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Chlorine in PDB 3nsj: The X-Ray Crystal Structure of Lymphocyte Perforin

Protein crystallography data

The structure of The X-Ray Crystal Structure of Lymphocyte Perforin, PDB code: 3nsj was solved by R.H.Law, J.C.Whisstock, T.T.Caradoc-Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.36 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.640, 109.800, 141.030, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 21.5

Other elements in 3nsj:

The structure of The X-Ray Crystal Structure of Lymphocyte Perforin also contains other interesting chemical elements:

Iodine (I) 4 atoms
Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The X-Ray Crystal Structure of Lymphocyte Perforin (pdb code 3nsj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the The X-Ray Crystal Structure of Lymphocyte Perforin, PDB code: 3nsj:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3nsj

Go back to Chlorine Binding Sites List in 3nsj
Chlorine binding site 1 out of 2 in the The X-Ray Crystal Structure of Lymphocyte Perforin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The X-Ray Crystal Structure of Lymphocyte Perforin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl720

b:82.3
occ:1.00
NH2 A:ARG498 3.1 64.7 1.0
NE A:ARG498 3.1 71.1 1.0
N A:THR508 3.4 67.4 1.0
CZ A:ARG498 3.5 78.5 1.0
CA A:VAL507 3.8 67.4 1.0
CG1 A:VAL507 3.8 70.4 1.0
O A:THR508 3.8 71.3 1.0
C A:VAL507 4.1 71.0 1.0
O A:GLU506 4.2 74.1 1.0
CB A:VAL507 4.2 70.6 1.0
CD A:ARG498 4.3 71.2 1.0
CA A:THR508 4.4 66.9 1.0
C A:THR508 4.4 71.4 1.0
CG2 A:VAL507 4.6 70.5 1.0
O A:HOH931 4.8 77.7 1.0
CB A:THR508 4.8 71.4 1.0
N A:VAL507 4.8 68.0 1.0
NH1 A:ARG498 4.8 62.5 1.0
C A:GLU506 4.9 73.5 1.0

Chlorine binding site 2 out of 2 in 3nsj

Go back to Chlorine Binding Sites List in 3nsj
Chlorine binding site 2 out of 2 in the The X-Ray Crystal Structure of Lymphocyte Perforin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The X-Ray Crystal Structure of Lymphocyte Perforin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl721

b:85.8
occ:1.00
OG A:SER419 3.1 84.3 1.0
O A:VAL417 3.1 74.3 1.0
N A:HIS521 3.6 75.5 1.0
CA A:TYR520 3.6 69.1 1.0
O A:SER519 3.7 68.3 1.0
C A:TYR520 3.8 76.6 1.0
N A:TYR520 3.9 68.3 1.0
C A:SER519 3.9 69.4 1.0
N A:SER419 4.0 68.1 1.0
C A:VAL417 4.1 74.8 1.0
CE2 A:PHE504 4.1 84.7 1.0
OG A:SER519 4.2 78.7 1.0
CB A:SER419 4.2 72.6 1.0
CG1 A:VAL417 4.4 76.2 1.0
CD2 A:PHE504 4.4 81.8 1.0
CB A:HIS521 4.4 77.7 1.0
CA A:HIS521 4.6 76.3 1.0
CA A:SER419 4.6 67.8 1.0
C A:VAL418 4.7 72.7 1.0
CA A:VAL418 4.7 69.6 1.0
O A:TYR520 4.7 76.6 1.0
CB A:SER519 4.7 67.6 1.0
CB A:VAL417 4.8 76.3 1.0
N A:VAL418 4.8 70.4 1.0
CB A:TYR520 4.9 70.1 1.0
CA A:SER519 5.0 63.7 1.0

Reference:

R.H.Law, N.Lukoyanova, I.Voskoboinik, T.T.Caradoc-Davies, K.Baran, M.A.Dunstone, M.E.D'angelo, E.V.Orlova, F.Coulibaly, S.Verschoor, K.A.Browne, A.Ciccone, M.J.Kuiper, P.I.Bird, J.A.Trapani, H.R.Saibil, J.C.Whisstock. The Structural Basis For Membrane Binding and Pore Formation By Lymphocyte Perforin. Nature V. 468 447 2010.
ISSN: ISSN 0028-0836
PubMed: 21037563
DOI: 10.1038/NATURE09518
Page generated: Sat Dec 12 09:58:08 2020

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