Chlorine in PDB 7kd2: Ricin Bound to Vhh Antibody V11B2

Enzymatic activity of Ricin Bound to Vhh Antibody V11B2

All present enzymatic activity of Ricin Bound to Vhh Antibody V11B2:
3.2.2.22;

Protein crystallography data

The structure of Ricin Bound to Vhh Antibody V11B2, PDB code: 7kd2 was solved by M.J.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.19 / 2.55
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.607, 99.559, 111.283, 90, 90, 90
R / Rfree (%) 22.7 / 28

Other elements in 7kd2:

The structure of Ricin Bound to Vhh Antibody V11B2 also contains other interesting chemical elements:

Zinc (Zn) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ricin Bound to Vhh Antibody V11B2 (pdb code 7kd2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Ricin Bound to Vhh Antibody V11B2, PDB code: 7kd2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 7kd2

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Chlorine binding site 1 out of 8 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:78.1
occ:1.00
 OD2 A:ASP100 3.3 65.7 1.0
CB A:ASP100 3.5 67.1 1.0
CG A:ASP100 3.7 66.5 1.0
O A:HOH443 3.7 45.3 1.0
CA A:PRO95 3.9 62.6 1.0
CB A:PRO95 4.0 62.4 1.0
N A:ASP96 4.4 68.1 1.0
O A:HOH447 4.5 42.8 1.0
CG1 A:VAL82 4.5 45.6 1.0
OD1 A:ASP100 4.7 66.7 1.0
OD2 A:ASP96 4.7 76.3 1.0
C A:PRO95 4.7 64.9 1.0
CA A:ASP100 4.8 68.3 1.0
CD1 A:ILE104 4.9 66.7 1.0
N A:PRO95 4.9 62.8 1.0
CG1 A:ILE104 5.0 68.4 1.0
CB A:VAL82 5.0 47.6 1.0

Chlorine binding site 2 out of 8 in 7kd2

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Chlorine binding site 2 out of 8 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:77.6
occ:1.00
 O A:HOH445 2.4 32.4 1.0
NH1 A:ARG193 2.9 50.0 1.0
OG1 A:THR190 3.0 54.2 1.0
CA B:GLY149 3.4 31.7 1.0
CA A:THR190 3.7 50.5 1.0
CD A:ARG193 3.8 54.8 1.0
CB A:THR190 4.0 51.7 1.0
N A:THR190 4.0 46.8 1.0
CZ A:ARG193 4.0 52.9 1.0
NE A:ARG189 4.2 59.3 1.0
N B:GLY149 4.2 30.1 1.0
NE A:ARG193 4.3 54.4 1.0
C A:ARG189 4.4 47.9 1.0
CG1 B:VAL145 4.4 42.2 1.0
O A:ARG189 4.5 47.5 1.0
CG A:ARG189 4.6 54.5 1.0
O A:GLY186 4.6 43.6 1.0
C B:GLY149 4.6 29.9 1.0
CB A:ARG193 4.6 55.1 1.0
O B:GLY149 4.8 31.1 1.0
CD A:ARG189 4.8 58.2 1.0
CG A:ARG193 4.8 58.0 1.0
CG2 A:THR190 4.8 52.7 1.0
CB A:ARG189 4.9 48.8 1.0
O A:HOH429 4.9 38.7 1.0

Chlorine binding site 3 out of 8 in 7kd2

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Chlorine binding site 3 out of 8 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:73.7
occ:1.00
 O A:HOH452 2.4 46.8 1.0
NE2 A:HIS94 2.6 75.7 1.0
O A:HOH457 2.7 46.6 1.0
CE1 A:HIS94 3.0 75.7 1.0
CD2 A:HIS94 3.8 72.2 1.0
ND1 A:HIS94 4.3 72.6 1.0
CG A:HIS94 4.7 69.9 1.0
O A:PRO95 4.8 64.0 1.0

Chlorine binding site 4 out of 8 in 7kd2

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Chlorine binding site 4 out of 8 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:81.5
occ:1.00
 N B:TYR69 3.1 35.8 1.0
OG B:SER70 3.3 52.0 1.0
CA B:TYR69 3.7 37.8 1.0
CB B:TYR69 3.7 38.6 1.0
N B:SER70 3.7 39.8 1.0
C B:TYR69 3.9 41.2 1.0
C B:GLY68 4.1 33.2 1.0
CD1 B:TYR69 4.2 41.2 1.0
CA B:GLY68 4.2 30.6 1.0
CG B:TYR69 4.4 39.5 1.0
CB B:SER70 4.5 47.9 1.0
O B:TYR69 4.7 44.9 1.0
CA B:SER70 4.7 42.9 1.0

