Calcium in PDB 4l3h: Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide

Enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide

All present enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide:
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide, PDB code: 4l3h was solved by E.T.Yukl, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	44.49 / 1.79
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	55.530, 83.520, 107.780, 109.94, 91.54, 105.78
*R / R_free (%)*	15.4 / 19.8

Other elements in 4l3h:

The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Sodium	(Na)	4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide (pdb code 4l3h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide, PDB code: 4l3h:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4l3h

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Calcium Binding Sites List in 4l3h

Calcium binding site 1 out of 2 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca401 b:38.0 occ:1.00	OD1	A:ASN66	2.0	34.0	1.0
	O	A:PRO277	2.3	38.9	1.0
	O	A:THR275	2.3	40.4	1.0
	O	A:HOH522	2.4	35.1	1.0
	O	A:HOH517	2.4	39.3	1.0
	O	A:HOH570	2.5	36.9	1.0
	O	A:HOH550	2.5	37.3	1.0
	CG	A:ASN66	3.1	39.4	1.0
	C	A:PRO277	3.5	41.7	1.0
	C	A:THR275	3.5	39.5	1.0
	ND2	A:ASN66	3.7	41.9	1.0
	C	A:GLY276	4.0	42.0	1.0
	N	A:PRO277	4.2	43.5	1.0
	CA	A:GLY276	4.2	39.9	1.0
	O	A:THR67	4.3	35.5	1.0
	O	A:HOH675	4.3	36.5	1.0
	N	A:GLY276	4.3	38.7	1.0
	O	A:GLY276	4.3	46.4	1.0
	CB	A:THR275	4.3	39.0	1.0
	CA	A:TYR278	4.3	41.1	1.0
	CB	A:ASN66	4.4	41.1	1.0
	N	A:TYR278	4.4	42.1	1.0
	OG1	A:THR275	4.5	36.6	1.0
	CA	A:PRO277	4.5	43.6	1.0
	CA	A:THR275	4.5	38.7	1.0
	O	A:HOH632	4.6	38.5	1.0
	O1A	A:HEC403	4.6	37.8	1.0
	O2A	A:HEC403	4.8	34.9	1.0
	CD1	A:TYR278	4.8	42.0	1.0
	CD	A:PRO277	4.8	45.2	1.0

Calcium binding site 2 out of 2 in 4l3h

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Calcium Binding Sites List in 4l3h

Calcium binding site 2 out of 2 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Ca401 b:23.8 occ:1.00	OD1	B:ASN66	2.2	21.6	1.0
	O	B:PRO277	2.3	23.9	1.0
	O	B:HOH511	2.3	27.4	1.0
	O	B:THR275	2.4	25.2	1.0
	O	B:HOH513	2.4	25.8	1.0
	O	B:HOH517	2.5	21.9	1.0
	O	B:HOH501	2.5	27.5	1.0
	CG	B:ASN66	3.3	23.8	1.0
	C	B:PRO277	3.5	24.5	1.0
	C	B:THR275	3.6	25.8	1.0
	ND2	B:ASN66	3.9	26.1	1.0
	C	B:GLY276	4.0	25.7	1.0
	N	B:PRO277	4.1	26.4	1.0
	CA	B:GLY276	4.2	26.7	1.0
	O	B:HOH581	4.2	30.8	1.0
	O	B:THR67	4.3	26.5	1.0
	N	B:GLY276	4.3	27.3	1.0
	O	B:GLY276	4.3	25.9	1.0
	CB	B:THR275	4.4	27.4	1.0
	CA	B:TYR278	4.4	24.6	1.0
	N	B:TYR278	4.4	24.1	1.0
	O	B:HOH506	4.4	27.5	1.0
	CA	B:PRO277	4.5	24.8	1.0
	OG1	B:THR275	4.5	25.0	1.0
	O1A	B:HEC403	4.6	24.3	1.0
	CB	B:ASN66	4.6	24.4	1.0
	CA	B:THR275	4.6	26.7	1.0
	CD	B:PRO277	4.7	28.2	1.0
	O2A	B:HEC403	4.7	22.9	1.0
	O	B:HOH565	4.7	32.3	1.0
	CD1	B:TYR278	4.8	25.1	1.0

Reference:

N.Abu Tarboush, E.T.Yukl, S.Shin, M.Feng, C.M.Wilmot, V.L.Davidson. Carboxyl Group of GLU113 Is Required For Stabilization of the Diferrous and Bis-Fe(IV) States of Maug. Biochemistry V. 52 6358 2013.
ISSN: ISSN 0006-2960
PubMed: 23952537
DOI: 10.1021/BI400905S

Page generated: Sun Jul 14 09:25:14 2024

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