Nickel in PDB 7d2b: Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with A Ni Ion Bound to the Active Site

Enzymatic activity of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with A Ni Ion Bound to the Active Site

All present enzymatic activity of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with A Ni Ion Bound to the Active Site:
2.3.2.5;

Protein crystallography data

The structure of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with A Ni Ion Bound to the Active Site, PDB code: 7d2b was solved by K.-F.Huang, J.-S.Huang, M.-L.Wu, W.-L.Hsieh, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	22.78 / 1.99
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	55.066, 71.26, 80.119, 90, 90, 90
*R / R_free (%)*	17.2 / 23.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with A Ni Ion Bound to the Active Site (pdb code 7d2b). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with A Ni Ion Bound to the Active Site, PDB code: 7d2b:

Nickel binding site 1 out of 1 in 7d2b

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Nickel Binding Sites List in 7d2b

Nickel binding site 1 out of 1 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with A Ni Ion Bound to the Active Site

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with A Ni Ion Bound to the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni400 b:31.6 occ:1.00	OE2	A:GLU184	2.1	25.3	1.0
	NE2	A:HIS322	2.1	21.0	1.0
	OD2	A:ASP144	2.1	18.3	1.0
	O	A:HOH701	2.1	39.2	1.0
	CG	A:ASP144	2.8	19.4	1.0
	CD	A:GLU184	2.9	23.2	1.0
	CD2	A:HIS322	2.9	19.9	1.0
	OD1	A:ASP144	2.9	18.4	1.0
	OE1	A:GLU184	3.0	24.9	1.0
	CE1	A:HIS322	3.2	20.0	1.0
	NE1	A:TRP321	3.8	24.6	1.0
	O	A:HOH531	3.9	23.9	1.0
	O	A:HOH672	4.0	40.8	1.0
	CG	A:HIS322	4.1	21.4	1.0
	ND1	A:HIS322	4.3	20.2	1.0
	CB	A:ASP144	4.3	18.5	1.0
	CG	A:GLU184	4.3	21.7	1.0
	CE2	A:TRP321	4.4	25.5	1.0
	OE1	A:GLU183	4.5	25.4	1.0
	O	A:HOH512	4.6	20.2	1.0
	CD1	A:TRP321	4.6	23.5	1.0
	CD2	A:LEU239	4.6	16.3	1.0
	CZ2	A:TRP321	4.7	25.4	1.0
	NE2	A:HIS128	4.8	20.0	1.0

Reference:

K.F.Huang, J.S.Huang, M.L.Wu, W.L.Hsieh, K.C.Hsu, H.L.Hsu, T.P.Ko, A.H-J Wang. A Unique Carboxylic-Acid Hydrogen-Bond Network (Cahbn) Confers Glutaminyl Cyclase Activity on M28 Family Enzymes. J.Mol.Biol. 66960 2021.
ISSN: ESSN 1089-8638
PubMed: 33774034
DOI: 10.1016/J.JMB.2021.166960

Page generated: Thu Oct 10 09:10:20 2024

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