Sodium in PDB 5yr5: Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin

Enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin

All present enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin:
3.4.11.18;

Protein crystallography data

The structure of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin, PDB code: 5yr5 was solved by V.Pillalamarri, T.Arya, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	31.24 / 1.60
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	47.392, 77.339, 47.464, 90.00, 87.95, 90.00
*R / R_free (%)*	17.7 / 20.1

Other elements in 5yr5:

The structure of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin also contains other interesting chemical elements:

Cobalt

(Co)

3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin (pdb code 5yr5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin, PDB code: 5yr5:

Sodium binding site 1 out of 1 in 5yr5

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Sodium Binding Sites List in 5yr5

Sodium binding site 1 out of 1 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na404 b:19.2 occ:1.00	O	A:VAL209	2.2	18.2	1.0
	O	A:SER363	2.3	19.5	1.0
	O	A:HOH440	2.3	19.3	1.0
	O	A:ASN207	2.3	19.3	1.0
	O	A:HOH436	3.2	19.5	1.0
	C	A:ASN207	3.3	19.6	1.0
	C	A:SER363	3.3	18.1	1.0
	C	A:VAL209	3.4	17.4	1.0
	N	A:ASN207	3.6	18.7	1.0
	C	A:VAL206	3.9	17.5	1.0
	N	A:SER363	3.9	20.1	1.0
	CA	A:ASN207	3.9	19.6	1.0
	N	A:VAL209	3.9	18.5	1.0
	O	A:SER205	4.0	17.3	1.0
	CA	A:SER363	4.0	19.5	1.0
	O	A:VAL206	4.1	19.4	1.0
	CA	A:VAL209	4.2	18.6	1.0
	CB	A:SER363	4.2	18.5	1.0
	O	A:HOH426	4.2	17.8	1.0
	N	A:GLU208	4.3	18.9	1.0
	C	A:SER205	4.3	17.0	1.0
	C	A:GLU208	4.4	18.1	1.0
	N	A:ILE210	4.4	17.7	1.0
	N	A:ALA364	4.4	17.9	1.0
	CD1	A:ILE225	4.5	22.5	1.0
	CA	A:VAL206	4.6	18.8	1.0
	N	A:VAL206	4.6	18.7	1.0
	CB	A:SER205	4.7	15.6	1.0
	CG1	A:ILE225	4.7	21.1	1.0
	CB	A:VAL209	4.7	18.9	1.0
	CA	A:ILE210	4.7	17.8	1.0
	CA	A:ALA364	4.7	17.1	1.0
	CA	A:GLU208	4.7	19.3	1.0
	OG	A:SER363	5.0	19.0	1.0
	O	A:GLU208	5.0	19.2	1.0

Reference:

V.Pillalamarri, T.Arya, N.Haque, S.C.Bala, A.K.Marapaka, A.Addlagatta. Discovery of Natural Product Ovalicin Sensitive Type 1 Methionine Aminopeptidases: Molecular and Structural Basis. Biochem. J. V. 476 991 2019.
ISSN: ESSN 1470-8728
PubMed: 30837307
DOI: 10.1042/BCJ20180874

Page generated: Tue Oct 8 01:25:07 2024

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