Bromine in PDB 6z8g: Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.

The structure of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure., PDB code: 6z8g was solved by C.E.Stebbins, A.Hempelmann, M.Van Straaten, J.Zeelen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.55 / 1.56
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.148, 68.407, 157.759, 90, 92.17, 90
R / Rfree (%)	22.6 / 23.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. (pdb code 6z8g). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 23 binding sites of Bromine where determined in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure., PDB code: 6z8g:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 23 in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br501 b:82.5 occ:1.00 NZ A:LYS307 3.5 43.8 1.0 CE A:LYS307 3.6 43.5 1.0 CG A:GLU320 3.9 39.7 1.0 CB A:GLU320 3.9 37.6 1.0 CD A:PRO317 4.0 39.0 1.0 OE2 A:GLU320 4.3 45.4 1.0 CB A:ALA316 4.3 30.8 1.0 CD1 A:LEU305 4.4 33.6 1.0 CD A:LYS307 4.4 39.3 1.0 CB A:LEU305 4.5 30.9 1.0 CD A:GLU320 4.6 43.9 1.0 CD2 A:LEU305 4.7 34.3 1.0 CG A:LEU305 4.7 33.2 1.0 CG A:PRO317 4.9 41.0 1.0 O A:LEU305 4.9 32.9 1.0 CA A:ALA316 4.9 32.3 1.0

Bromine binding site 2 out of 23 in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br502 b:81.2 occ:0.93 O A:HOH633 3.2 36.2 1.0 O A:HOH647 3.5 38.2 1.0 CE A:LYS83 3.7 33.9 1.0 CA A:ALA328 3.9 29.3 1.0 O A:SER327 3.9 34.6 1.0 C A:SER327 3.9 33.6 1.0 CB A:SER327 4.0 35.4 1.0 N A:ALA328 4.0 30.5 1.0 CB A:ALA328 4.2 27.2 1.0 CD2 A:LEU304 4.2 31.8 1.0 CG A:LYS83 4.4 29.5 1.0 CD A:LYS83 4.5 31.9 1.0 O A:HOH819 4.5 47.5 1.0 NZ A:LYS83 4.6 36.5 1.0 CA A:SER327 4.6 34.4 1.0

Bromine binding site 3 out of 23 in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br503 b:103.5 occ:0.79 OG1 A:THR79 3.1 39.7 1.0 N A:MET80 3.9 33.4 1.0 SD A:MET80 3.9 40.0 1.0 CB A:THR79 3.9 37.4 1.0 C A:THR79 4.1 33.8 1.0 NZ A:LYS83 4.1 36.5 1.0 CA A:MET80 4.1 34.4 1.0 CB A:MET80 4.1 35.0 1.0 O A:THR79 4.4 33.2 1.0 CE A:LYS83 4.4 33.9 1.0 CG A:MET80 4.6 35.6 1.0 CA A:THR79 4.6 33.8 1.0 CG2 A:VAL77 5.0 32.2 1.0

Bromine binding site 4 out of 23 in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br504 b:81.8 occ:0.94 N A:GLY141 3.2 40.9 1.0 NE2 A:HIS221 3.5 51.2 1.0 CA A:GLY141 3.6 45.1 1.0 C A:GLY141 3.8 48.4 1.0 CD2 A:HIS221 3.8 49.7 1.0 CB A:GLU139 4.0 41.8 1.0 O A:GLY141 4.0 49.4 1.0 O A:ASN219 4.0 49.5 1.0 CA A:ASN219 4.1 53.8 1.0 N A:PHE140 4.2 40.0 1.0 C A:ASN219 4.2 51.2 1.0 C A:GLU139 4.2 37.2 1.0 N A:GLY142 4.3 49.4 1.0 O A:ALA218 4.4 52.8 1.0 C A:PHE140 4.4 40.7 1.0 CA A:GLU139 4.4 39.3 1.0 O A:THR220 4.7 39.9 1.0 CE1 A:HIS221 4.8 51.5 1.0 O A:GLU139 4.8 36.6 1.0 CA A:PHE140 4.8 41.5 1.0 CG A:GLU139 4.8 41.2 1.0 CB A:ASN219 4.9 54.9 1.0 OE1 A:GLU139 4.9 47.1 1.0 N A:THR220 5.0 43.2 1.0

Bromine binding site 5 out of 23 in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br505 b:48.9 occ:0.52 O A:HOH736 3.3 43.2 1.0 O A:HOH732 3.5 37.7 1.0 CA A:GLU64 3.7 24.5 1.0 N A:GLU64 3.9 22.2 1.0 O A:SER63 3.9 20.3 1.0 CZ3 A:TRP371 3.9 23.3 1.0 CB A:LEU368 3.9 23.8 1.0 C A:SER63 4.0 20.9 1.0 OG A:SER67 4.0 29.6 1.0 NH1 B:ARG99 4.1 21.5 1.0 CB A:SER67 4.3 25.4 1.0 CB A:GLU64 4.3 26.9 1.0 CD2 A:LEU368 4.4 21.4 1.0 O A:HOH739 4.5 44.1 1.0 CE3 A:TRP371 4.5 23.3 1.0 CB A:SER63 4.5 21.3 1.0 CG A:LEU368 4.5 22.4 1.0 CD1 A:LEU368 4.6 21.8 1.0 CG A:GLU64 4.6 31.0 1.0 CA A:LEU368 4.7 23.4 1.0 N A:LEU368 4.8 24.5 1.0 C A:GLU64 4.9 23.8 1.0 CA A:SER63 4.9 20.5 1.0

