Manganese in PDB 5jr6: The Xray Crystal Structure of P. Falciparum Aminopeptidase P in Complex with Apstatin

The structure of The Xray Crystal Structure of P. Falciparum Aminopeptidase P in Complex with Apstatin, PDB code: 5jr6 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)	42.79 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.220, 99.930, 105.170, 90.00, 105.21, 90.00
R / Rfree (%)	19.7 / 24.1

The binding sites of Manganese atom in the The Xray Crystal Structure of P. Falciparum Aminopeptidase P in Complex with Apstatin (pdb code 5jr6). 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 in Complex with Apstatin, PDB code: 5jr6:
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 in Complex with Apstatin


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 in Complex with Apstatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:62.1 occ:1.00 OD1 A:ASP581 2.4 38.3 1.0 OE2 A:GLU690 2.4 39.0 1.0 NE2 A:HIS644 2.4 31.7 1.0 OE2 A:GLU676 2.5 53.7 1.0 O2 F:01B1 2.7 43.8 1.0 O3 F:01B1 2.8 79.8 1.0 OE1 A:GLU676 2.9 51.4 1.0 CD A:GLU676 3.0 52.2 1.0 C3 F:01B1 3.2 70.3 1.0 CG A:ASP581 3.2 33.6 1.0 CD2 A:HIS644 3.3 34.1 1.0 MN A:MN802 3.4 42.5 1.0 CD A:GLU690 3.4 42.9 1.0 CE1 A:HIS644 3.4 28.6 1.0 C2 F:01B1 3.4 35.7 1.0 OD2 A:ASP581 3.6 36.1 1.0 OE1 A:GLU690 3.8 35.7 1.0 C1 F:01B1 4.0 51.7 1.0 N2 F:01B1 4.0 54.3 1.0 N F:PRO2 4.1 81.1 1.0 OG A:SER674 4.1 32.3 1.0 NE2 A:HIS653 4.2 53.9 1.0 CB A:SER674 4.2 31.2 1.0 CB A:ASP581 4.3 31.0 1.0 ND1 A:HIS644 4.5 33.0 1.0 CG A:HIS644 4.5 36.5 1.0 CG A:GLU676 4.5 33.6 1.0 CG A:GLU690 4.6 40.9 1.0 CD2 A:HIS653 4.7 47.0 1.0 CA F:PRO2 4.7 83.1 1.0 CD F:PRO2 5.0 77.5 1.0

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


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 in Complex with Apstatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:42.5 occ:1.00 O2 F:01B1 2.0 43.8 1.0 OD2 A:ASP581 2.0 36.1 1.0 OD1 A:ASP570 2.0 30.0 1.0 OE1 A:GLU690 2.2 35.7 1.0 CG A:ASP570 2.7 36.0 1.0 OD2 A:ASP570 2.7 35.8 1.0 CG A:ASP581 2.9 33.6 1.0 CD A:GLU690 3.0 42.9 1.0 N2 F:01B1 3.1 54.3 1.0 OE2 A:GLU690 3.1 39.0 1.0 OD1 A:ASP581 3.2 38.3 1.0 C2 F:01B1 3.3 35.7 1.0 MN A:MN801 3.4 62.1 1.0 OG1 A:THR583 3.5 29.1 1.0 C1 F:01B1 3.8 51.7 1.0 CZ A:PHE537 3.8 39.6 1.0 OE1 A:GLU676 4.1 51.4 1.0 CB A:ASP570 4.2 27.2 1.0 C3 F:01B1 4.3 70.3 1.0 CB A:ASP581 4.3 31.0 1.0 N A:VAL582 4.3 34.3 1.0 CE2 A:PHE537 4.4 33.4 1.0 CG A:GLU690 4.4 40.9 1.0 C A:ASP581 4.5 33.4 1.0 CE1 A:PHE537 4.5 41.6 1.0 O A:VAL582 4.5 31.5 1.0 C A:VAL582 4.6 32.1 1.0 CA A:ASP581 4.7 27.6 1.0 CA A:ASP570 4.7 34.9 1.0 O3 F:01B1 4.8 79.8 1.0 N A:THR583 4.8 31.1 1.0 CB A:THR583 4.9 26.3 1.0 CB A:GLU690 4.9 32.6 1.0 CA A:VAL582 4.9 35.9 1.0 C6 F:01B1 4.9 72.4 1.0 N A:SER571 4.9 33.2 1.0 C A:ASP570 5.0 36.8 1.0 O A:ASP581 5.0 30.4 1.0

