Manganese in PDB 5m1d: Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor

Enzymatic activity of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor

All present enzymatic activity of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor:
4.1.1.98;

Protein crystallography data

The structure of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor, PDB code: 5m1d was solved by S.A.Marshall, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	137.32 / 2.70
*Space group*	P 4₃ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	194.199, 194.199, 107.598, 90.00, 90.00, 90.00
*R / R_free (%)*	19.5 / 22.6

Other elements in 5m1d:

The structure of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor (pdb code 5m1d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor, PDB code: 5m1d:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5m1d

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Manganese Binding Sites List in 5m1d

Manganese binding site 1 out of 3 in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor

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 N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn501 b:1.0 occ:0.50	OE2	A:GLU241	1.9	0.2	1.0
	OE1	A:GLU241	1.9	0.6	1.0
	OD1	A:ASN175	2.0	0.4	1.0
	ND2	A:ASN175	2.0	0.4	1.0
	CG	A:ASN175	2.2	0.0	1.0
	CD	A:GLU241	2.3	0.9	1.0
	O3P	A:4LU502	2.3	99.2	1.0
	O	A:HOH614	3.4	85.6	1.0
	CB	A:ASN175	3.6	0.9	1.0
	NA	A:NA503	3.7	60.5	0.5
	CG	A:GLU241	3.8	0.7	1.0
	P	A:4LU502	3.8	0.8	1.0
	O	A:LEU176	3.9	92.3	1.0
	CA	A:ASN175	4.0	0.8	1.0
	N	A:LEU176	4.1	96.5	1.0
	O5'	A:4LU502	4.5	0.2	1.0
	C	A:ASN175	4.5	97.9	1.0
	C	A:LEU176	4.6	89.5	1.0
	O2P	A:4LU502	4.6	87.2	1.0
	O1P	A:4LU502	4.7	83.3	1.0
	O	A:LEU239	4.7	0.2	1.0
	CB	A:GLU241	4.7	0.2	1.0
	O	A:HOH604	4.8	67.5	1.0
	O	A:PRO236	4.9	0.7	1.0
	CG2	A:VAL235	4.9	0.0	1.0

Manganese binding site 2 out of 3 in 5m1d

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Manganese Binding Sites List in 5m1d

Manganese binding site 2 out of 3 in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor

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 N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn501 b:95.5 occ:1.00	O	B:HOH615	1.9	96.8	1.0
	OD1	B:ASN175	1.9	69.4	1.0
	OE1	B:GLU241	2.0	0.5	1.0
	OE2	B:GLU241	2.0	96.0	1.0
	O	B:HOH610	2.2	60.6	1.0
	CD	B:GLU241	2.3	79.5	1.0
	O3P	B:4LU502	2.3	52.4	1.0
	CG	B:ASN175	3.1	57.4	1.0
	NA	B:NA503	3.5	66.7	1.0
	P	B:4LU502	3.7	53.7	1.0
	CG	B:GLU241	3.8	74.8	1.0
	ND2	B:ASN175	3.8	56.7	1.0
	O	B:HOH657	3.8	64.7	1.0
	O2P	B:4LU502	4.2	59.8	1.0
	CB	B:ASN175	4.2	56.5	1.0
	O	B:LEU176	4.3	52.8	1.0
	O	B:PRO236	4.4	85.7	1.0
	O5'	B:4LU502	4.5	52.2	1.0
	CG2	B:VAL235	4.5	88.5	1.0
	O	B:VAL235	4.6	71.3	1.0
	CA	B:ASN175	4.7	58.9	1.0
	O	B:LEU239	4.7	88.5	1.0
	N	B:LEU176	4.7	54.9	1.0
	O1P	B:4LU502	4.8	46.9	1.0
	OD1	B:ASP237	4.9	72.7	1.0
	CA	B:ASP237	4.9	76.8	1.0
	CB	B:GLU241	4.9	70.6	1.0

Manganese binding site 3 out of 3 in 5m1d

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Manganese Binding Sites List in 5m1d

Manganese binding site 3 out of 3 in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor

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 N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mn501 b:0.4 occ:0.50	OE2	C:GLU241	1.9	0.7	1.0
	OD1	C:ASN175	1.9	0.3	1.0
	OE1	C:GLU241	1.9	0.0	1.0
	CD	C:GLU241	2.2	0.7	1.0
	O3P	C:4LU502	2.9	95.7	1.0
	CG	C:ASN175	3.0	0.9	1.0
	NA	C:NA503	3.6	56.8	0.5
	CG	C:GLU241	3.7	0.1	1.0
	ND2	C:ASN175	3.8	0.3	1.0
	CB	C:ASN175	4.0	0.2	1.0
	P	C:4LU502	4.1	0.6	1.0
	O	C:LEU176	4.2	0.1	1.0
	O2P	C:4LU502	4.3	0.7	1.0
	O	C:PRO236	4.3	0.6	1.0
	CA	C:ASN175	4.4	0.3	1.0
	O	C:LEU239	4.4	0.6	1.0
	CG2	C:VAL235	4.5	0.8	1.0
	N	C:LEU176	4.5	0.1	1.0
	CB	C:GLU241	4.7	0.8	1.0
	O	C:VAL235	4.8	0.8	1.0
	CA	C:ASP237	4.9	0.1	1.0
	C	C:ASN175	5.0	0.8	1.0

Reference:

S.A.Marshall, K.Fisher, A.Ni Cheallaigh, M.D.White, K.A.Payne, D.A.Parker, S.E.Rigby, D.Leys. Oxidative Maturation and Structural Characterization of Prenylated Fmn Binding By Ubid, A Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis. J. Biol. Chem. V. 292 4623 2017.
ISSN: ESSN 1083-351X
PubMed: 28057757
DOI: 10.1074/JBC.M116.762732

Page generated: Sun Oct 6 01:53:53 2024

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