Zinc in PDB 6mv5: Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9 (E32K)

The structure of Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9 (E32K), PDB code: 6mv5 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)	48.00 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.449, 100.420, 86.590, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 23.9

The structure of Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9 (E32K) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9 (E32K) (pdb code 6mv5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9 (E32K), PDB code: 6mv5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9 (E32K)


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 N-Terminal Peptide From PCSK9 (E32K) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:43.7 occ:1.00 OD1 H:ASP53 2.0 39.9 1.0 O3 H:SO4303 2.0 88.3 1.0 OE1 P:GLU48 2.0 55.1 1.0 OE2 P:GLU48 2.0 51.3 1.0 O4 H:SO4303 2.1 84.1 1.0 CD P:GLU48 2.3 52.7 1.0 CB H:ASP53 2.4 41.5 1.0 S H:SO4303 2.4 83.9 1.0 CG H:ASP53 2.5 38.7 1.0 O2 H:SO4303 3.0 85.3 1.0 O P:HOH101 3.4 41.1 1.0 CA H:ASP53 3.5 39.9 1.0 OD2 H:ASP53 3.6 37.2 1.0 O1 H:SO4303 3.8 87.1 1.0 CG P:GLU48 3.8 56.8 1.0 O H:HOH434 4.2 32.8 1.0 O H:HOH407 4.2 54.2 1.0 N H:ASP53 4.4 38.8 1.0 NH1 H:ARG52 4.5 33.2 1.0 CB P:GLU48 4.6 64.3 1.0 C H:ASP53 4.7 41.7 1.0 O H:ASP53 4.9 41.5 1.0 CD H:ARG52 4.9 30.2 1.0 O H:SER52C 5.0 41.5 1.0

Zinc binding site 2 out of 4 in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9 (E32K)


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 N-Terminal Peptide From PCSK9 (E32K) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:0.3 occ:1.00 OD1 L:ASN137 2.0 97.8 1.0 OD1 L:ASN138 2.0 0.9 1.0 NE2 H:HIS164 2.0 92.5 1.0 ND2 L:ASN138 2.0 0.2 1.0 ND2 L:ASN137 2.0 0.8 1.0 CG L:ASN138 2.2 1.0 1.0 CG L:ASN137 2.3 98.4 1.0 CE1 H:HIS164 3.0 89.8 1.0 CD2 H:HIS164 3.0 91.8 1.0 CB L:ASN138 3.6 96.7 1.0 CB L:ASN137 3.7 93.7 1.0 OG L:SER174 3.8 69.3 1.0 N L:ASN138 3.8 88.1 1.0 ND1 H:HIS164 4.0 87.3 1.0 CG H:HIS164 4.1 88.5 1.0 CA L:ASN138 4.3 89.3 1.0 C L:ASN137 4.3 88.9 1.0 CA L:ASN137 4.3 86.1 1.0 OG1 H:THR183 4.7 90.8 1.0

Zinc binding site 3 out of 4 in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9 (E32K)


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 N-Terminal Peptide From PCSK9 (E32K) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn302 b:0.3 occ:1.00 OE1 L:GLU81 2.0 80.6 1.0 OE1 L:GLU79 2.0 96.3 1.0 OE2 L:GLU79 2.0 97.0 1.0 CD L:GLU79 2.3 94.5 1.0 CD L:GLU81 3.2 79.1 1.0 CG L:GLU79 3.8 90.0 1.0 NH2 L:ARG61 4.0 49.0 1.0 NH1 L:ARG61 4.0 51.2 1.0 CG L:GLU81 4.0 76.7 1.0 OE2 L:GLU81 4.1 79.6 1.0 CZ L:ARG61 4.4 48.9 1.0 CB L:GLU79 4.6 82.6 1.0

Zinc binding site 4 out of 4 in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9 (E32K)


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 N-Terminal Peptide From PCSK9 (E32K) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn303 b:0.7 occ:1.00 NE2 L:HIS189 1.7 98.6 1.0 OD1 L:ASP185 2.0 0.8 1.0 OD2 L:ASP185 2.0 0.9 1.0 O3 L:SO4304 2.0 93.2 1.0 CG L:ASP185 2.3 0.4 1.0 CE1 L:HIS189 2.3 0.1 1.0 CD2 L:HIS189 2.9 98.3 1.0 S L:SO4304 3.4 92.3 1.0 ND1 L:HIS189 3.5 0.5 1.0 CB L:ASP185 3.8 0.7 1.0 CG L:HIS189 3.9 0.5 1.0 O2 L:SO4304 3.9 92.6 1.0 O L:ASP185 4.1 0.6 1.0 O4 L:SO4304 4.2 93.0 1.0 O1 L:SO4304 4.3 92.4 1.0 CD L:LYS188 4.4 0.5 1.0 CA L:ASP185 4.4 0.6 1.0 CB L:LYS188 4.6 0.6 1.0 C L:ASP185 4.6 0.1 1.0

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