Zinc in PDB 6eed: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion

Protein crystallography data

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion, PDB code: 6eed was solved by N.Drinkwater, S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.80 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.149, 109.230, 117.920, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18

Other elements in 6eed:

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion (pdb code 6eed). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion, PDB code: 6eed:

Zinc binding site 1 out of 1 in 6eed

Go back to Zinc Binding Sites List in 6eed
Zinc binding site 1 out of 1 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:12.8
occ:0.80
OE1 A:GLU519 2.0 10.7 1.0
O A:J6A1102 2.0 10.2 1.0
NE2 A:HIS500 2.1 10.7 1.0
NE2 A:HIS496 2.1 10.4 1.0
OAC A:J6A1102 2.2 11.0 1.0
CD A:GLU519 2.8 12.0 1.0
C A:J6A1102 2.8 9.2 1.0
OE2 A:GLU519 2.8 13.5 1.0
NAS A:J6A1102 2.9 10.7 1.0
CD2 A:HIS496 3.0 9.1 1.0
CE1 A:HIS500 3.1 10.8 1.0
CD2 A:HIS500 3.1 9.5 1.0
CE1 A:HIS496 3.2 11.2 1.0
O A:HOH1277 3.4 12.4 1.0
OE1 A:GLU463 4.1 11.5 1.0
OH A:TYR580 4.1 10.7 1.0
CE2 A:TYR580 4.1 11.0 1.0
ND1 A:HIS500 4.2 11.0 1.0
CG A:HIS496 4.2 9.4 1.0
CG A:HIS500 4.2 10.3 1.0
CG A:GLU519 4.2 11.6 1.0
CA A:J6A1102 4.3 10.9 1.0
ND1 A:HIS496 4.3 9.8 1.0
OE1 A:GLU497 4.4 11.6 1.0
CZ A:TYR580 4.6 11.1 1.0
CD A:GLU463 4.7 11.0 1.0
N A:J6A1102 4.7 11.8 1.0
OE2 A:GLU463 4.8 12.9 1.0
CG2 A:THR522 4.8 11.8 1.0
OE2 A:GLU497 4.8 11.2 1.0
O2 A:PO41115 4.9 49.4 0.8
CB A:GLU519 4.9 11.6 1.0
CA A:GLU519 4.9 11.1 1.0
NZ A:LYS518 4.9 11.6 1.0

Reference:

N.B.Vinh, N.Drinkwater, T.R.Malcolm, M.Kassiou, L.Lucantoni, P.M.Grin, G.S.Butler, S.Duffy, C.M.Overall, V.M.Avery, P.J.Scammells, S.Mcgowan. Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. V. 62 622 2019.
ISSN: ISSN 1520-4804
PubMed: 30537832
DOI: 10.1021/ACS.JMEDCHEM.8B01310
Page generated: Wed Dec 16 11:42:48 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy