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Silicon in PDB 1nd0: Cationic Cyclization Antibody 4C6 Complex with Transition State Analog

Protein crystallography data

The structure of Cationic Cyclization Antibody 4C6 Complex with Transition State Analog, PDB code: 1nd0 was solved by X.Zhu, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.45
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.572, 95.164, 141.058, 75.51, 88.64, 89.28
R / Rfree (%) 24.2 / 28.6

Silicon Binding Sites:

The binding sites of Silicon atom in the Cationic Cyclization Antibody 4C6 Complex with Transition State Analog (pdb code 1nd0). This binding sites where shown within 5.0 Angstroms radius around Silicon atom.
In total 4 binding sites of Silicon where determined in the Cationic Cyclization Antibody 4C6 Complex with Transition State Analog, PDB code: 1nd0:
Jump to Silicon binding site number: 1; 2; 3; 4;

Silicon binding site 1 out of 4 in 1nd0

Go back to Silicon Binding Sites List in 1nd0
Silicon binding site 1 out of 4 in the Cationic Cyclization Antibody 4C6 Complex with Transition State Analog


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Cationic Cyclization Antibody 4C6 Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Si401

b:55.8
occ:1.00
SI A:DP4401 0.0 55.8 1.0
C7 A:DP4401 1.8 56.8 1.0
C4 A:DP4401 1.8 52.9 1.0
C8 A:DP4401 1.8 55.8 1.0
C9 A:DP4401 1.8 61.1 1.0
C13 A:DP4401 2.8 63.8 1.0
C3 A:DP4401 2.8 50.6 1.0
C10 A:DP4401 2.8 65.2 1.0
C5 A:DP4401 2.8 50.8 1.0
C2 A:DP4401 4.2 50.1 1.0
C6 A:DP4401 4.2 48.6 1.0
C12 A:DP4401 4.3 69.0 1.0
C11 A:DP4401 4.3 69.3 1.0
C1 A:DP4401 4.7 48.3 1.0
CD2 B:LEU95 4.7 25.9 1.0
N1 A:DP4401 4.8 71.8 1.0
CA A:GLY91 5.0 22.1 1.0

Silicon binding site 2 out of 4 in 1nd0

Go back to Silicon Binding Sites List in 1nd0
Silicon binding site 2 out of 4 in the Cationic Cyclization Antibody 4C6 Complex with Transition State Analog


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 2 of Cationic Cyclization Antibody 4C6 Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Si402

b:55.2
occ:1.00
SI C:DP4402 0.0 55.2 1.0
C7 C:DP4402 1.8 55.9 1.0
C4 C:DP4402 1.8 51.9 1.0
C8 C:DP4402 1.8 54.5 1.0
C9 C:DP4402 1.8 59.9 1.0
C13 C:DP4402 2.8 63.3 1.0
C3 C:DP4402 2.8 50.0 1.0
C10 C:DP4402 2.8 63.9 1.0
C5 C:DP4402 2.8 50.0 1.0
C2 C:DP4402 4.2 49.5 1.0
C6 C:DP4402 4.2 49.7 1.0
C12 C:DP4402 4.3 67.5 1.0
C11 C:DP4402 4.3 68.0 1.0
C1 C:DP4402 4.7 48.6 1.0
CD2 D:LEU95 4.8 29.4 1.0
N1 C:DP4402 4.8 70.2 1.0

Silicon binding site 3 out of 4 in 1nd0

Go back to Silicon Binding Sites List in 1nd0
Silicon binding site 3 out of 4 in the Cationic Cyclization Antibody 4C6 Complex with Transition State Analog


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 3 of Cationic Cyclization Antibody 4C6 Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Si403

b:55.6
occ:1.00
SI E:DP4403 0.0 55.6 1.0
C4 E:DP4403 1.8 52.7 1.0
C8 E:DP4403 1.8 55.0 1.0
C7 E:DP4403 1.8 56.5 1.0
C9 E:DP4403 1.8 60.6 1.0
C3 E:DP4403 2.8 50.2 1.0
C13 E:DP4403 2.8 63.7 1.0
C5 E:DP4403 2.8 51.3 1.0
C10 E:DP4403 2.8 63.6 1.0
C2 E:DP4403 4.2 50.5 1.0
C6 E:DP4403 4.2 49.4 1.0
C12 E:DP4403 4.3 67.6 1.0
C11 E:DP4403 4.3 68.3 1.0
CD2 F:LEU95 4.7 25.0 1.0
C1 E:DP4403 4.7 49.7 1.0
N1 E:DP4403 4.8 70.4 1.0

Silicon binding site 4 out of 4 in 1nd0

Go back to Silicon Binding Sites List in 1nd0
Silicon binding site 4 out of 4 in the Cationic Cyclization Antibody 4C6 Complex with Transition State Analog


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 4 of Cationic Cyclization Antibody 4C6 Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Si404

b:54.7
occ:1.00
SI G:DP4404 0.0 54.7 1.0
C4 G:DP4404 1.8 51.5 1.0
C7 G:DP4404 1.8 55.8 1.0
C8 G:DP4404 1.8 53.9 1.0
C9 G:DP4404 1.8 59.8 1.0
C13 G:DP4404 2.8 62.8 1.0
C3 G:DP4404 2.8 49.6 1.0
C5 G:DP4404 2.8 49.7 1.0
C10 G:DP4404 2.8 63.8 1.0
C2 G:DP4404 4.2 48.0 1.0
C6 G:DP4404 4.2 48.8 1.0
C12 G:DP4404 4.3 67.8 1.0
C11 G:DP4404 4.3 67.7 1.0
C1 G:DP4404 4.7 48.0 1.0
CD2 H:LEU95 4.7 26.5 1.0
N1 G:DP4404 4.8 70.3 1.0
CA G:GLY91 5.0 23.7 1.0

Reference:

X.Zhu, A.Heine, F.Monnat, K.N.Houk, K.D.Janda, I.A.Wilson. Structural Basis For Antibody Catalysis of A Cationic Cyclization Reaction J.Mol.Biol. V. 329 69 2003.
ISSN: ISSN 0022-2836
PubMed: 12742019
DOI: 10.1016/S0022-2836(03)00406-6
Page generated: Wed Dec 16 02:09:29 2020

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