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Chlorine 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:

Zinc (Zn) 27 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40, PDB code: 4ong:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 4ong

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Chlorine binding site 1 out of 11 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl316

b:24.5
occ:1.00
ZN H:ZN304 2.2 26.7 1.0
N1 H:IMD314 3.2 26.9 1.0
N H:PRO206 3.6 17.5 1.0
CA H:PRO206 3.6 20.9 1.0
O H:HOH401 3.6 15.7 1.0
CL H:CL317 3.7 27.2 1.0
C H:HIS205 3.8 13.0 1.0
C5 H:IMD314 3.8 27.0 1.0
CE H:LYS211 3.8 29.8 1.0
CB H:ALA204 3.8 16.0 1.0
N H:HIS205 3.9 14.8 1.0
O H:HIS205 4.0 13.3 1.0
O H:THR210 4.0 16.2 1.0
CG H:LYS211 4.0 22.4 1.0
CG H:PRO206 4.0 21.7 1.0
CD H:PRO206 4.1 16.1 1.0
CB H:PRO206 4.2 21.3 1.0
C H:ALA204 4.3 13.9 1.0
C2 H:IMD314 4.3 29.2 1.0
N H:THR210 4.4 18.2 1.0
CA H:ALA204 4.4 14.1 1.0
CA H:HIS205 4.5 12.6 1.0
C H:THR210 4.5 14.9 1.0
CD H:LYS211 4.6 26.0 1.0
CA H:SER209 4.7 17.1 1.0
C H:SER209 4.7 18.3 1.0
C H:PRO206 4.8 21.8 1.0

Chlorine binding site 2 out of 11 in 4ong

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Chlorine binding site 2 out of 11 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl317

b:27.2
occ:1.00
ZN H:ZN304 2.2 26.7 1.0
N1 H:IMD314 3.5 26.9 1.0
O H:HOH401 3.6 15.7 1.0
O H:HOH515 3.6 37.3 1.0
CL H:CL316 3.7 24.5 1.0
OG H:SER209 3.8 29.5 1.0
O H:PRO206 3.8 18.5 1.0
CA H:SER209 3.8 17.1 1.0
CA H:PRO206 3.9 20.9 1.0
CB H:SER209 4.0 24.8 1.0
C2 H:IMD314 4.0 29.2 1.0
CB H:PRO206 4.3 21.3 1.0
C H:PRO206 4.4 21.8 1.0
C5 H:IMD314 4.5 27.0 1.0
N H:SER209 4.7 16.0 1.0
C H:SER209 4.8 18.3 1.0

Chlorine binding site 3 out of 11 in 4ong

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Chlorine binding site 3 out of 11 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl318

b:28.1
occ:1.00
ZN H:ZN305 2.2 53.7 1.0
OG H:SER162 3.2 38.3 1.0
O H:HOH405 3.3 32.3 1.0
ND2 H:ASN202 3.4 18.3 1.0
CA H:ASN161 3.4 21.7 1.0
C H:ASN161 3.5 23.4 1.0
N H:SER162 3.5 25.1 1.0
CL H:CL319 3.6 43.5 1.0
O H:HOH518 3.6 56.2 1.0
CB H:SER162 4.0 35.6 1.0
CB H:THR200 4.0 19.4 1.0
O H:ASN161 4.1 18.4 1.0
OD1 H:ASN202 4.2 28.9 1.0
CG H:ASN202 4.2 22.4 1.0
CG2 H:THR200 4.2 16.4 1.0
N H:ASN161 4.3 17.7 1.0
CA H:SER162 4.3 27.9 1.0
OD1 H:ASN161 4.4 21.2 1.0
O H:HOH445 4.4 25.2 1.0
CB H:ASN161 4.4 18.4 1.0
OG1 H:THR200 4.6 22.4 1.0
CG H:ASN161 4.8 20.9 1.0
O H:THR200 4.9 17.3 1.0

Chlorine binding site 4 out of 11 in 4ong

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Chlorine binding site 4 out of 11 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl319

b:43.5
occ:1.00
ZN H:ZN305 2.2 53.7 1.0
CG H:ASP213 3.4 23.4 1.0
CB H:ASP213 3.4 18.7 1.0
O H:HOH518 3.5 56.2 1.0
O H:HOH405 3.5 32.3 1.0
CL H:CL318 3.6 28.1 1.0
OD2 H:ASP213 3.7 28.1 1.0
OD1 H:ASP213 3.8 23.1 1.0
ND2 H:ASN202 3.8 18.3 1.0
CG2 H:THR200 4.2 16.4 1.0
O H:HOH406 4.5 40.7 1.0
ZN H:ZN301 4.8 35.8 0.5
OG H:SER162 4.9 38.3 1.0
CA H:ASP213 4.9 18.4 1.0
CB H:THR200 5.0 19.4 1.0

Chlorine binding site 5 out of 11 in 4ong

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Chlorine binding site 5 out of 11 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl320

b:31.7
occ:1.00
ZN H:ZN308 2.2 0.7 0.3
NZ H:LYS65 3.1 35.1 1.0
N H:TYR60 3.2 19.6 1.0
C4 H:IMD315 3.4 28.5 1.0
CA H:TYR59 3.5 19.0 1.0
N3 H:IMD315 3.6 26.5 1.0
C H:TYR59 3.8 23.3 1.0
O H:TYR60 3.8 20.1 1.0
O H:THR58 4.1 23.9 1.0
CE H:LYS65 4.1 36.5 1.0
CA H:TYR60 4.2 22.4 1.0
CD2 H:TYR60 4.2 23.5 1.0
CB H:TYR59 4.2 19.6 1.0
CB H:TYR60 4.3 22.5 1.0
CD H:LYS65 4.4 34.5 1.0
C H:TYR60 4.5 24.1 1.0
CD1 H:TYR59 4.5 23.3 1.0
N H:TYR59 4.6 23.5 1.0
CZ L:PHE99 4.6 27.7 1.0
CG H:TYR60 4.7 22.8 1.0
C H:THR58 4.7 26.1 1.0
CG H:TYR59 4.7 22.2 1.0
C5 H:IMD315 4.7 30.6 1.0
C2 H:IMD315 4.9 28.7 1.0

Chlorine binding site 6 out of 11 in 4ong

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Chlorine binding site 6 out of 11 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
L:Cl316

b:28.1
occ:1.00
ZN L:ZN304 2.2 30.1 1.0
ND1 L:HIS203 3.5 22.4 1.0
N L:ALA117 3.6 24.2 1.0
C L:ALA116 3.6 24.8 1.0
CL L:CL317 3.7 31.7 1.0
CE1 L:HIS203 3.7 22.9 1.0
O L:ALA116 3.8 22.3 1.0
O L:HOH406 3.8 24.3 1.0
CB L:ASP115 3.8 22.3 1.0
CA L:ALA117 3.9 21.6 1.0
N L:ALA116 3.9 24.5 1.0
CB L:ALA117 4.1 25.7 1.0
C L:ASP115 4.2 24.4 1.0
CA L:ALA116 4.2 22.6 1.0
O L:TYR145 4.3 20.0 1.0
CA L:ASP115 4.6 23.5 1.0
O L:ASP115 4.6 26.8 1.0
CG L:ASP115 4.7 25.3 1.0
CG L:HIS203 4.8 21.4 1.0
OD2 L:ASP115 4.9 24.0 1.0
O L:HOH450 5.0 30.7 1.0

Chlorine binding site 7 out of 11 in 4ong

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Chlorine binding site 7 out of 11 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
L:Cl317

b:31.7
occ:1.00
ZN L:ZN304 2.2 30.1 1.0
ND1 L:HIS203 3.3 22.4 1.0
O L:HOH406 3.4 24.3 1.0
CL L:CL316 3.7 28.1 1.0
CA L:THR202 3.7 28.4 1.0
CD L:PRO118 3.8 20.4 1.0
CE1 L:HIS203 3.8 22.9 1.0
N L:HIS203 3.8 27.9 1.0
CD1 L:ILE149 4.0 21.2 1.0
CB L:ALA117 4.1 25.7 1.0
C L:THR202 4.2 25.9 1.0
CA L:ALA117 4.2 21.6 1.0
CG L:HIS203 4.3 21.4 1.0
O L:ALA201 4.4 25.5 1.0
OG1 L:THR202 4.4 34.4 1.0
N L:THR202 4.6 23.7 1.0
CB L:THR202 4.6 32.9 1.0
C L:ALA201 4.8 24.0 1.0
CG L:PRO118 4.8 17.7 1.0
CG1 L:ILE149 4.8 23.4 1.0
N L:PRO118 4.8 21.4 1.0
CB L:HIS203 4.8 28.4 1.0
NE2 L:HIS203 4.9 21.9 1.0
CA L:HIS203 4.9 30.3 1.0

