Dithiopyrophosphate- 1.8 A (pdb code 3c86). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total only one binding site of Cobalt was determined in the Opda From Agrobacterium Radiobacter with Bound Product Diethyl Thiophosphate From Crystal Soaking with Tetraethyl Dithiopyrophosphate- 1.8 A, PDB code: 3c86:

Cobalt binding site 1 out of 1 in 3c86

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Cobalt Binding Sites List in 3c86

Cobalt binding site 1 out of 1 in the Opda From Agrobacterium Radiobacter with Bound Product Diethyl Thiophosphate From Crystal Soaking with Tetraethyl Dithiopyrophosphate- 1.8 A

Mono view

Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Opda From Agrobacterium Radiobacter with Bound Product Diethyl Thiophosphate From Crystal Soaking with Tetraethyl Dithiopyrophosphate- 1.8 A within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Co801 b:18.7 occ:0.80	O	A:HOH1085	2.0	19.9	0.8
	OQ2	A:KCX169	2.0	18.0	1.0
	NE2	A:HIS230	2.1	19.0	1.0
	ND1	A:HIS201	2.2	16.0	1.0
	S1	A:DPJ1	2.4	18.8	0.5
	CE1	A:HIS201	3.0	19.1	1.0
	CE1	A:HIS230	3.0	18.9	1.0
	CX	A:KCX169	3.1	19.9	1.0
	CD2	A:HIS230	3.1	17.2	1.0
	CG	A:HIS201	3.2	18.1	1.0
	OQ1	A:KCX169	3.4	17.1	1.0
	NH2	A:ARG254	3.5	36.1	1.0
	FE	A:FE2800	3.5	16.0	0.8
	P2	A:DPJ1	3.6	30.0	0.5
	CB	A:HIS201	3.6	16.4	1.0
	O4	A:DPJ1	3.8	22.2	0.5
	NE1	A:TRP131	4.1	20.7	1.0
	ND1	A:HIS230	4.2	17.3	1.0
	CE1	A:HIS55	4.2	16.4	1.0
	NE2	A:HIS201	4.2	18.6	1.0
	NE2	A:HIS55	4.2	17.4	1.0
	O3	A:DPJ1	4.2	21.1	0.5
	CG	A:HIS230	4.2	17.4	1.0
	OD2	A:ASP301	4.2	19.6	1.0
	NZ	A:KCX169	4.2	18.4	1.0
	CD2	A:HIS201	4.3	14.6	1.0
	CZ	A:ARG254	4.4	36.0	1.0
	CA	A:HIS201	4.4	16.5	1.0
	CD1	A:TRP131	4.7	20.2	1.0
	CE	A:KCX169	4.8	18.7	1.0
	CG	A:ASP301	4.9	17.6	1.0
	OD1	A:ASP301	4.9	18.0	1.0
	NE	A:ARG254	4.9	30.9	1.0

Reference:

C.J.Jackson, J.L.Foo, H.K.Kim, P.D.Carr, J.W.Liu, G.Salem, D.L.Ollis. In Crystallo Capture of A Michaelis Complex and Product-Binding Modes of A Bacterial Phosphotriesterase J.Mol.Biol. V. 375 1189 2008.
ISSN: ISSN 0022-2836
PubMed: 18082180
DOI: 10.1016/J.JMB.2007.10.061

Page generated: Tue Jul 30 15:51:03 2024

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