Chlorine binding site 5 out of 8 in 7kd2

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Chlorine binding site 5 out of 8 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:67.6
occ:1.00
 O B:HOH477 3.2 37.8 1.0
O B:LEU48 3.2 39.0 1.0
O B:ARG58 3.4 39.0 1.0
OG1 B:THR50 3.4 40.0 1.0
N B:ASN60 3.7 48.8 1.0
C B:LEU48 3.8 39.4 1.0
N B:THR50 3.8 37.2 1.0
CA B:SER59 3.9 39.0 1.0
N B:TRP49 4.2 35.8 1.0
CA B:TRP49 4.2 35.5 1.0
C B:ARG58 4.2 39.9 1.0
CG2 B:ILE10 4.3 40.2 1.0
C B:TRP49 4.3 38.8 1.0
CB B:LEU48 4.3 42.2 1.0
C B:SER59 4.3 44.4 1.0
CB B:THR50 4.4 37.9 1.0
N B:SER59 4.5 38.9 1.0
O B:HOH488 4.6 49.6 1.0
CA B:THR50 4.7 36.3 1.0
CA B:LEU48 4.7 42.4 1.0
CA B:ASN60 4.8 48.8 1.0
O B:ALA45 4.8 47.3 1.0
CB B:SER59 4.9 33.7 1.0

Chlorine binding site 6 out of 8 in 7kd2

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Chlorine binding site 6 out of 8 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:75.0
occ:1.00
 NH1 B:ARG27 2.6 62.8 1.0
NH2 B:ARG27 2.7 63.0 1.0
NE2 B:HIS29 2.9 60.7 1.0
CZ B:ARG27 3.0 62.0 1.0
CE1 B:HIS29 3.3 61.0 1.0
CD2 B:HIS29 4.1 58.2 1.0
NE B:ARG27 4.4 59.9 1.0
ND1 B:HIS29 4.6 58.1 1.0

Chlorine binding site 7 out of 8 in 7kd2

Go back to Chlorine Binding Sites List in 7kd2
Chlorine binding site 7 out of 8 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:102.7
occ:1.00
 NH2 B:ARG16 3.2 26.1 1.0
NH1 B:ARG16 3.2 25.6 1.0
O B:THR110 3.3 42.0 1.0
O B:HOH462 3.3 31.8 1.0
O B:PRO209 3.4 44.9 1.0
CZ B:ARG16 3.6 27.9 1.0
O B:GLY208 3.9 51.3 1.0
C B:PRO209 3.9 45.3 1.0
C B:THR110 4.0 38.7 1.0
CA B:PRO209 4.3 47.7 1.0
O B:HOH407 4.3 34.2 1.0
CB B:ALA210 4.7 44.0 1.0
CA B:THR110 4.8 36.5 1.0
N B:ALA210 4.8 44.4 1.0
N B:SER111 4.8 37.7 1.0
CA B:SER111 4.8 36.5 1.0
NE B:ARG16 4.9 31.6 1.0
C B:GLY208 4.9 47.6 1.0

Chlorine binding site 8 out of 8 in 7kd2

Go back to Chlorine Binding Sites List in 7kd2
Chlorine binding site 8 out of 8 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl203

b:64.0
occ:1.00
 OE2 C:GLU60 3.4 79.6 1.0
N C:LEU47 3.4 52.4 1.0
NH2 B:ARG236 3.9 53.9 1.0
CG C:GLU46 3.9 63.6 1.0
CA C:GLU46 3.9 56.2 1.0
O C:LEU47 4.0 56.3 1.0
CD2 B:LEU242 4.1 37.8 1.0
CB C:GLU46 4.1 59.4 1.0
C C:GLU46 4.1 54.3 1.0
CB C:LEU47 4.1 50.6 1.0
CA C:LEU47 4.3 53.1 1.0
NE2 B:GLN244 4.5 46.9 1.0
CD C:GLU60 4.5 82.8 1.0
C C:LEU47 4.6 54.6 1.0
CZ B:ARG236 4.9 52.6 1.0
NE B:ARG236 4.9 49.5 1.0

Reference:

M.J.Rudolph, A.Y.Poon, S.Kavaliauskiene, A.G.Myrann, C.Reynolds-Peterson, S.A.Davis, K.Sandvig, D.J.Vance, N.J.Mantis. Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies That Bridge Ricin'S A-B Subunit Interface. J.Mol.Biol. V. 433 67086 2021.
ISSN: ESSN 1089-8638
PubMed: 34089718
DOI: 10.1016/J.JMB.2021.167086
Page generated: Mon Jul 29 23:30:50 2024

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