Chlorine binding site 8 out of 11 in 4ong

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Chlorine binding site 8 out of 11 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
L:Cl318

b:44.9
occ:1.00
ZN L:ZN306 2.2 60.8 1.0
O L:HOH426 3.2 21.9 1.0
OD2 L:ASP170 3.3 45.3 1.0
O L:HOH410 3.4 23.3 1.0
O L:HOH409 3.5 40.4 1.0
CG L:ASP170 3.6 36.7 1.0
CA L:GLY89 3.8 20.8 1.0
OD1 L:ASP170 3.8 35.3 1.0
CG L:LEU90 3.9 28.3 1.0
CE L:LYS108 4.1 43.3 1.0
C L:GLY89 4.1 20.0 1.0
N L:LEU90 4.2 19.7 1.0
CG L:PRO45 4.2 28.5 1.0
CG L:LYS108 4.3 30.1 1.0
CD1 L:LEU90 4.5 27.6 1.0
CB L:ASP170 4.5 29.3 1.0
CD L:LYS108 4.6 36.1 1.0
CD L:PRO45 4.6 25.2 1.0
CD2 L:LEU90 4.6 30.8 1.0
O L:GLY89 4.7 20.8 1.0
O L:HOH468 4.7 33.2 1.0
O L:GLN43 4.8 22.4 1.0
N L:GLY89 4.8 21.1 1.0
O L:HOH455 4.8 22.8 1.0
CB L:LEU90 4.8 22.8 1.0
N L:PRO45 4.9 24.1 1.0
O L:HOH462 5.0 24.5 1.0

Chlorine binding site 9 out of 11 in 4ong

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Chlorine binding site 9 out of 11 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
L:Cl319

b:33.2
occ:1.00
ZN L:ZN302 2.2 29.9 1.0
CL L:CL320 3.4 40.1 1.0
O L:HOH524 3.6 45.7 1.0
NE2 L:HIS194 3.6 22.7 1.0
CD L:ARG193 3.9 21.8 1.0
CD2 L:HIS194 4.2 18.2 1.0
CG L:GLU190 4.2 33.3 1.0
CA L:GLU190 4.3 20.7 1.0
CB L:ARG193 4.3 17.9 1.0
CB L:GLU190 4.3 25.1 1.0
O L:GLU190 4.6 24.3 1.0
CE1 L:HIS194 4.7 24.3 1.0
CG L:ARG193 4.7 18.1 1.0
OE2 L:GLU190 4.7 42.9 1.0
CD L:GLU190 4.8 43.6 1.0
NE L:ARG193 4.9 23.5 1.0
C L:GLU190 5.0 22.9 1.0

Chlorine binding site 10 out of 11 in 4ong

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Chlorine binding site 10 out of 11 in the Fab Fragment of 3D6 in Complex with Amyloid Beta 1-40


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
L:Cl320

b:40.1
occ:1.00
ZN L:ZN302 2.2 29.9 1.0
O L:HOH500 2.8 60.2 1.0
NE2 L:HIS194 3.3 22.7 1.0
CL L:CL319 3.4 33.2 1.0
O L:HOH524 3.5 45.7 1.0
CD2 L:HIS194 3.7 18.2 1.0
CB L:GLU190 3.7 25.1 1.0
NH1 L:ARG160 3.8 50.6 1.0
CD L:GLU190 3.9 43.6 1.0
OE2 L:GLU190 4.0 42.9 1.0
CG L:GLU190 4.1 33.3 1.0
OE1 L:GLU190 4.2 49.3 1.0
CE1 L:HIS194 4.5 24.3 1.0
CA L:GLU190 4.6 20.7 1.0
O L:GLU190 4.7 24.3 1.0
O L:HOH520 4.9 55.7 1.0
C L:GLU190 4.9 22.9 1.0
CG L:HIS194 4.9 20.0 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: Sat Dec 12 11:01:21 2020

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