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

Go back to

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

Go back to

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

Go back to

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

Go back to

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: Sun Dec 13 10:39:12 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy