Zinc in PDB 6e4z: Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9

The structure of Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9, PDB code: 6e4z was solved by M.H.Ultsch, D.K.Kirchhofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.42 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.929, 99.782, 86.328, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.6

The binding sites of Zinc atom in the Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9 (pdb code 6e4z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9, PDB code: 6e4z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:44.7 occ:1.00 OD1 H:ASP53 1.9 52.8 1.0 OE2 P:GLU48 2.0 46.3 1.0 CD P:GLU48 2.8 59.1 1.0 CG H:ASP53 3.0 43.4 1.0 OE1 P:GLU48 3.0 44.8 1.0 O P:HOH101 3.3 43.8 1.0 CB H:ASP53 3.5 30.9 1.0 CA H:ASP53 4.0 38.4 1.0 OD2 H:ASP53 4.0 39.0 1.0 O H:HOH418 4.1 53.7 1.0 CG P:GLU48 4.2 62.4 1.0 O H:HOH417 4.4 40.7 1.0 NH1 H:ARG52 4.6 34.4 1.0 N H:ASP53 4.8 37.5 1.0 O H:SER52C 4.9 43.5 1.0

Zinc binding site 2 out of 5 in the Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:0.3 occ:1.00 OD1 L:ASN138 2.0 94.2 1.0 NE2 H:HIS164 2.1 83.8 1.0 OD1 L:ASN137 2.1 83.2 1.0 CD2 H:HIS164 2.5 81.5 1.0 CG L:ASN137 3.0 86.5 1.0 O L:HOH414 3.0 86.0 1.0 CG L:ASN138 3.1 88.2 1.0 ND2 L:ASN137 3.1 93.2 1.0 CE1 H:HIS164 3.3 78.5 1.0 ND2 L:ASN138 3.7 90.6 1.0 CG H:HIS164 3.8 82.5 1.0 OG L:SER174 4.1 59.4 1.0 ND1 H:HIS164 4.2 77.4 1.0 CB L:ASN138 4.3 80.6 1.0 CB L:ASN137 4.4 80.1 1.0 OG1 H:THR183 4.5 80.9 1.0 N L:ASN138 4.5 56.8 1.0 O H:GLY162 4.6 71.1 1.0 CA L:ASN138 4.9 75.8 1.0 CA L:ASN137 4.9 77.9 1.0 C L:ASN137 5.0 63.7 1.0

Zinc binding site 3 out of 5 in the Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn302 b:0.1 occ:1.00 OD2 L:ASP185 2.1 1.0 1.0 NE2 L:HIS189 2.1 95.4 1.0 O1 L:SO4305 2.3 99.3 1.0 CD2 L:HIS189 3.0 88.3 1.0 CG L:ASP185 3.1 0.7 1.0 CE1 L:HIS189 3.1 0.7 1.0 S L:SO4305 3.4 76.6 1.0 OD1 L:ASP185 3.5 0.1 1.0 O4 L:SO4305 3.6 91.0 1.0 O2 L:SO4305 3.8 82.3 1.0 O L:ASP185 4.1 0.4 1.0 CG L:HIS189 4.2 90.0 1.0 ND1 L:HIS189 4.2 95.9 1.0 CE L:LYS188 4.3 0.4 1.0 CB L:ASP185 4.4 0.5 1.0 O3 L:SO4305 4.6 75.7 1.0 CB L:LYS188 4.7 97.5 1.0 CA L:ASP185 4.8 0.6 1.0 C L:ASP185 4.9 0.6 1.0 NZ L:LYS188 4.9 0.4 1.0

Zinc binding site 4 out of 5 in the Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn303 b:0.4 occ:1.00 OE2 L:GLU81 2.0 0.1 1.0 OE1 L:GLU81 2.0 98.0 1.0 CD L:GLU81 2.3 95.2 1.0 O L:HOH438 2.6 78.7 1.0 CG L:GLU81 3.8 79.3 1.0 CG L:PRO59 4.5 44.8 1.0 NH2 L:ARG61 4.5 50.5 1.0 OE1 L:GLU79 4.5 85.4 1.0 CB L:GLU81 4.6 70.5 1.0 NH1 L:ARG61 4.9 52.7 1.0

Zinc binding site 5 out of 5 in the Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Anti-PCSK9 Fab 6E2 Bound to the Modified N-Terminal Peptide From PCSK9 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn304 b:0.2 occ:1.00 OE2 P:GLU49 2.0 89.0 1.0 NE2 L:HIS27D 2.0 86.3 1.0 O1P P:SEP47 2.7 98.9 0.5 O L:HOH442 2.9 64.0 1.0 CD2 L:HIS27D 3.0 81.9 1.0 CE1 L:HIS27D 3.0 90.0 1.0 O3P P:SEP47 3.0 0.4 0.5 OG P:SEP47 3.0 96.7 0.5 O2P P:SEP47 3.0 0.8 0.5 CD P:GLU49 3.1 97.3 1.0 O3P P:SEP47 3.1 93.9 0.5 P P:SEP47 3.2 0.3 0.5 P P:SEP47 3.4 0.5 0.5 CG P:GLU49 3.7 95.5 1.0 CB P:SEP47 3.8 80.9 0.5 CB P:SEP47 3.9 80.7 0.5 OE1 P:GLU49 4.0 0.2 1.0 ND1 L:HIS27D 4.1 85.8 1.0 CG L:HIS27D 4.1 78.5 1.0 OG P:SEP47 4.2 91.4 0.5 OH L:TYR32 4.4 67.2 1.0 O P:SEP47 4.4 70.6 0.5 O P:SEP47 4.5 70.1 0.5 O1P P:SEP47 4.8 98.9 0.5 O2P P:SEP47 4.8 0.9 0.5 CA P:SEP47 5.0 67.5 0.5 CA P:SEP47 5.0 67.3 0.5

M.Ultsch, W.Li, C.Eigenbrot, P.Di Lello, M.T.Lipari, S.Gerhardy, A.P.Ahyoung, J.Quinn, Y.Franke, Y.Chen, M.Kong Beltran, A.Peterson, D.Kirchhofer. Identification of A Helical Segment Within the Intrinsically Disordered Region of the PCSK9 Prodomain. J. Mol. Biol. V. 431 885 2019.
ISSN: ESSN 1089-8638
PubMed: 30653992
DOI: 10.1016/J.JMB.2018.11.025