Manganese in PDB 5jqk: The Xray Crystal Structure of P. Falciparum Aminopeptidase P

The structure of The Xray Crystal Structure of P. Falciparum Aminopeptidase P, PDB code: 5jqk 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)	44.99 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.740, 100.070, 106.660, 90.00, 105.37, 90.00
R / Rfree (%)	18.9 / 22.6

The binding sites of Manganese atom in the The Xray Crystal Structure of P. Falciparum Aminopeptidase P (pdb code 5jqk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Xray Crystal Structure of P. Falciparum Aminopeptidase P, PDB code: 5jqk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Xray Crystal Structure of P. Falciparum Aminopeptidase P


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Xray Crystal Structure of P. Falciparum Aminopeptidase P within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:30.1 occ:1.00 OD1 A:ASP581 1.9 39.9 1.0 OE2 A:GLU690 2.0 33.7 1.0 O2 A:PO4803 2.1 31.6 1.0 NE2 A:HIS644 2.2 28.4 1.0 OE2 A:GLU676 2.3 36.4 1.0 CG A:ASP581 2.9 33.9 1.0 CD A:GLU676 3.0 43.7 1.0 CD A:GLU690 3.0 31.3 1.0 CD2 A:HIS644 3.1 31.6 1.0 P A:PO4803 3.1 42.5 1.0 CE1 A:HIS644 3.2 29.8 1.0 MN A:MN802 3.2 28.7 1.0 OE1 A:GLU676 3.2 47.2 1.0 O3 A:PO4803 3.3 47.2 1.0 OD2 A:ASP581 3.4 34.6 1.0 OE1 A:GLU690 3.4 25.9 1.0 O1 A:PO4803 3.7 43.8 1.0 OG A:SER674 4.1 32.8 1.0 CB A:SER674 4.1 32.9 1.0 CB A:ASP581 4.1 33.3 1.0 ND1 A:HIS644 4.3 29.8 1.0 CG A:HIS644 4.3 32.3 1.0 CG A:GLU690 4.3 34.4 1.0 CG A:GLU676 4.4 33.5 1.0 O4 A:PO4803 4.4 39.3 1.0 NE2 A:HIS653 4.5 42.4 1.0 CD2 A:HIS653 4.8 37.2 1.0 OD2 A:ASP570 4.9 36.9 1.0

Manganese binding site 2 out of 4 in the The Xray Crystal Structure of P. Falciparum Aminopeptidase P


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Xray Crystal Structure of P. Falciparum Aminopeptidase P within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:28.7 occ:1.00 OD2 A:ASP581 1.9 34.6 1.0 OD1 A:ASP570 2.0 35.0 1.0 O2 A:PO4803 2.1 31.6 1.0 OE1 A:GLU690 2.1 25.9 1.0 OD2 A:ASP570 2.4 36.9 1.0 CG A:ASP570 2.5 33.8 1.0 CG A:ASP581 2.8 33.9 1.0 CD A:GLU690 2.9 31.3 1.0 OD1 A:ASP581 3.0 39.9 1.0 OE2 A:GLU690 3.1 33.7 1.0 MN A:MN801 3.2 30.1 1.0 P A:PO4803 3.2 42.5 1.0 OG1 A:THR583 3.5 34.6 1.0 O1 A:PO4803 3.5 43.8 1.0 O4 A:PO4803 3.7 39.3 1.0 CZ A:PHE537 3.7 32.5 1.0 CB A:ASP570 4.0 29.5 1.0 OE1 A:GLU676 4.1 47.2 1.0 N A:VAL582 4.2 32.1 1.0 CB A:ASP581 4.2 33.3 1.0 CE2 A:PHE537 4.4 32.5 1.0 CE1 A:PHE537 4.4 31.8 1.0 CG A:GLU690 4.4 34.4 1.0 O A:VAL582 4.4 37.5 1.0 C A:VAL582 4.5 35.5 1.0 O3 A:PO4803 4.5 47.2 1.0 C A:ASP581 4.5 34.8 1.0 CA A:ASP581 4.6 37.5 1.0 CA A:ASP570 4.7 34.6 1.0 CD A:GLU676 4.8 43.7 1.0 OE2 A:GLU676 4.8 36.4 1.0 CA A:VAL582 4.8 36.1 1.0 N A:THR583 4.8 35.5 1.0 N A:SER571 4.8 30.2 1.0 CB A:THR583 4.9 33.3 1.0 CB A:GLU690 4.9 27.4 1.0 C A:ASP570 4.9 33.2 1.0

