Manganese in PDB 1d3v: Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog

Enzymatic activity of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog

All present enzymatic activity of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog, PDB code: 1d3v was solved by J.D.Cox, N.N.Kim, A.M.Traish, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.00 / 1.70
*Space group*	P 3
*Cell size a, b, c (Å), α, β, γ (°)*	91.300, 91.300, 69.900, 90.00, 90.00, 120.00
*R / R_free (%)*	15.7 / 17.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog (pdb code 1d3v). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog, PDB code: 1d3v:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1d3v

Go back to

Manganese Binding Sites List in 1d3v

Manganese binding site 1 out of 4 in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn500 b:9.5 occ:1.00	OD2	A:ASP124	2.1	7.5	1.0
	ND1	A:HIS101	2.2	10.8	1.0
	O1	A:ABH551	2.2	20.0	1.0
	OD2	A:ASP128	2.2	8.2	1.0
	O2	A:ABH551	2.4	17.6	1.0
	OD2	A:ASP232	2.4	10.4	1.0
	B	A:ABH551	2.8	18.4	1.0
	CE1	A:HIS101	3.1	10.3	1.0
	CG	A:ASP124	3.2	6.7	1.0
	CG	A:ASP128	3.2	6.8	1.0
	CG	A:HIS101	3.2	11.6	1.0
	CG	A:ASP232	3.3	9.6	1.0
	MN	A:MN501	3.4	10.5	1.0
	OD1	A:ASP124	3.5	5.8	1.0
	OD1	A:ASP128	3.5	5.6	1.0
	CB	A:HIS101	3.5	11.7	1.0
	O3	A:ABH551	3.6	19.9	1.0
	CB	A:ASP232	3.6	9.5	1.0
	CE	A:ABH551	4.1	18.6	1.0
	NE2	A:HIS101	4.3	9.9	1.0
	CD2	A:HIS101	4.3	11.6	1.0
	NE1	A:TRP122	4.3	10.4	1.0
	CB	A:ASP124	4.5	6.8	1.0
	OD1	A:ASP232	4.5	9.3	1.0
	O	A:HIS141	4.5	10.7	1.0
	CB	A:ASP128	4.6	7.3	1.0
	CZ2	A:TRP122	4.6	10.4	1.0
	CE2	A:TRP122	4.8	10.6	1.0
	CG	A:GLU277	4.8	11.0	1.0
	CA	A:ASP232	5.0	9.8	1.0

Manganese binding site 2 out of 4 in 1d3v

Go back to

Manganese Binding Sites List in 1d3v

Manganese binding site 2 out of 4 in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn501 b:10.5 occ:1.00	OD2	A:ASP234	2.2	9.1	1.0
	O1	A:ABH551	2.2	20.0	1.0
	OD2	A:ASP232	2.3	10.4	1.0
	OD1	A:ASP124	2.3	5.8	1.0
	ND1	A:HIS126	2.5	9.0	1.0
	OD1	A:ASP234	2.6	10.4	1.0
	CG	A:ASP234	2.7	10.3	1.0
	O3	A:ABH551	2.9	19.9	1.0
	B	A:ABH551	3.1	18.4	1.0
	CG	A:ASP124	3.2	6.7	1.0
	CG	A:ASP232	3.2	9.6	1.0
	CE1	A:HIS126	3.4	7.5	1.0
	MN	A:MN500	3.4	9.5	1.0
	OD2	A:ASP124	3.5	7.5	1.0
	CG	A:HIS126	3.6	8.7	1.0
	OD1	A:ASP232	3.8	9.3	1.0
	CB	A:HIS126	3.9	8.3	1.0
	O2	A:ABH551	4.1	17.6	1.0
	N	A:HIS126	4.2	7.9	1.0
	CB	A:ASP232	4.2	9.5	1.0
	CE	A:ABH551	4.2	18.6	1.0
	CB	A:ASP234	4.2	9.4	1.0
	CD	A:ABH551	4.3	17.3	1.0
	N	A:ALA125	4.3	8.9	1.0
	NE2	A:HIS126	4.6	8.2	1.0
	O	A:HOH555	4.6	8.5	1.0
	CB	A:ASP124	4.6	6.8	1.0
	OD1	A:ASP128	4.7	5.6	1.0
	CA	A:HIS126	4.7	8.4	1.0
	CD2	A:HIS126	4.7	7.5	1.0
	OD2	A:ASP128	4.9	8.2	1.0
	CB	A:ALA125	4.9	8.2	1.0
	CA	A:ASP124	5.0	8.4	1.0
	C	A:ALA125	5.0	7.8	1.0
	O	A:HOH645	5.0	18.6	1.0

