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Bromine in PDB 5itf: Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant

Protein crystallography data

The structure of Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant, PDB code: 5itf was solved by K.P.Bzymek, J.C.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.14 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.010, 82.210, 211.900, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.3

Bromine Binding Sites:

The binding sites of Bromine atom in the Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant (pdb code 5itf). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant, PDB code: 5itf:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in 5itf

Go back to Bromine Binding Sites List in 5itf
Bromine binding site 1 out of 3 in the Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br3

b:56.2
occ:0.43
 BR E:6DU3 0.0 56.2 0.4
CD2 E:6DU3 1.0 52.7 0.6
CE2 E:6DU3 1.8 52.8 0.6
CD1 E:6DU3 2.0 52.8 0.4
CG E:6DU3 2.2 51.1 0.6
CG E:6DU3 2.9 51.0 0.4
CB E:6DU3 2.9 46.7 0.6
CE1 E:6DU3 3.0 53.0 0.4
CZ E:6DU3 3.1 53.2 0.6
CB E:6DU3 3.1 47.3 0.4
OH A:TYR87 3.2 40.2 1.0
CD1 E:6DU3 3.3 52.5 0.6
CA E:6DU3 3.4 43.6 0.6
CA E:6DU3 3.4 43.9 0.4
C E:ARG9 3.5 28.3 1.0
O E:ARG9 3.6 30.1 1.0
O A:HOH440 3.6 30.3 1.0
CD2 E:LEU10 3.6 42.7 1.0
CE1 E:6DU3 3.7 53.6 0.6
N E:LEU10 3.7 36.0 1.0
NE2 B:GLN39 3.8 46.1 1.0
N E:ARG9 3.9 41.7 1.0
CG E:LEU10 4.0 34.8 1.0
CA E:ARG9 4.0 31.4 1.0
C E:ARG8 4.0 54.6 1.0
O E:ARG8 4.0 62.9 1.0
CA E:LEU10 4.1 33.0 1.0
CD2 E:6DU3 4.2 52.9 0.4
N E:ASP4 4.2 38.6 1.0
CZ E:6DU3 4.2 53.9 0.4
C E:6DU3 4.2 41.4 0.6
C E:6DU3 4.3 41.7 0.4
CD B:GLN39 4.3 41.2 1.0
OD2 A:ASP85 4.4 45.5 1.0
OE1 A:GLN38 4.4 44.2 1.0
CZ A:TYR87 4.5 35.3 1.0
N E:6DU3 4.5 48.7 0.6
N E:6DU3 4.5 48.7 0.4
CB E:LEU10 4.6 29.7 1.0
CE2 E:6DU3 4.7 54.0 0.4
CA E:ARG8 4.7 54.2 1.0
CG B:GLN39 4.8 30.2 1.0
OE1 B:GLN39 4.9 41.9 1.0

Bromine binding site 2 out of 3 in 5itf

Go back to Bromine Binding Sites List in 5itf
Bromine binding site 2 out of 3 in the Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br3