Manganese binding site 3 out of 4 in the The Xray Crystal Structure of P. Falciparum Aminopeptidase P


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Xray Crystal Structure of P. Falciparum Aminopeptidase P within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn801 b:40.1 occ:1.00 OD2 B:ASP581 2.0 48.0 1.0 OE2 B:GLU690 2.1 50.3 1.0 O4 B:PO4803 2.2 49.3 1.0 NE2 B:HIS644 2.2 55.2 1.0 OE2 B:GLU676 2.3 55.1 1.0 CG B:ASP581 3.0 48.0 1.0 CD B:GLU676 3.0 55.3 1.0 CD B:GLU690 3.1 45.5 1.0 CE1 B:HIS644 3.1 52.6 1.0 OE1 B:GLU676 3.1 55.1 1.0 P B:PO4803 3.1 53.2 1.0 MN B:MN802 3.2 37.1 1.0 CD2 B:HIS644 3.2 54.8 1.0 O2 B:PO4803 3.3 58.7 1.0 OE1 B:GLU690 3.4 35.0 1.0 O3 B:PO4803 3.5 52.0 1.0 OD1 B:ASP581 3.6 37.7 1.0 CB B:SER674 4.0 39.4 1.0 OG B:SER674 4.0 41.7 1.0 CB B:ASP581 4.1 40.8 1.0 ND1 B:HIS644 4.2 54.6 1.0 CG B:HIS644 4.3 55.8 1.0 CG B:GLU690 4.3 36.8 1.0 CG B:GLU676 4.4 49.9 1.0 O1 B:PO4803 4.5 59.5 1.0 NE2 B:HIS653 4.6 56.5 1.0 CD2 B:HIS653 4.9 56.8 1.0

Manganese binding site 4 out of 4 in the The Xray Crystal Structure of P. Falciparum Aminopeptidase P


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Xray Crystal Structure of P. Falciparum Aminopeptidase P within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn802 b:37.1 occ:1.00 OE1 B:GLU690 1.9 35.0 1.0 OD1 B:ASP581 2.0 37.7 1.0 OD1 B:ASP570 2.0 46.7 1.0 O4 B:PO4803 2.0 49.3 1.0 OD2 B:ASP570 2.6 50.6 1.0 CG B:ASP570 2.7 50.0 1.0 CG B:ASP581 2.8 48.0 1.0 CD B:GLU690 2.9 45.5 1.0 OD2 B:ASP581 3.0 48.0 1.0 OE2 B:GLU690 3.1 50.3 1.0 MN B:MN801 3.2 40.1 1.0 P B:PO4803 3.3 53.2 1.0 OG1 B:THR583 3.4 49.0 1.0 O3 B:PO4803 3.7 52.0 1.0 O1 B:PO4803 3.7 59.5 1.0 CZ B:PHE537 3.8 48.1 1.0 OE1 B:GLU676 4.0 55.1 1.0 CB B:ASP570 4.2 42.1 1.0 CB B:ASP581 4.2 40.8 1.0 N B:VAL582 4.2 45.9 1.0 CG B:GLU690 4.3 36.8 1.0 O B:VAL582 4.4 41.1 1.0 C B:VAL582 4.4 36.0 1.0 CE1 B:PHE537 4.4 42.8 1.0 C B:ASP581 4.4 41.7 1.0 CE2 B:PHE537 4.5 41.9 1.0 O2 B:PO4803 4.5 58.7 1.0 CA B:ASP581 4.6 42.1 1.0 CB B:GLU690 4.7 35.5 1.0 CA B:VAL582 4.7 36.8 1.0 N B:THR583 4.8 38.8 1.0 CD B:GLU676 4.8 55.3 1.0 CA B:ASP570 4.8 42.9 1.0 CB B:THR583 4.8 43.6 1.0 OE2 B:GLU676 4.8 55.1 1.0 N B:SER571 4.9 42.9 1.0 C B:ASP570 5.0 45.4 1.0

N.Drinkwater, K.K.Sivaraman, R.S.Bamert, W.Rut, K.Mohamed, N.B.Vinh, P.J.Scammells, M.Drag, S.Mcgowan. Structure and Substrate Fingerprint of Aminopeptidase P From Plasmodium Falciparum. Biochem.J. V. 473 3189 2016.
ISSN: ESSN 1470-8728
PubMed: 27462122
DOI: 10.1042/BCJ20160550