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

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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

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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

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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

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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

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