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Zinc in PDB 6e4y: Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9, Unmodified

Protein crystallography data

The structure of Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9, Unmodified, PDB code: 6e4y 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) 48.01 / 2.24
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.378, 100.527, 86.715, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.5

Other elements in 6e4y:

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

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9, Unmodified (pdb code 6e4y). 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, Unmodified, PDB code: 6e4y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6e4y

Go back to Zinc Binding Sites List in 6e4y
Zinc binding site 1 out of 4 in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9, Unmodified


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, Unmodified within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:47.0
occ:1.00
OE2 P:GLU48 1.9 46.9 1.0
OD1 H:ASP53 2.1 46.2 1.0
CD P:GLU48 2.7 70.1 1.0
OE1 P:GLU48 2.9 43.4 1.0
CG H:ASP53 3.1 42.4 1.0
O P:HOH201 3.4 43.0 1.0
CB H:ASP53 3.5 37.2 1.0
CA H:ASP53 3.8 39.2 1.0
OD2 H:ASP53 4.1 44.0 1.0
O H:HOH421 4.1 52.9 1.0
CG P:GLU48 4.2 70.1 1.0
O H:HOH412 4.4 39.0 1.0
NH1 H:ARG52 4.6 37.8 1.0
N H:ASP53 4.7 40.2 1.0
O H:SER52C 4.8 43.2 1.0
CB P:GLU48 4.8 68.9 1.0
C H:ASP53 5.0 44.6 1.0

Zinc binding site 2 out of 4 in 6e4y

Go back to Zinc Binding Sites List in 6e4y
Zinc binding site 2 out of 4 in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9, Unmodified


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, Unmodified within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn301

b:98.8
occ:1.00
OD1 L:ASN138 2.2 94.2 1.0
OD1 L:ASN137 2.3 89.1 1.0
NE2 H:HIS164 2.3 90.7 1.0
CD2 H:HIS164 2.6 89.7 1.0
CG L:ASN137 3.0 95.4 1.0
ND2 L:ASN137 3.0 88.6 1.0
CG L:ASN138 3.4 0.4 1.0
CE1 H:HIS164 3.6 89.1 1.0
CG H:HIS164 3.9 86.3 1.0
OG L:SER174 4.0 75.1 1.0
ND2 L:ASN138 4.2 94.5 1.0
OG1 H:THR183 4.2 0.1 1.0
O H:GLY162 4.4 91.7 1.0
ND1 H:HIS164 4.4 87.7 1.0
CB L:ASN137 4.4 73.0 1.0
CB L:ASN138 4.5 78.7 1.0
N L:ASN138 4.5 72.7 1.0
C H:GLY162 5.0 93.5 1.0
CB H:THR183 5.0 0.3 1.0

Zinc binding site 3 out of 4 in 6e4y

Go back to Zinc Binding Sites List in 6e4y
Zinc binding site 3 out of 4 in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9, Unmodified


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, Unmodified within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn302

b:1.0
occ:1.00
OE2 L:GLU81 2.8 0.9 1.0
CD L:GLU81 3.3 0.5 1.0
O L:HOH417 3.4 71.1 1.0
OE1 L:GLU79 3.4 86.0 1.0
OE1 L:GLU81 3.5 89.2 1.0
NH1 L:ARG61 3.7 63.9 1.0
NH2 L:ARG61 3.9 58.7 1.0
OE2 L:GLU79 4.0 93.4 1.0
CD L:GLU79 4.1 96.5 1.0
CZ L:ARG61 4.3 69.5 1.0
CG L:GLU81 4.4 77.1 1.0
CG L:PRO59 4.6 49.9 1.0

Zinc binding site 4 out of 4 in 6e4y

Go back to Zinc Binding Sites List in 6e4y
Zinc binding site 4 out of 4 in the Anti-PCSK9 Fab 6E2 Bound to the N-Terminal Peptide From PCSK9, Unmodified


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, Unmodified within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:0.9
occ:1.00
OE2 P:GLU40 2.4 85.9 1.0
OD1 P:ASP37 3.3 91.5 1.0
CD P:GLU40 3.5 95.0 1.0
OE1 P:GLU40 4.0 94.3 1.0
CG P:ASP37 4.4 88.7 1.0
CG P:GLU40 4.8 72.0 1.0

Reference:

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
Page generated: Wed Dec 16 11:41:49 2020

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