Manganese binding site 3 out of 4 in 1d3v

Go back to

Manganese Binding Sites List in 1d3v

Manganese binding site 3 out of 4 in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn502 b:9.6 occ:1.00	OD2	B:ASP128	2.2	8.7	1.0
	OD2	B:ASP124	2.2	8.8	1.0
	O1	B:ABH552	2.2	16.9	1.0
	ND1	B:HIS101	2.2	9.9	1.0
	OD2	B:ASP232	2.3	11.2	1.0
	O2	B:ABH552	2.4	15.9	1.0
	B	B:ABH552	2.9	15.8	1.0
	CG	B:ASP128	3.1	7.3	1.0
	CE1	B:HIS101	3.2	8.6	1.0
	CG	B:ASP124	3.2	8.8	1.0
	CG	B:HIS101	3.2	10.2	1.0
	CG	B:ASP232	3.3	10.4	1.0
	OD1	B:ASP128	3.4	6.3	1.0
	MN	B:MN503	3.4	9.3	1.0
	CB	B:HIS101	3.5	11.3	1.0
	OD1	B:ASP124	3.6	7.5	1.0
	CB	B:ASP232	3.7	9.6	1.0
	O3	B:ABH552	3.7	14.7	1.0
	CE	B:ABH552	4.1	15.8	1.0
	NE2	B:HIS101	4.4	9.2	1.0
	NE1	B:TRP122	4.4	9.0	1.0
	CD2	B:HIS101	4.4	9.9	1.0
	OD1	B:ASP232	4.4	10.4	1.0
	O	B:HIS141	4.4	8.8	1.0
	CB	B:ASP124	4.5	8.3	1.0
	CB	B:ASP128	4.5	7.2	1.0
	CZ2	B:TRP122	4.6	10.1	1.0
	CE2	B:TRP122	4.8	9.3	1.0
	CG	B:GLU277	4.9	11.2	1.0
	CA	B:ASP232	5.0	9.2	1.0

Manganese binding site 4 out of 4 in 1d3v

Go back to

Manganese Binding Sites List in 1d3v

Manganese binding site 4 out of 4 in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn503 b:9.3 occ:1.00	OD1	B:ASP234	2.1	10.4	1.0
	O1	B:ABH552	2.2	16.9	1.0
	OD1	B:ASP124	2.3	7.5	1.0
	OD2	B:ASP232	2.3	11.2	1.0
	ND1	B:HIS126	2.4	9.0	1.0
	OD2	B:ASP234	2.6	9.1	1.0
	CG	B:ASP234	2.7	10.2	1.0
	O3	B:ABH552	3.0	14.7	1.0
	B	B:ABH552	3.2	15.8	1.0
	CG	B:ASP124	3.2	8.8	1.0
	CE1	B:HIS126	3.2	7.9	1.0
	CG	B:ASP232	3.3	10.4	1.0
	MN	B:MN502	3.4	9.6	1.0
	OD2	B:ASP124	3.4	8.8	1.0
	CG	B:HIS126	3.5	7.3	1.0
	OD1	B:ASP232	3.8	10.4	1.0
	CB	B:HIS126	3.9	8.3	1.0
	N	B:HIS126	4.1	7.7	1.0
	O2	B:ABH552	4.1	15.9	1.0
	CB	B:ASP234	4.2	9.6	1.0
	N	B:ALA125	4.2	8.3	1.0
	CE	B:ABH552	4.3	15.8	1.0
	CB	B:ASP232	4.3	9.6	1.0
	CD	B:ABH552	4.4	16.0	1.0
	NE2	B:HIS126	4.4	8.6	1.0
	OD1	B:ASP128	4.6	6.3	1.0
	CD2	B:HIS126	4.6	7.2	1.0
	CB	B:ASP124	4.6	8.3	1.0
	O	B:HOH667	4.6	10.9	1.0
	CA	B:HIS126	4.6	8.1	1.0
	CB	B:ALA125	4.8	8.2	1.0
	C	B:ALA125	4.9	7.1	1.0
	CA	B:ALA125	4.9	7.9	1.0
	OD2	B:ASP128	4.9	8.7	1.0
	CA	B:ASP124	5.0	9.3	1.0

Reference:

J.D.Cox, N.N.Kim, A.M.Traish, D.W.Christianson. Arginase-Boronic Acid Complex Highlights A Physiological Role in Erectile Function. Nat.Struct.Biol. V. 6 1043 1999.
ISSN: ISSN 1072-8368
PubMed: 10542097
DOI: 10.1038/14929

Page generated: Sat Oct 5 10:03:36 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO

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