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

Protein crystallography data

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) and Catalytic Zinc Ion, PDB code: 6eab 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) 35.36 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.030, 109.101, 118.240, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 19.1

Other elements in 6eab:

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) 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 (6J) and Catalytic Zinc Ion (pdb code 6eab). 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 (6J) and Catalytic Zinc Ion, PDB code: 6eab:

Zinc binding site 1 out of 1 in 6eab

Go back to Zinc Binding Sites List in 6eab
Zinc binding site 1 out of 1 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) 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 (6J) and Catalytic Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:13.2
occ:0.80
O A:J2D1102 2.0 13.7 1.0
OE1 A:GLU519 2.0 10.9 1.0
NE2 A:HIS496 2.1 10.5 1.0
NE2 A:HIS500 2.1 11.1 1.0
OAC A:J2D1102 2.1 13.9 1.0
C A:J2D1102 2.8 11.8 1.0
CD A:GLU519 2.8 11.1 1.0
NAQ A:J2D1102 2.9 10.9 1.0
OE2 A:GLU519 2.9 14.6 1.0
CD2 A:HIS496 3.0 11.6 1.0
CD2 A:HIS500 3.0 10.7 1.0
CE1 A:HIS496 3.1 11.2 1.0
CE1 A:HIS500 3.1 8.9 1.0
O A:HOH1240 3.5 14.1 1.0
OH A:TYR580 4.1 11.4 1.0
OE1 A:GLU463 4.1 12.4 1.0
CG A:HIS496 4.2 9.6 1.0
CE2 A:TYR580 4.2 15.3 1.0
ND1 A:HIS496 4.2 10.5 1.0
CG A:HIS500 4.2 9.3 1.0
ND1 A:HIS500 4.2 9.3 1.0
CA A:J2D1102 4.2 11.1 1.0
CG A:GLU519 4.3 8.8 1.0
OE1 A:GLU497 4.4 12.9 1.0
CZ A:TYR580 4.6 11.3 1.0
N A:J2D1102 4.6 12.8 1.0
CD A:GLU463 4.7 13.3 1.0
OE2 A:GLU463 4.8 16.9 1.0
OE2 A:GLU497 4.8 12.2 1.0
CG2 A:THR522 4.8 11.5 1.0
CB A:THR522 4.9 10.1 1.0
CB A:GLU519 4.9 9.4 1.0
CA A:GLU519 4.9 10.4 1.0
NZ A:LYS518 5.0 9.2 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: Mon Oct 28 20:03:28 2024

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