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Zinc in PDB 4ong: Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40

Protein crystallography data

The structure of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40, PDB code: 4ong was solved by H.Feinberg, J.W.Saldanha, L.Diep, A.Goel, A.Widom, G.M.Veldman, W.I.Weis, D.Schenk, G.S.Basi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.47 / 2.20
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 40.040, 84.940, 175.690, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.7

Other elements in 4ong:

The structure of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Zinc atom in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 (pdb code 4ong). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 27 binding sites of Zinc where determined in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40, PDB code: 4ong:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 27 in 4ong

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Zinc binding site 1 out of 27 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:35.8
occ:0.50
OD2 H:ASP213 2.0 28.1 1.0
O H:HOH406 2.1 40.7 1.0
CG H:ASP213 3.0 23.4 1.0
OD1 H:ASP213 3.2 23.1 1.0
O H:HOH511 3.6 39.9 1.0
CB H:ASP213 4.3 18.7 1.0
CB H:LYS211 4.6 15.6 1.0
CL H:CL319 4.8 43.5 1.0
N H:ASP213 4.8 14.8 1.0

Zinc binding site 2 out of 27 in 4ong

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Zinc binding site 2 out of 27 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn302

b:41.9
occ:1.00
OD2 H:ASP62 2.0 50.3 1.0
OD1 H:ASP62 2.0 52.6 1.0
N1 H:IMD315 2.0 30.7 1.0
O H:HOH403 2.1 29.6 1.0
O H:HOH402 2.1 25.8 1.0
CG H:ASP62 2.4 47.7 1.0
C5 H:IMD315 2.8 30.6 1.0
C2 H:IMD315 3.2 28.7 1.0
CB H:ASP62 3.9 32.0 1.0
C4 H:IMD315 4.1 28.5 1.0
N3 H:IMD315 4.2 26.5 1.0
O H:HOH412 4.3 27.1 1.0
O H:HOH494 4.3 34.2 1.0
CA H:ASP62 4.7 30.9 1.0
N H:ASP62 4.8 21.4 1.0

Zinc binding site 3 out of 27 in 4ong

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Zinc binding site 3 out of 27 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn303

b:35.2
occ:0.50
ZN L:ZN314 1.8 44.2 0.5
OD2 L:ASP172 2.0 54.4 1.0
NE2 H:HIS170 2.0 34.8 1.0
O L:HOH405 2.1 35.9 1.0
O L:HOH407 2.1 29.0 1.0
CD2 H:HIS170 3.0 26.5 1.0
CE1 H:HIS170 3.0 37.1 1.0
CG L:ASP172 3.3 44.1 1.0
O L:HOH404 3.5 18.3 1.0
OD1 L:ASN143 3.9 33.5 1.0
ND1 H:HIS170 4.1 34.4 1.0
CG H:HIS170 4.1 26.3 1.0
CB L:ASP172 4.1 36.0 1.0
OD1 L:ASP172 4.1 42.5 1.0
O L:HOH508 4.4 33.6 1.0
CG L:ASN143 4.7 26.9 1.0
ND2 L:ASN143 4.7 30.6 1.0
CD L:LYS174 4.7 73.1 1.0
O H:VAL169 5.0 21.5 1.0

Zinc binding site 4 out of 27 in 4ong

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Zinc binding site 4 out of 27 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn304

b:26.7
occ:1.00
N1 H:IMD314 2.1 26.9 1.0
O H:HOH401 2.1 15.7 1.0
CL H:CL317 2.2 27.2 1.0
CL H:CL316 2.2 24.5 1.0
C2 H:IMD314 2.8 29.2 1.0
C5 H:IMD314 3.3 27.0 1.0
N3 H:IMD314 4.0 27.6 1.0
CE H:LYS211 4.1 29.8 1.0
C4 H:IMD314 4.3 28.2 1.0
CA H:PRO206 4.4 20.9 1.0
CA H:SER209 4.6 17.1 1.0
CB H:PRO206 4.9 21.3 1.0
NZ H:LYS211 4.9 31.4 1.0
C H:SER209 4.9 18.3 1.0

Zinc binding site 5 out of 27 in 4ong

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Zinc binding site 5 out of 27 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn305

b:53.7
occ:1.00
O H:HOH518 2.1 56.2 1.0
O H:HOH405 2.1 32.3 1.0
CL H:CL319 2.2 43.5 1.0
CL H:CL318 2.2 28.1 1.0
OG H:SER162 4.0 38.3 1.0
ND2 H:ASN202 4.4 18.3 1.0
CG2 H:THR200 4.8 16.4 1.0
CB H:THR200 5.0 19.4 1.0

Zinc binding site 6 out of 27 in 4ong

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Zinc binding site 6 out of 27 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn306

b:62.5
occ:1.00
OD1 H:ASP179 2.0 74.8 1.0
O H:HOH407 2.1 34.5 1.0
CG H:ASP179 2.9 73.9 1.0
OD2 H:ASP179 3.1 73.6 1.0
OG H:SER118 4.0 25.9 1.0
O H:HOH513 4.2 47.9 1.0
O H:HOH460 4.3 28.1 1.0
CB H:ASP179 4.4 54.7 1.0
CD2 H:LEU176 4.6 36.0 1.0
CZ H:PHE152 4.6 22.4 1.0
CB H:SER118 4.6 21.8 1.0
CE1 H:PHE152 4.8 20.8 1.0
CA H:ASP179 4.9 53.0 1.0

Zinc binding site 7 out of 27 in 4ong

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Zinc binding site 7 out of 27 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn307

b:39.4
occ:0.50
CG P:GLU3 1.0 33.9 0.5
CD P:GLU3 1.7 26.0 0.5
CB P:GLU3 1.8 31.7 0.5
O P:HOH105 2.1 31.2 0.5
O L:HOH476 2.1 22.6 0.5
O L:HOH475 2.1 26.9 0.5
O P:HOH102 2.1 14.8 0.5
CA P:GLU3 2.2 33.8 0.5
OE1 P:GLU3 2.4 23.0 0.5
C P:GLU3 2.5 34.9 0.5
N P:PHE4 2.5 29.8 0.5
N P:GLU3 2.5 32.2 0.5
OE2 P:GLU3 2.5 21.5 0.5
O L:HOH474 2.7 29.8 0.5
CD2 P:PHE4 3.3 18.2 0.5
O P:GLU3 3.5 36.1 0.5
NH2 L:ARG101 3.6 34.7 0.5
O P:ASP1 3.6 19.7 0.5
CG P:PHE4 3.7 20.9 0.5
CA P:PHE4 3.7 29.5 0.5
C P:ALA2 3.7 27.3 0.5
CE2 P:PHE4 3.7 16.8 0.5
C P:ASP1 3.8 21.6 0.5
CB P:PHE4 4.1 25.4 0.5
N P:ALA2 4.2 22.6 0.5
CD1 P:PHE4 4.3 14.2 0.5
CA P:ASP1 4.4 22.9 0.5
CZ P:PHE4 4.4 12.6 0.5
O P:ALA2 4.4 25.2 0.5
CD2 H:TYR59 4.5 23.7 1.0
CB H:SER50 4.5 23.1 1.0
N P:ASP1 4.5 21.1 0.5
OG H:SER50 4.6 26.0 1.0
CA P:ALA2 4.6 26.1 0.5
CZ L:ARG101 4.6 29.5 0.5
CE1 P:PHE4 4.7 10.9 0.5
CE2 H:TYR59 4.7 27.0 1.0
CG H:TYR59 4.7 22.2 1.0
O P:HOH101 4.8 25.6 1.0
C P:PHE4 4.9 31.9 0.5

Zinc binding site 8 out of 27 in 4ong

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Zinc binding site 8 out of 27 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn308

b:0.7
occ:0.30
N3 H:IMD315 2.0 26.5 1.0
CL H:CL320 2.2 31.7 1.0
C4 H:IMD315 2.7 28.5 1.0
C2 H:IMD315 3.2 28.7 1.0
NZ H:LYS65 3.6 35.1 1.0
C5 H:IMD315 4.0 30.6 1.0
CE H:LYS65 4.1 36.5 1.0
N1 H:IMD315 4.2 30.7 1.0
CZ L:PHE99 4.3 27.7 1.0
CE2 L:PHE99 4.4 31.7 1.0
CD H:LYS65 4.6 34.5 1.0
O H:TYR60 4.7 20.1 1.0

Zinc binding site 9 out of 27 in 4ong

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Zinc binding site 9 out of 27 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn309

b:58.2
occ:0.50
O H:HOH416 2.1 23.7 1.0
O H:HOH478 2.1 29.4 0.5
O P:PHE4 3.6 38.0 0.5
CB P:PHE4 4.4 25.4 0.5
C P:PHE4 4.5 31.9 0.5
O H:HOH439 4.5 27.1 1.0
CA P:PHE4 4.7 29.5 0.5
OG H:SER53 4.7 34.9 1.0
CD1 P:PHE4 4.7 14.2 0.5
CD H:ARG52 4.9 46.0 1.0

Zinc binding site 10 out of 27 in 4ong

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Zinc binding site 10 out of 27 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn310

b:0.9
occ:1.00
O H:HOH410 2.1 51.2 1.0
O H:HOH409 2.1 23.1 1.0
O H:HOH408 2.1 34.6 1.0
O H:HOH463 2.1 36.1 1.0
OG1 H:THR113 3.3 26.8 1.0
CB H:THR113 4.3 25.1 1.0
N H:THR114 4.4 18.9 1.0
CA H:THR113 4.5 24.1 1.0
O H:GLY9 4.6 27.0 1.0
N H:GLY9 4.8 22.5 1.0
C H:GLY9 4.8 24.9 1.0
CA H:GLY9 4.8 21.8 1.0
O H:HOH495 4.9 36.5 1.0
CD H:PRO155 4.9 22.6 1.0
C H:THR113 5.0 21.5 1.0

Reference:

H.Feinberg, J.W.Saldanha, L.Diep, A.Goel, A.Widom, G.M.Veldman, W.I.Weis, D.Schenk, G.S.Basi. Crystal Structure Reveals Conservation of Amyloid-Beta Conformation Recognized By 3D6 Following Humanization to Bapineuzumab. Alzheimers Res Ther V. 6 31 2014.
PubMed: 25024748
DOI: 10.1186/ALZRT261
Page generated: Wed Dec 16 05:39:19 2020

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