Manganese in PDB 4wp8: Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion

Enzymatic activity of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion

All present enzymatic activity of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion:
4.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion, PDB code: 4wp8 was solved by D.V.Barathy, N.G.Bharambe, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	55.96 / 1.65
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	51.970, 55.960, 54.070, 90.00, 106.35, 90.00
*R / R_free (%)*	17.2 / 21.5

Other elements in 4wp8:

The structure of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion (pdb code 4wp8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion, PDB code: 4wp8:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4wp8

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Manganese Binding Sites List in 4wp8

Manganese binding site 1 out of 2 in the Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion

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 Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn301 b:14.4 occ:1.00	OD1	A:ASP61	2.1	17.0	1.0
	OD2	A:ASP105	2.1	15.7	1.0
	O3G	A:ZDA303	2.1	19.4	1.0
	O2B	A:ZDA303	2.2	14.2	1.0
	O2A	A:ZDA303	2.2	16.1	1.0
	O	A:ILE62	2.2	14.2	1.0
	CG	A:ASP61	3.1	17.2	1.0
	CG	A:ASP105	3.2	15.1	1.0
	PB	A:ZDA303	3.3	15.4	1.0
	PA	A:ZDA303	3.3	16.4	1.0
	C	A:ILE62	3.3	14.6	1.0
	PG	A:ZDA303	3.4	19.5	1.0
	O	A:HOH503	3.5	10.4	1.0
	OD2	A:ASP61	3.5	21.6	1.0
	O3A	A:ZDA303	3.6	16.7	1.0
	O	A:HOH401	3.6	15.9	1.0
	OD1	A:ASP105	3.6	15.2	1.0
	O3B	A:ZDA303	3.7	18.0	1.0
	N	A:ILE62	3.9	14.1	1.0
	OG	A:SER65	4.0	14.3	1.0
	O2G	A:ZDA303	4.1	20.2	1.0
	CA	A:ILE62	4.1	14.1	1.0
	NH1	A:ARG143	4.2	27.7	1.0
	O1A	A:ZDA303	4.2	20.9	1.0
	C	A:ASP61	4.3	14.1	1.0
	N	A:GLU63	4.4	15.1	1.0
	CB	A:ASP61	4.4	15.4	1.0
	CB	A:SER65	4.5	14.3	1.0
	CB	A:ASP105	4.5	14.8	1.0
	N	A:SER65	4.5	14.7	1.0
	N	A:GLU64	4.5	15.8	1.0
	O3'	A:ZDA303	4.5	17.6	1.0
	O	A:HOH448	4.6	19.8	1.0
	O1G	A:ZDA303	4.6	19.3	1.0
	O1B	A:ZDA303	4.6	15.4	1.0
	CA	A:GLU63	4.6	16.1	1.0
	CA	A:ASP61	4.7	14.4	1.0
	CB	A:ILE62	4.7	14.3	1.0
	O	A:ASP61	4.8	14.1	1.0
	C	A:GLU63	4.8	15.5	1.0

Manganese binding site 2 out of 2 in 4wp8

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Manganese Binding Sites List in 4wp8

Manganese binding site 2 out of 2 in the Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion

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 Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with 2'5'-Dd-3'-Atp and Manganese Ion within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn301 b:14.4 occ:1.00	O3G	B:ZDA302	2.0	13.7	0.5
	O1B	B:ZDA302	2.1	12.3	0.5
	OD2	B:ASP105	2.2	15.4	1.0
	OD1	B:ASP61	2.2	16.1	1.0
	O	B:ILE62	2.2	13.6	1.0
	O1A	B:ZDA302	2.2	14.7	0.5
	O1A	B:ZDA302	2.3	13.2	0.5
	O1B	B:ZDA302	2.4	13.8	0.5
	O3G	B:ZDA302	2.4	15.8	0.5
	PB	B:ZDA302	3.1	12.3	0.5
	CG	B:ASP61	3.2	18.1	1.0
	CG	B:ASP105	3.2	15.2	1.0
	PG	B:ZDA302	3.2	13.8	0.5
	PB	B:ZDA302	3.4	14.7	0.5
	C	B:ILE62	3.4	14.7	1.0
	PA	B:ZDA302	3.5	15.0	0.5
	PA	B:ZDA302	3.5	13.9	0.5
	O3B	B:ZDA302	3.5	12.9	0.5
	O	B:HOH403	3.6	17.8	1.0
	O3A	B:ZDA302	3.6	12.8	0.5
	OD1	B:ASP105	3.6	14.7	1.0
	PG	B:ZDA302	3.6	16.2	0.5
	OD2	B:ASP61	3.6	21.0	1.0
	O3A	B:ZDA302	3.7	14.7	0.5
	O3B	B:ZDA302	3.8	15.4	0.5
	N	B:ILE62	3.9	14.2	1.0
	O1G	B:ZDA302	4.0	14.4	0.5
	OG	B:SER65	4.0	17.7	1.0
	NH1	B:ARG143	4.1	25.2	1.0
	CA	B:ILE62	4.2	14.9	1.0
	O2A	B:ZDA302	4.3	15.5	0.5
	C	B:ASP61	4.3	14.8	1.0
	O1G	B:ZDA302	4.3	16.6	0.5
	O2G	B:ZDA302	4.4	13.9	0.5
	N	B:GLU63	4.4	16.0	1.0
	CB	B:ASP61	4.5	15.8	1.0
	CB	B:SER65	4.5	16.6	1.0
	O2B	B:ZDA302	4.5	12.5	0.5
	O3'	B:ZDA302	4.5	13.5	0.5
	N	B:SER65	4.5	16.7	1.0
	CB	B:ASP105	4.5	15.0	1.0
	N	B:GLU64	4.5	17.2	1.0
	O2A	B:ZDA302	4.6	13.1	0.5
	C3'	B:ZDA302	4.6	14.0	0.5
	CA	B:GLU63	4.6	17.8	1.0
	CB	B:ILE62	4.7	14.9	1.0
	CA	B:ASP61	4.7	15.2	1.0
	O3'	B:ZDA302	4.7	15.8	0.5
	O2B	B:ZDA302	4.7	13.9	0.5
	O2G	B:ZDA302	4.7	16.2	0.5
	C	B:GLU63	4.8	17.8	1.0
	O	B:ASP61	4.8	15.9	1.0

Reference:

D.V.Barathy, N.G.Bharambe, W.Syed, A.Zaveri, S.S.Visweswariah, M.Cola Sigmaf O, S.Misquith, K.Suguna. Autoinhibitory Mechanism and Activity-Related Structural Changes in A Mycobacterial Adenylyl Cyclase J.Struct.Biol. V. 190 304 2015.
ISSN: ESSN 1095-8657
PubMed: 25916753
DOI: 10.1016/J.JSB.2015.04.013

Page generated: Sat Oct 5 22:51:35 2024

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