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Chlorine in PDB 4lgr: Ricin A Chain Bound to Camelid Nanobody (VHH3)

Enzymatic activity of Ricin A Chain Bound to Camelid Nanobody (VHH3)

All present enzymatic activity of Ricin A Chain Bound to Camelid Nanobody (VHH3):
3.2.2.22;

Protein crystallography data

The structure of Ricin A Chain Bound to Camelid Nanobody (VHH3), PDB code: 4lgr was solved by M.J.Rudolph, J.Cheung, M.Franklin, F.Burshteyn, M.Cassidy, E.Gary, N.Mantis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.22 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.345, 77.423, 121.805, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.4

Other elements in 4lgr:

The structure of Ricin A Chain Bound to Camelid Nanobody (VHH3) also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ricin A Chain Bound to Camelid Nanobody (VHH3) (pdb code 4lgr). 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 A Chain Bound to Camelid Nanobody (VHH3), PDB code: 4lgr:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4lgr

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Chlorine binding site 1 out of 8 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ricin A Chain Bound to Camelid Nanobody (VHH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:58.4
occ:1.00
 NE2 A:HIS94 2.5 33.6 1.0
CD2 A:HIS94 3.2 37.0 1.0
O A:HOH484 3.2 36.6 1.0
CE1 A:HIS94 3.6 38.5 1.0
CG A:HIS94 4.4 29.7 1.0
ND1 A:HIS94 4.6 39.0 1.0

Chlorine binding site 2 out of 8 in 4lgr

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Chlorine binding site 2 out of 8 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ricin A Chain Bound to Camelid Nanobody (VHH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:72.8
occ:1.00
 NH2 A:ARG193 2.9 50.7 1.0
NE A:ARG193 2.9 46.8 1.0
CZ A:ARG193 3.3 52.6 1.0
CD A:ARG193 4.1 39.4 1.0
CB A:ARG189 4.1 26.5 1.0
OG1 A:THR190 4.2 32.9 1.0
NE A:ARG189 4.3 37.7 1.0
N A:THR190 4.3 22.1 1.0
C A:ARG189 4.3 24.2 1.0
O A:ARG189 4.4 23.1 1.0
CA A:THR190 4.5 23.6 1.0
NH2 A:ARG189 4.5 57.4 1.0
NH1 A:ARG193 4.6 56.2 1.0
CB A:ARG193 4.7 29.6 1.0
CG1 A:VAL18 4.7 35.6 1.0
CZ A:ARG189 4.8 54.7 1.0
CA A:ARG189 4.9 22.4 1.0
CG A:ARG193 5.0 33.2 1.0

Chlorine binding site 3 out of 8 in 4lgr

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Chlorine binding site 3 out of 8 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ricin A Chain Bound to Camelid Nanobody (VHH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:40.4
occ:1.00
 O A:HOH437 2.1 41.6 1.0
ND1 A:HIS40 2.2 56.7 1.0
O A:HOH482 2.5 49.5 1.0
CG A:HIS40 3.1 56.6 1.0
CE1 A:HIS40 3.2 58.4 1.0
CB A:HIS40 3.4 55.7 1.0
CA A:HIS40 3.6 56.5 1.0
CD2 A:HIS40 4.3 56.0 1.0
NE2 A:HIS40 4.3 58.2 1.0
C A:GLN223 4.4 54.3 1.0
N A:GLY224 4.4 49.6 1.0
O A:GLN223 4.5 64.6 1.0
N A:HIS40 4.5 54.6 1.0
CA A:GLY224 4.6 44.6 1.0
C A:HIS40 4.6 50.8 1.0
CA A:GLN223 4.9 52.8 1.0
O A:HIS40 4.9 53.1 1.0

Chlorine binding site 4 out of 8 in 4lgr

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Chlorine binding site 4 out of 8 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ricin A Chain Bound to Camelid Nanobody (VHH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:48.1
occ:1.00
 OG1 A:THR71 2.8 19.2 1.0
O A:HOH431 2.9 33.2 1.0
C A:VAL70 3.4 16.3 1.0
OE1 A:GLU61 3.5 60.5 1.0
N A:THR71 3.5 14.4 1.0
CA A:VAL70 3.6 14.5 1.0
C A:SER69 3.6 20.7 1.0
O A:SER69 3.6 20.2 1.0
N A:VAL70 3.7 13.8 1.0
CB A:SER69 3.7 29.2 1.0
O A:VAL70 3.8 15.8 1.0
CB A:THR71 3.9 15.7 1.0
CD A:GLU61 4.0 49.1 1.0
CG A:GLU61 4.1 21.1 1.0
O A:HOH478 4.1 41.8 1.0
CA A:THR71 4.2 12.4 1.0
O A:ARG85 4.3 14.6 1.0
CA A:SER69 4.3 20.4 1.0
OG A:SER69 5.0 34.8 1.0