b:56.0
occ:0.57
 BR E:6DU3 0.0 56.0 0.6
CD2 E:6DU3 0.9 52.9 0.4
CE2 E:6DU3 1.7 54.0 0.4
CD1 E:6DU3 2.0 52.5 0.6
CG E:6DU3 2.2 51.0 0.4
CE1 E:6DU3 2.9 53.6 0.6
CG E:6DU3 2.9 51.1 0.6
CZ E:6DU3 2.9 53.9 0.4
CB E:6DU3 3.0 47.3 0.4
CB E:6DU3 3.1 46.7 0.6
O E:6DU3 3.2 45.0 0.6
CD1 E:6DU3 3.3 52.8 0.4
O E:6DU3 3.3 45.0 0.4
O B:GLN39 3.4 36.6 1.0
C B:SER40 3.4 35.6 1.0
N B:PRO41 3.5 35.1 1.0
C E:6DU3 3.5 41.4 0.6
CE1 E:6DU3 3.5 53.0 0.4
C E:6DU3 3.5 41.7 0.4
CD2 E:LEU5 3.7 43.6 1.0
CD B:PRO41 3.7 31.1 1.0
CA B:SER40 3.8 35.1 1.0
O B:SER40 3.8 39.7 1.0
CG E:LEU5 3.8 43.4 1.0
C B:GLN39 3.9 34.7 1.0
CA E:6DU3 3.9 43.9 0.4
CA E:6DU3 4.0 43.6 0.6
CA B:PRO41 4.0 34.4 1.0
CG B:PRO41 4.0 31.6 1.0
N B:SER40 4.0 33.0 1.0
N E:LEU5 4.0 36.9 1.0
N E:ASP4 4.1 38.6 1.0
C E:ASP4 4.1 34.3 1.0
CZ E:6DU3 4.2 53.2 0.6
CD2 E:6DU3 4.2 52.7 0.6
CA E:LEU5 4.3 48.7 1.0
O E:ASP4 4.5 35.2 1.0
CA E:ASP4 4.5 39.9 1.0
CB B:PRO41 4.6 32.1 1.0
CG B:GLN39 4.7 30.2 1.0
CB E:LEU5 4.7 42.0 1.0
CE2 E:6DU3 4.7 52.8 0.6
CB B:GLN39 4.9 25.8 1.0
N E:6DU3 4.9 48.7 0.4
N E:6DU3 4.9 48.7 0.6
CD1 E:LEU5 5.0 47.9 1.0
CA B:GLN39 5.0 31.6 1.0

Bromine binding site 3 out of 3 in 5itf

Go back to Bromine Binding Sites List in 5itf
Bromine binding site 3 out of 3 in the Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br3

b:66.2
occ:1.00
 BR F:6DU3 0.0 66.2 1.0
CD1 F:6DU3 2.0 55.9 1.0
CG F:6DU3 2.9 50.2 1.0
CE1 F:6DU3 3.0 53.1 1.0
CB F:6DU3 3.1 48.7 1.0
O D:GLN39 3.5 39.1 1.0
C F:6DU3 3.6 38.1 1.0
O F:6DU3 3.7 37.9 1.0
N F:ASP4 3.9 38.0 1.0
C D:SER40 3.9 37.9 1.0
C F:ASP4 3.9 37.5 1.0
N D:PRO41 4.0 36.4 1.0
CA F:6DU3 4.0 38.9 1.0
C D:GLN39 4.0 36.5 1.0
CD2 F:LEU5 4.0 45.9 1.0
O F:ASP4 4.0 37.6 1.0
N F:LEU5 4.1 51.4 1.0
CG F:LEU5 4.1 45.2 1.0
CD D:PRO41 4.1 25.3 1.0
CA D:SER40 4.1 34.8 1.0
O D:SER40 4.2 41.7 1.0
N D:SER40 4.2 35.8 1.0
CD2 F:6DU3 4.2 42.5 1.0
CZ F:6DU3 4.2 56.2 1.0
CG D:GLN39 4.3 30.1 1.0
CA F:LEU5 4.3 51.0 1.0
CA F:ASP4 4.4 38.1 1.0
CG D:PRO41 4.4 25.8 1.0
CA D:PRO41 4.5 37.5 1.0
CB D:GLN39 4.7 32.1 1.0
CE2 F:6DU3 4.8 52.3 1.0
CB F:LEU5 4.8 46.8 1.0
CA D:GLN39 5.0 36.7 1.0

Reference:

K.P.Bzymek, K.A.Avery, Y.Ma, D.A.Horne, J.C.Williams. Natural and Non-Natural Amino-Acid Side-Chain Substitutions: Affinity and Diffraction Studies of Meditope-Fab Complexes. Acta Crystallogr F Struct V. 72 820 2016BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 27834791
DOI: 10.1107/S2053230X16016149
Page generated: Thu Jul 11 00:05:19 2024

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