Manganese in PDB 9ixf: Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86.

Enzymatic activity of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86.

All present enzymatic activity of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86.:
3.5.3.25;

Protein crystallography data

The structure of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86., PDB code: 9ixf was solved by K.Oda, Y.Matoba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	43.92 / 1.75
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	45.876, 46.683, 58.222, 85.39, 86.78, 70.54
*R / R_free (%)*	15.8 / 20.1

Other elements in 9ixf:

The structure of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86. also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86. (pdb code 9ixf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86., PDB code: 9ixf:

Manganese binding site 1 out of 1 in 9ixf

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Manganese Binding Sites List in 9ixf

Manganese binding site 1 out of 1 in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86.

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 Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn401 b:8.1 occ:0.82	O	A:HOH608	2.1	13.8	1.0
	OD2	A:ASP109	2.2	8.5	1.0
	OD2	A:ASP113	2.2	11.5	1.0
	OD2	A:ASP198	2.3	12.7	1.0
	O	A:HOH551	2.3	11.1	1.0
	SG	A:CYS86	2.5	11.9	1.0
	CG	A:ASP113	3.1	12.3	1.0
	CG	A:ASP109	3.1	9.5	1.0
	CG	A:ASP198	3.2	10.2	1.0
	MG	A:MG402	3.3	6.0	0.9
	OD1	A:ASP113	3.4	10.3	1.0
	CB	A:CYS86	3.4	11.1	1.0
	OD1	A:ASP109	3.5	8.5	1.0
	CB	A:ASP198	3.5	10.7	1.0
	OH	A:TYR107	3.9	11.2	1.0
	O	A:GLY126	4.3	18.1	1.0
	OE2	A:GLU241	4.3	17.0	1.0
	OD1	A:ASP198	4.3	9.7	1.0
	CD	A:GLU241	4.4	17.3	1.0
	CE1	A:TYR107	4.5	11.0	1.0
	CB	A:ASP109	4.5	7.8	1.0
	CB	A:ASP113	4.5	12.1	1.0
	OE1	A:GLU241	4.6	15.5	1.0
	CZ	A:TYR107	4.7	11.8	1.0
	OD2	A:ASP200	4.8	12.3	1.0
	O	A:HOH693	4.8	27.1	1.0
	CA	A:CYS86	4.9	12.1	1.0
	NE2	A:HIS196	4.9	16.4	1.0
	CA	A:ASP198	5.0	10.5	1.0

Reference:

K.Oda, Y.Matoba. Copper Inactivates Dcsb By Oxidizing the Metal Ligand CYS86 to Sulfinic Acid. Febs J. 2024.
ISSN: ISSN 1742-464X
DOI: 10.1111/FEBS.17325

Page generated: Wed Nov 27 20:28:12 2024

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