Bromine binding site 6 out of 23 in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br506 b:89.0 occ:0.56 OD1 A:ASN326 2.7 33.6 1.0 NH2 A:ARG291 2.8 29.8 1.0 O A:ASN322 3.5 33.3 1.0 CG A:ASN326 3.6 33.8 1.0 CG2 A:ILE325 3.7 28.8 1.0 CA A:GLU332 3.8 38.9 1.0 N A:GLU332 3.9 38.5 1.0 CG A:GLU332 3.9 44.3 1.0 CB A:ASN322 3.9 36.6 1.0 CA A:ASN322 3.9 33.2 1.0 CB A:ILE325 4.0 27.0 1.0 CZ A:ARG291 4.0 34.7 1.0 OD1 A:ASN322 4.1 39.3 1.0 ND2 A:ASN326 4.1 36.7 1.0 C A:ASN322 4.1 33.4 1.0 CG A:ASN322 4.2 38.5 1.0 NH1 A:ARG291 4.3 37.4 1.0 N A:ASN326 4.4 28.9 1.0 CB A:GLU332 4.4 41.8 1.0 CD1 A:ILE325 4.7 26.8 1.0 CB A:ASN326 4.8 31.7 1.0 CA A:ASN326 4.9 29.0 1.0 C A:GLU332 4.9 38.7 1.0 C A:ILE325 4.9 31.8 1.0 CG1 A:ILE325 5.0 26.3 1.0

Bromine binding site 7 out of 23 in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. within 5.0Å range: probe atom residue distance (Å) B Occ B:Br502 b:81.9 occ:1.00 OG B:SER277 3.2 23.7 1.0 CB B:SER277 3.3 20.9 1.0 O B:HOH738 3.4 41.6 1.0 N B:SER277 3.5 19.9 1.0 CA B:GLY275 3.6 24.6 1.0 C B:GLY275 3.6 25.4 1.0 N B:ALA276 3.8 20.4 1.0 BR B:BR503 3.8 86.5 0.8 O B:ARG272 3.9 23.0 1.0 CA B:SER277 4.0 20.4 1.0 O B:GLY275 4.0 24.7 1.0 CA B:ARG272 4.1 21.6 1.0 N B:GLY275 4.4 23.8 1.0 O B:HOH617 4.4 25.1 1.0 C B:ARG272 4.5 21.8 1.0 C B:ALA276 4.5 19.1 1.0 O B:ILE271 4.6 19.3 1.0 CB B:ARG272 4.7 22.5 1.0 CA B:ALA276 4.7 20.3 1.0 C B:SER277 5.0 19.5 1.0 N B:THR278 5.0 21.8 1.0

Bromine binding site 8 out of 23 in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. within 5.0Å range: probe atom residue distance (Å) B Occ B:Br503 b:86.5 occ:0.76 CD B:ARG272 3.7 24.6 1.0 OG B:SER277 3.8 23.7 1.0 CG B:ARG272 3.8 23.6 1.0 BR B:BR502 3.8 81.9 1.0 CB B:LEU179 4.1 28.4 1.0 CB B:SER277 4.1 20.9 1.0 O B:LEU179 4.3 29.9 1.0 CB B:ARG272 4.4 22.5 1.0 CD1 B:LEU179 4.4 29.6 1.0 CD2 B:LEU179 4.6 28.1 1.0 CG B:LEU179 4.6 28.9 1.0 C B:LEU179 4.8 30.2 1.0 CA B:LEU179 4.9 28.3 1.0 NE B:ARG272 4.9 24.3 1.0 CA B:ARG272 5.0 21.6 1.0

Bromine binding site 9 out of 23 in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. within 5.0Å range: probe atom residue distance (Å) B Occ B:Br504 b:64.1 occ:0.36 O B:THR150 3.6 56.4 1.0 CG2 B:THR150 3.9 60.1 1.0 C B:THR150 4.7 55.5 1.0

Bromine binding site 10 out of 23 in the Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of VSG13 Soaked in 0.5 M Used to Phase VSG13 to Solve the Structure. within 5.0Å range: probe atom residue distance (Å) B Occ B:Br505 b:79.5 occ:1.00 C B:PHE140 2.9 51.9 1.0 BR B:BR506 3.1 113.4 0.9 N B:PHE140 3.2 52.2 1.0 O B:ALA218 3.5 47.5 1.0 CA B:PHE140 3.6 52.2 1.0 C B:GLU139 3.6 65.5 1.0 O B:PHE140 3.9 53.0 1.0 CB B:GLU139 4.0 64.7 1.0 CA B:GLU139 4.1 63.8 1.0 O B:GLU139 4.2 67.6 1.0 CB B:PHE140 4.3 50.7 1.0 CA B:ASN219 4.4 45.5 1.0 CG B:GLU139 4.5 64.2 1.0 C B:ASN219 4.6 44.1 1.0 C B:ALA218 4.6 46.9 1.0 O B:THR220 4.7 40.4 1.0 O B:ASN219 4.8 43.0 1.0 CD2 B:HIS221 4.9 53.3 1.0 NE2 B:HIS221 5.0 55.2 1.0 N B:ASN219 5.0 42.5 1.0

J.Zeelen, M.Van Straaten, J.Verdi, A.Hempelmann, H.Hashemi, K.Perez, P.D.Jeffrey, S.Halg, N.Wiedemar, P.Maser, F.N.Papavasiliou, C.E.Stebbins. Structure of Trypanosome Coat Protein Vsgsur and Function in Suramin Resistance. Nat Microbiol V. 6 392 2021.
ISSN: ESSN 2058-5276
PubMed: 33462435
DOI: 10.1038/S41564-020-00844-1