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


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 in Complex with Apstatin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn801 b:74.5 occ:1.00 OE2 B:GLU690 2.3 53.5 1.0 OD2 B:ASP581 2.5 66.8 1.0 OE2 B:GLU676 2.5 53.6 1.0 NE2 B:HIS644 2.6 58.9 1.0 O2 B:PO4803 2.6 74.3 1.0 O4 B:PO4803 2.9 82.3 1.0 OE1 B:GLU676 2.9 73.3 1.0 CD B:GLU676 3.0 65.1 1.0 CG B:ASP581 3.2 57.7 1.0 CD B:GLU690 3.2 48.4 1.0 P B:PO4803 3.2 73.4 1.0 MN B:MN802 3.4 57.9 1.0 OD1 B:ASP581 3.5 54.7 1.0 CE1 B:HIS644 3.5 54.0 1.0 OE1 B:GLU690 3.5 40.9 1.0 CD2 B:HIS644 3.6 55.2 1.0 O3 B:PO4803 3.9 66.2 1.0 OG B:SER674 4.0 47.2 1.0 CB B:SER674 4.2 42.6 1.0 CB B:ASP581 4.3 53.9 1.0 CG B:GLU676 4.5 58.3 1.0 NE2 B:HIS653 4.5 70.7 1.0 CG B:GLU690 4.5 38.9 1.0 O1 B:PO4803 4.6 79.1 1.0 ND1 B:HIS644 4.6 59.2 1.0 CG B:HIS644 4.7 55.1 1.0 CD2 B:HIS653 4.8 66.1 1.0

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


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 in Complex with Apstatin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn802 b:57.9 occ:1.00 O4 B:PO4803 1.8 82.3 1.0 OD1 B:ASP581 1.8 54.7 1.0 OE1 B:GLU690 2.0 40.9 1.0 OD1 B:ASP570 2.1 64.0 1.0 CG B:ASP570 2.8 56.6 1.0 CG B:ASP581 2.9 57.7 1.0 OD2 B:ASP570 2.9 49.5 1.0 CD B:GLU690 2.9 48.4 1.0 P B:PO4803 3.2 73.4 1.0 OE2 B:GLU690 3.2 53.5 1.0 OD2 B:ASP581 3.3 66.8 1.0 MN B:MN801 3.4 74.5 1.0 OG1 B:THR583 3.4 54.8 1.0 O3 B:PO4803 3.8 66.2 1.0 CZ B:PHE537 3.9 56.2 1.0 O2 B:PO4803 4.0 74.3 1.0 OE1 B:GLU676 4.1 73.3 1.0 O1 B:PO4803 4.1 79.1 1.0 N B:VAL582 4.1 42.8 1.0 O B:VAL582 4.2 55.8 1.0 CB B:ASP581 4.2 53.9 1.0 CB B:ASP570 4.3 47.6 1.0 CG B:GLU690 4.3 38.9 1.0 C B:VAL582 4.3 41.7 1.0 CE2 B:PHE537 4.4 53.9 1.0 C B:ASP581 4.4 41.9 1.0 CA B:ASP581 4.6 49.2 1.0 CE1 B:PHE537 4.6 51.9 1.0 CB B:GLU690 4.7 37.4 1.0 N B:THR583 4.8 40.4 1.0 CB B:THR583 4.8 51.3 1.0 CA B:VAL582 4.8 41.1 1.0 CA B:ASP570 4.8 52.5 1.0 N B:SER571 4.9 50.1 1.0 CD B:GLU676 5.0 65.1 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