Atomistry » Chlorine » PDB 4lb8-4lht » 4lgr
Atomistry »
  Chlorine »
    PDB 4lb8-4lht »
      4lgr »

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

Go back to Chlorine Binding Sites List in 4lgr
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

Go back to Chlorine Binding Sites List in 4lgr
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

Go back to Chlorine Binding Sites List in 4lgr
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

Go back to Chlorine Binding Sites List in 4lgr
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

Go back to Chlorine Binding Sites List in 4lgr
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

Go back to Chlorine Binding Sites List in 4lgr
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

Go back to Chlorine Binding Sites List in 4lgr
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

Go back to Chlorine Binding Sites List in 4lgr
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: Sat Dec 12 10:52:50 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy