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Bromine in PDB 3c9a: High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz

Protein crystallography data

The structure of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz, PDB code: 3c9a was solved by D.E.Klein, S.E.Stayrook, F.Shi, K.Narayan, M.A.Lemmon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.76 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.991, 51.275, 69.985, 84.23, 74.82, 75.67
R / Rfree (%) 19.5 / 24

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Bromine atom in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz (pdb code 3c9a). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 18 binding sites of Bromine where determined in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz, PDB code: 3c9a:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 18 in 3c9a

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Bromine binding site 1 out of 18 in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2

b:21.4
occ:0.73
 N A:CYS260 3.4 24.1 1.0
N A:CYS139 3.4 21.1 1.0
NH2 A:ARG135 3.4 16.5 1.0
O A:HOH574 3.5 39.6 1.0
O A:HOH584 3.5 29.0 1.0
CA A:ARG138 3.8 19.2 1.0
CB A:CYS260 4.0 23.8 1.0
CA A:THR144 4.0 26.6 1.0
C A:ARG138 4.1 19.6 1.0
C A:THR144 4.2 25.3 1.0
CB A:ARG138 4.2 18.9 1.0
O A:ARG143 4.3 29.2 1.0
CA A:CYS260 4.3 24.1 1.0
CB A:CYS139 4.3 22.2 1.0
CZ A:ARG135 4.4 14.8 1.0
CA A:CYS139 4.4 21.9 1.0
O A:CYS137 4.5 15.3 1.0
CG A:ARG138 4.5 19.3 1.0
SG A:CYS139 4.5 21.2 1.0
OE1 A:GLU110 4.6 22.0 1.0
CG2 A:THR144 4.7 27.4 1.0
O A:HOH533 4.7 36.9 1.0
CB A:THR144 4.8 26.6 1.0
O A:CYS139 4.8 23.5 1.0
NH1 A:ARG135 4.8 17.7 1.0
N A:ARG138 4.9 16.8 1.0
N A:THR144 5.0 27.8 1.0

Bromine binding site 2 out of 18 in 3c9a

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Bromine binding site 2 out of 18 in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br3

b:20.7
occ:0.50
 O A:HOH708 3.2 49.3 1.0
O A:HOH695 3.3 30.3 1.0
O A:HOH552 3.3 25.9 1.0
N A:ILE102 3.6 14.7 1.0
CB A:ARG101 3.7 15.7 1.0
CA A:ARG101 3.8 15.9 1.0
O A:ILE102 3.9 15.4 1.0
CG A:ARG101 4.0 15.8 1.0
O A:HOH626 4.0 28.7 1.0
C A:ARG101 4.2 15.4 1.0
CD A:ARG101 4.5 15.8 1.0
CA A:ILE102 4.6 15.2 1.0
C A:ILE102 4.6 15.6 1.0

Bromine binding site 3 out of 18 in 3c9a

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Bromine binding site 3 out of 18 in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br4

b:28.1
occ:0.33
 CD A:PRO331 3.1 16.3 1.0
O B:HOH702 3.1 36.7 1.0
O B:HOH474 3.3 23.1 1.0
CE2 A:TYR339 3.4 14.4 1.0
CG A:PRO331 3.5 15.1 1.0
O B:HOH524 3.6 31.7 1.0
NE2 B:HIS392 3.7 14.2 1.0
NZ B:LYS366 3.8 26.2 1.0
N A:PRO331 3.9 14.6 1.0
CA A:GLU330 4.1 14.4 1.0
CD2 A:TYR339 4.2 14.1 1.0
O B:HOH436 4.3 18.8 1.0
O A:ARG329 4.3 13.9 1.0
C A:GLU330 4.3 14.1 1.0
OH B:TYR411 4.4 16.8 1.0
OH A:TYR339 4.4 15.1 1.0
CD2 B:HIS392 4.4 13.6 1.0
OD2 B:ASP372 4.5 23.6 1.0
CZ A:TYR339 4.5 14.5 1.0
CE1 B:HIS392 4.7 14.4 1.0
N A:GLU330 4.7 12.8 1.0
C A:ARG329 4.8 13.1 1.0
CE B:LYS366 4.8 26.4 1.0
CB A:PRO331 4.9 16.2 1.0
CA A:PRO331 4.9 15.3 1.0
CG A:ARG329 5.0 11.9 1.0
NE A:ARG329 5.0 15.7 1.0

Bromine binding site 4 out of 18 in 3c9a

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Bromine binding site 4 out of 18 in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br6

b:21.8
occ:0.32
 O A:HOH444 3.2 20.6 1.0
N A:LYS356 3.6 24.1 1.0
CB A:CYS415 3.8 16.0 1.0
CD A:PRO383 3.9 16.6 1.0
SG A:CYS415 3.9 17.2 1.0
CA A:ARG355 4.0 25.5 1.0
O A:GLN354 4.0 22.3 1.0
CG A:PRO383 4.1 18.3 1.0
O A:HOH496 4.2 29.6 1.0
O A:HOH638 4.2 46.6 1.0
C A:ARG355 4.3 24.7 1.0
CA A:LYS356 4.4 23.5 1.0
CB A:CYS353 4.6 18.2 1.0
C A:GLN354 4.7 23.4 1.0
N A:ARG355 4.8 24.2 1.0
CB A:ARG355 4.9 26.4 1.0
N A:GLN357 5.0 20.5 1.0

Bromine binding site 5 out of 18 in 3c9a

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Bromine binding site 5 out of 18 in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br7

b:20.1
occ:0.35
 N A:SER395 3.3 20.4 1.0
O A:HOH562 3.4 42.2 1.0
CB A:GLN394 3.8 19.0 1.0
CG A:GLN394 3.8 20.8 1.0
CB A:SER395 3.8 22.4 1.0
OG A:SER395 3.9 26.6 1.0
CA A:GLN394 4.0 19.6 1.0
CA A:SER395 4.2 22.1 1.0
C A:GLN394 4.2 19.5 1.0
O A:SER395 4.6 23.3 1.0
CD A:GLN394 4.6 23.1 1.0
O A:HOH796 4.7 44.2 1.0
C A:SER395 4.9 21.9 1.0

Bromine binding site 6 out of 18 in 3c9a

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Bromine binding site 6 out of 18 in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br8

b:18.3
occ:0.34
 O A:HOH535 3.1 30.5 1.0
O A:HOH627 3.4 37.9 1.0
N A:TYR104 3.4 13.8 1.0
CD1 A:TYR104 3.8 15.7 1.0
CA A:LEU103 3.8 14.4 1.0
O A:GLY107 3.9 18.7 1.0
CB A:LEU103 4.0 15.1 1.0
CG A:LEU103 4.1 16.7 1.0
CB A:TYR104 4.1 15.0 1.0
C A:LEU103 4.1 13.9 1.0
O A:HOH531 4.2 23.6 1.0
O A:TYR104 4.2 16.6 1.0
CA A:TYR104 4.2 14.6 1.0
CA A:ASP108 4.3 17.8 1.0
O A:HOH602 4.4 40.8 1.0
CG A:TYR104 4.4 14.9 1.0
O A:HOH458 4.5 24.9 1.0
O A:HOH552 4.5 25.9 1.0
CD2 A:LEU103 4.7 15.6 1.0
CB A:ASP108 4.7 17.7 1.0
C A:TYR104 4.7 15.0 1.0
CE1 A:TYR104 4.8 16.6 1.0
O A:ILE102 4.9 15.4 1.0
C A:GLY107 4.9 17.6 1.0
O A:HOH678 4.9 49.2 1.0

Bromine binding site 7 out of 18 in 3c9a

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Bromine binding site 7 out of 18 in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br9

b:30.0
occ:0.43
 O A:HOH752 3.3 58.9 1.0
OG A:SER263 3.3 28.6 1.0
O A:HOH788 3.3 84.7 1.0
N A:GLU267 3.4 33.3 1.0
C A:GLY265 3.6 30.4 1.0
CA A:GLY265 3.6 28.9 1.0
N A:ASP268 3.7 30.8 1.0
CB A:GLU267 3.8 34.5 1.0
N A:VAL266 3.8 31.4 1.0
CB A:SER263 3.8 26.0 1.0
CA A:GLU267 3.9 33.9 1.0
N A:GLY265 3.9 27.9 1.0
O A:GLY265 4.0 29.8 1.0
C A:GLU267 4.1 32.6 1.0
CB A:ASP268 4.3 29.2 1.0
C A:VAL266 4.4 33.1 1.0
O A:HOH663 4.4 40.5 1.0
CA A:ASP268 4.5 29.2 1.0
CA A:VAL266 4.6 32.6 1.0
CG A:ASP268 4.6 28.1 1.0
CG A:GLU267 4.8 36.1 1.0
O A:HOH699 4.8 44.1 1.0
O A:GLU267 5.0 32.7 1.0

Bromine binding site 8 out of 18 in 3c9a

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Bromine binding site 8 out of 18 in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br10

b:21.6
occ:0.33
 O A:HOH519 2.7 33.8 1.0
O A:HOH455 3.0 25.3 1.0
N A:CYS382 3.2 16.5 1.0
O A:HOH743 3.3 43.9 1.0
N A:CYS388 3.6 17.3 1.0
CB A:CYS382 3.6 15.7 1.0
CB A:CYS388 3.8 17.8 1.0
SG A:CYS382 3.8 17.9 1.0
CA A:CYS382 4.0 16.5 1.0
CA A:GLN381 4.1 17.2 1.0
C A:GLN381 4.2 15.9 1.0
CA A:CYS388 4.3 16.8 1.0
C A:ARG387 4.4 17.4 1.0
CA A:ARG387 4.4 18.2 1.0
O A:HOH571 4.5 48.4 1.0
O A:CYS382 4.7 17.6 1.0
O A:CYS380 4.7 15.4 1.0
CB A:GLN381 4.8 17.6 1.0
O A:HIS386 4.8 18.2 1.0
C A:CYS382 4.8 16.6 1.0

Bromine binding site 9 out of 18 in 3c9a

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Bromine binding site 9 out of 18 in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br17

b:21.2
occ:0.18
 O A:HOH639 2.7 33.5 1.0
OG A:SER412 2.9 22.7 1.0
OG1 A:THR410 3.1 21.1 1.0
BR C:BR18 3.3 20.3 0.3
CG2 C:THR57 3.3 19.7 1.0
CB A:THR410 3.6 17.6 1.0
C A:TYR411 3.7 16.2 1.0
C A:THR410 3.8 16.5 1.0
N A:TYR411 3.8 15.2 1.0
O A:THR410 3.9 15.2 1.0
N A:SER412 3.9 16.2 1.0
CA A:GLY400 4.0 26.6 1.0
CA A:TYR411 4.0 15.7 1.0
O A:TYR411 4.1 15.0 1.0
O A:HOH568 4.1 39.4 1.0
CB A:SER412 4.2 16.9 1.0
CB C:THR57 4.2 20.9 1.0
N A:GLY400 4.3 25.3 1.0
CA A:THR410 4.3 17.0 1.0
O A:HOH618 4.4 46.1 1.0
CA A:SER412 4.6 16.4 1.0
O A:ILE398 4.7 22.8 1.0
CG2 A:THR410 4.9 19.3 1.0
O A:HOH611 5.0 34.7 1.0

Bromine binding site 10 out of 18 in 3c9a

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Bromine binding site 10 out of 18 in the High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of High Resolution Crystal Structure of Argos Bound to the Egf Domain of Spitz within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1

b:15.8
occ:0.75
 O B:HOH478 3.3 17.8 1.0
O B:HOH597 3.3 26.4 1.0
N B:CYS260 3.3 14.6 1.0
N B:CYS139 3.4 15.9 1.0
NH2 B:ARG135 3.6 17.4 1.0
CA B:ARG138 3.7 15.4 1.0
O B:HOH530 3.8 37.8 1.0
CA B:THR144 3.9 14.0 1.0
C B:ARG138 4.1 14.9 1.0
CB B:CYS260 4.1 15.9 1.0
C B:THR144 4.1 14.9 1.0
CB B:ARG138 4.1 14.7 1.0
CG2 B:THR144 4.1 15.5 1.0
OE1 B:GLU110 4.3 24.3 1.0
CG B:ARG138 4.3 16.9 1.0
CA B:CYS260 4.3 15.9 1.0
O B:ARG143 4.4 15.9 1.0
CB B:CYS139 4.4 15.9 1.0
CA B:CYS139 4.5 15.1 1.0
O B:HOH445 4.5 23.8 1.0
CZ B:ARG135 4.6 16.5 1.0
O B:CYS137 4.6 13.2 1.0
CB B:THR144 4.6 15.1 1.0
SG B:CYS139 4.6 16.9 1.0
O B:CYS139 4.8 15.6 1.0
N B:ARG138 4.9 14.9 1.0
N B:THR144 4.9 14.3 1.0

Reference:

D.E.Klein, S.E.Stayrook, F.Shi, K.Narayan, M.A.Lemmon. Structural Basis For Egfr Ligand Sequestration By Argos. Nature V. 453 1271 2008.
ISSN: ISSN 0028-0836
PubMed: 18500331
DOI: 10.1038/NATURE06978
Page generated: Wed Jul 10 19:11:50 2024

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