Cobalt in PDB 2xdm: Crystal Structure of A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor

Enzymatic activity of Crystal Structure of A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor

All present enzymatic activity of Crystal Structure of A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor:
3.4.16.4;

Protein crystallography data

The structure of Crystal Structure of A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor, PDB code: 2xdm was solved by M.Rocaboy, E.Sauvage, R.Herman, F.Kerff, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	32.43 / 2.40
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	103.308, 91.568, 106.871, 90.00, 94.37, 90.00
*R / R_free (%)*	19.948 / 26.225

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor (pdb code 2xdm). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor, PDB code: 2xdm:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 2xdm

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Cobalt Binding Sites List in 2xdm

Cobalt binding site 1 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor

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 A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Co610 b:64.9 occ:1.00	NE2	A:HIS247	2.1	30.9	1.0
	O	A:GLU188	2.2	24.9	1.0
	OE1	A:GLU251	2.2	33.3	1.0
	CE1	A:HIS247	3.0	31.0	1.0
	CD	A:GLU251	3.1	32.8	1.0
	CD2	A:HIS247	3.1	30.3	1.0
	C	A:GLU188	3.3	24.9	1.0
	OE2	A:GLU251	3.3	30.9	1.0
	O	A:ALA186	4.1	24.3	1.0
	ND1	A:HIS247	4.1	31.2	1.0
	CB	A:GLU188	4.2	24.5	1.0
	CG	A:HIS247	4.2	29.8	1.0
	CA	A:GLU188	4.2	24.7	1.0
	N	A:GLY189	4.3	25.0	1.0
	CA	A:GLY189	4.3	25.2	1.0
	CG	A:GLU251	4.3	32.0	1.0
	N	A:GLU188	4.5	24.3	1.0
	C	A:GLY189	4.6	25.1	1.0
	O	A:GLY189	4.9	25.5	1.0
	N	A:TYR190	5.0	25.3	1.0

Cobalt binding site 2 out of 4 in 2xdm

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Cobalt Binding Sites List in 2xdm

Cobalt binding site 2 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor

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 A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Co611 b:97.9 occ:1.00	O	A:ALA402	2.7	28.9	1.0
	CG2	A:VAL406	2.9	31.6	1.0
	ND1	A:HIS462	3.1	40.0	1.0
	CB	A:HIS462	3.1	36.6	1.0
	CG	A:HIS462	3.2	37.7	1.0
	O	A:GLN463	3.4	37.0	1.0
	C	A:ALA402	3.7	28.7	1.0
	CE1	A:HIS462	4.0	41.0	1.0
	O	A:GLU404	4.0	29.4	1.0
	N	A:GLN463	4.1	38.4	1.0
	CA	A:ALA402	4.1	29.3	1.0
	CA	A:HIS462	4.2	38.1	1.0
	CD2	A:HIS462	4.3	38.5	1.0
	CB	A:VAL406	4.3	30.3	1.0
	C	A:GLN463	4.4	37.5	1.0
	C	A:HIS462	4.5	38.2	1.0
	NE2	A:HIS462	4.6	40.9	1.0
	CB	A:ALA402	4.7	28.8	1.0
	N	A:ALA403	4.8	28.2	1.0
	CA	A:GLN463	4.9	38.6	1.0
	CG1	A:VAL406	4.9	32.0	1.0
	CD	A:PRO465	5.0	36.5	1.0

Cobalt binding site 3 out of 4 in 2xdm

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Cobalt Binding Sites List in 2xdm

Cobalt binding site 3 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor

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 A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Co610 b:45.8 occ:1.00	OE2	D:GLU251	2.2	43.5	1.0
	O	D:GLU188	2.3	35.3	1.0
	NE2	D:HIS247	2.5	34.7	1.0
	CD	D:GLU251	2.9	41.8	1.0
	OE1	D:GLU251	2.9	41.6	1.0
	CE1	D:HIS247	3.4	35.7	1.0
	CD2	D:HIS247	3.5	35.5	1.0
	C	D:GLU188	3.6	35.3	1.0
	O	D:ALA186	4.0	37.3	1.0
	CG	D:GLU251	4.4	41.7	1.0
	CA	D:GLU188	4.4	35.6	1.0
	N	D:GLY189	4.5	35.3	1.0
	CB	D:GLU188	4.5	36.3	1.0
	ND1	D:HIS247	4.5	34.2	1.0
	CA	D:GLY189	4.6	35.2	1.0
	CG	D:HIS247	4.6	35.0	1.0
	N	D:GLU188	4.6	35.2	1.0
	C	D:ALA186	5.0	36.8	1.0
	CD2	D:LEU248	5.0	33.2	1.0

Cobalt binding site 4 out of 4 in 2xdm

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Cobalt Binding Sites List in 2xdm

Cobalt binding site 4 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor

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 A Complex Between Actinomadura R39 Dd Peptidase and A Peptidoglycan Mimetic Boronate Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Co611 b:46.4 occ:1.00	ND1	D:HIS462	3.2	55.3	1.0
	CG2	D:VAL406	3.6	42.3	1.0
	CB	D:HIS462	4.0	56.5	1.0
	CG	D:HIS462	4.0	55.7	1.0
	CE1	D:HIS462	4.2	55.0	1.0
	O	D:ALA402	4.4	43.8	1.0
	CA	D:HIS462	4.7	58.6	1.0
	O	D:GLN463	4.7	60.2	1.0
	N	D:GLN463	4.9	60.3	1.0

Reference:

L.Dzhekieva, M.Rocaboy, F.Kerff, P.Charlier, E.Sauvage, R.F.Pratt. Crystal Structure of A Complex Between the Actinomadura R39 Dd-Peptidase and A Peptidoglycan- Mimetic Boronate Inhibitor: Interpretation of A Transition State Analogue in Terms of Catalytic Mechanism. Biochemistry V. 49 6411 2010.
ISSN: ISSN 0006-2960
PubMed: 20608745
DOI: 10.1021/BI100757C

Page generated: Tue Jul 30 15:33:27 2024

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