Chlorine binding site 5 out of 8 in 4lgr

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Chlorine binding site 5 out of 8 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ricin A Chain Bound to Camelid Nanobody (VHH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:39.0
occ:1.00
 O A:HOH438 2.6 34.8 1.0
O A:HOH409 2.9 25.5 1.0
O A:HOH401 2.9 20.8 1.0
N A:THR12 3.2 18.9 1.0
CD1 A:PHE11 3.5 16.4 1.0
CA A:PHE11 3.5 15.8 1.0
CG2 A:THR12 3.8 22.6 1.0
C A:PHE11 3.8 20.1 1.0
CE1 A:PHE11 4.0 19.4 1.0
O A:HOH559 4.1 56.9 1.0
O A:ASN10 4.1 22.2 1.0
CG A:PHE11 4.1 20.7 1.0
O A:THR12 4.2 19.2 1.0
CB A:PHE11 4.3 18.2 1.0
CA A:THR12 4.3 16.6 1.0
O A:HOH428 4.5 25.3 1.0
N A:PHE11 4.5 16.6 1.0
CB A:SER20 4.5 26.9 1.0
O A:HOH475 4.6 37.4 1.0
O A:HOH492 4.6 40.4 1.0
CB A:THR12 4.6 22.0 1.0
OG A:SER20 4.6 21.1 1.0
C A:ASN10 4.7 22.6 1.0
C A:THR12 4.8 18.8 1.0
O A:SER20 4.8 21.7 1.0
O A:HOH531 4.9 39.4 1.0

Chlorine binding site 6 out of 8 in 4lgr

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Chlorine binding site 6 out of 8 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Ricin A Chain Bound to Camelid Nanobody (VHH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:71.9
occ:1.00
 OE2 A:GLU99 2.5 60.9 1.0
OE1 A:GLU99 3.0 55.0 1.0
CD A:GLU99 3.1 53.9 1.0
NH1 A:ARG48 4.4 58.7 1.0
CG A:GLU99 4.6 39.8 1.0
NH2 A:ARG48 4.7 61.3 1.0

Chlorine binding site 7 out of 8 in 4lgr

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Chlorine binding site 7 out of 8 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Ricin A Chain Bound to Camelid Nanobody (VHH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:47.0
occ:1.00
 O B:HOH366 2.4 55.6 1.0
O B:HOH334 2.4 51.8 1.0
O B:HOH307 3.0 31.3 1.0
O B:HOH370 4.0 61.7 1.0

Chlorine binding site 8 out of 8 in 4lgr

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Chlorine binding site 8 out of 8 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Ricin A Chain Bound to Camelid Nanobody (VHH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl205

b:65.9
occ:1.00
 OG B:SER7 2.8 34.4 1.0
O B:VAL5 2.8 33.9 1.0
CD2 B:HIS21 2.9 40.0 0.5
O B:HIS21 3.3 33.2 0.5
O B:HIS21 3.5 31.8 0.5
CB B:SER7 3.5 38.1 1.0
N B:SER7 3.6 33.7 1.0
C B:GLU6 3.7 36.9 1.0
C B:VAL5 3.7 37.5 1.0
N B:ALA23 3.8 31.7 1.0
CG B:HIS21 3.8 37.1 0.5
NE2 B:HIS21 3.8 40.3 0.5
C B:HIS21 3.9 30.4 0.5
C B:HIS21 3.9 30.4 0.5
CA B:GLU6 4.0 33.3 1.0
O B:GLU6 4.1 42.2 1.0
CB B:HIS21 4.2 30.6 0.5
CA B:SER7 4.2 32.0 1.0
CA B:CYS22 4.2 28.3 1.0
CB B:HIS21 4.2 30.7 0.5
CB B:ALA23 4.2 42.7 1.0
CG1 B:VAL5 4.2 43.4 1.0
N B:GLU6 4.3 33.4 1.0
N B:CYS22 4.3 28.8 1.0
C B:CYS22 4.3 29.4 1.0
CB B:VAL5 4.6 40.9 1.0
CA B:ALA23 4.6 34.2 1.0
CA B:HIS21 4.7 26.9 0.5
CA B:HIS21 4.7 27.1 0.5
CA B:VAL5 4.8 32.8 1.0
ND1 B:HIS21 4.9 44.3 0.5
CE1 B:HIS21 5.0 49.2 0.5

Reference:

M.J.Rudolph, D.J.Vance, J.Cheung, M.C.Franklin, F.Burshteyn, M.S.Cassidy, E.N.Gary, C.Herrera, C.B.Shoemaker, N.J.Mantis. Crystal Structures of Ricin Toxin'S Enzymatic Subunit (Rta) in Complex with Neutralizing and Non-Neutralizing Single-Chain Antibodies. J.Mol.Biol. V. 426 3057 2014.
ISSN: ISSN 0022-2836
PubMed: 24907552
DOI: 10.1016/J.JMB.2014.05.026
Page generated: Sun Jul 21 18:55:51 2024

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