Cobalt in PDB 2r1m: Opda From Agrobacterium Radiobacter with Bound Product Diethyl Phosphate From Crystal Soaking with Diethyl 4- Methoxyphenyl Phosphate (450H)- 2.5 A

Enzymatic activity of Opda From Agrobacterium Radiobacter with Bound Product Diethyl Phosphate From Crystal Soaking with Diethyl 4- Methoxyphenyl Phosphate (450H)- 2.5 A

All present enzymatic activity of Opda From Agrobacterium Radiobacter with Bound Product Diethyl Phosphate From Crystal Soaking with Diethyl 4- Methoxyphenyl Phosphate (450H)- 2.5 A:
3.1.8.1;

Protein crystallography data

The structure of Opda From Agrobacterium Radiobacter with Bound Product Diethyl Phosphate From Crystal Soaking with Diethyl 4- Methoxyphenyl Phosphate (450H)- 2.5 A, PDB code: 2r1m 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 / 2.50
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	109.096, 109.096, 61.880, 90.00, 90.00, 120.00
*R / R_free (%)*	15.5 / 22.5

Other elements in 2r1m:

The structure of Opda From Agrobacterium Radiobacter with Bound Product Diethyl Phosphate From Crystal Soaking with Diethyl 4- Methoxyphenyl Phosphate (450H)- 2.5 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 Phosphate From Crystal Soaking with Diethyl 4- Methoxyphenyl Phosphate (450H)- 2.5 A (pdb code 2r1m). 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 Phosphate From Crystal Soaking with Diethyl 4- Methoxyphenyl Phosphate (450H)- 2.5 A, PDB code: 2r1m:

Cobalt binding site 1 out of 1 in 2r1m

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Cobalt Binding Sites List in 2r1m

Cobalt binding site 1 out of 1 in the Opda From Agrobacterium Radiobacter with Bound Product Diethyl Phosphate From Crystal Soaking with Diethyl 4- Methoxyphenyl Phosphate (450H)- 2.5 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 Phosphate From Crystal Soaking with Diethyl 4- Methoxyphenyl Phosphate (450H)- 2.5 A within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Co801 b:33.3 occ:1.00	OQ2	A:KCX169	2.1	39.8	1.0
	ND1	A:HIS201	2.2	21.2	1.0
	NE2	A:HIS230	2.2	34.0	1.0
	O2	A:DPF1	2.7	17.1	0.5
	O4	A:DPF1	2.8	10.8	0.5
	CX	A:KCX169	2.9	30.4	1.0
	CE1	A:HIS201	3.0	24.7	1.0
	OQ1	A:KCX169	3.1	29.4	1.0
	CE1	A:HIS230	3.2	29.5	1.0
	P1	A:DPF1	3.2	25.4	0.5
	CD2	A:HIS230	3.3	32.9	1.0
	CG	A:HIS201	3.3	28.0	1.0
	FE	A:FE2800	3.5	27.2	1.0
	NH2	A:ARG254	3.5	33.2	1.0
	CB	A:HIS201	3.7	22.7	1.0
	NE1	A:TRP131	4.0	22.8	1.0
	OD2	A:ASP301	4.1	30.2	1.0
	NE2	A:HIS55	4.1	21.4	1.0
	CE1	A:HIS55	4.1	23.4	1.0
	NE2	A:HIS201	4.2	26.9	1.0
	NZ	A:KCX169	4.2	24.6	1.0
	ND1	A:HIS230	4.3	31.6	1.0
	CD2	A:HIS201	4.3	27.4	1.0
	CG	A:HIS230	4.4	30.4	1.0
	O1	A:DPF1	4.4	19.4	0.5
	O3	A:DPF1	4.5	19.4	0.5
	CA	A:HIS201	4.5	23.8	1.0
	CZ	A:ARG254	4.6	40.8	1.0
	CD1	A:TRP131	4.6	26.0	1.0
	CE	A:KCX169	4.8	24.2	1.0
	C1	A:DPF1	4.8	10.4	0.5
	CG	A:ASP301	4.9	30.4	1.0
	OD1	A:ASP301	4.9	36.2	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 15:29:43 2024

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