Bromine in PDB 7vgu: Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3 : Structure Obtained 1 Msec After Photoexcitation with Bromide Ion

The structure of Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3 : Structure Obtained 1 Msec After Photoexcitation with Bromide Ion, PDB code: 7vgu was solved by T.Hosaka, E.Nango, T.Nakane, F.Luo, T.Kimura-Someya, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.36 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.3, 51.1, 78.4, 90, 131.5, 90
R / Rfree (%)	18.2 / 21.1

The binding sites of Bromine atom in the Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3 : Structure Obtained 1 Msec After Photoexcitation with Bromide Ion (pdb code 7vgu). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3 : Structure Obtained 1 Msec After Photoexcitation with Bromide Ion, PDB code: 7vgu:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3 : Structure Obtained 1 Msec After Photoexcitation with Bromide Ion


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3 : Structure Obtained 1 Msec After Photoexcitation with Bromide Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br309 b:34.4 occ:0.70 OD1 A:ASN98 1.2 44.3 0.2 CG A:ASN98 1.9 49.2 0.2 CB A:ASN98 2.7 29.3 0.2 ND2 A:ASN98 2.9 37.1 0.2 O A:ASN98 3.0 29.6 0.2 ND2 A:ASN98 3.1 37.1 0.8 C A:ASN98 3.2 28.1 0.2 NZ A:LYS235 3.2 26.0 0.8 OG1 A:THR102 3.5 39.0 0.8 CA A:ASN98 3.5 23.8 0.2 CG2 A:THR102 3.6 29.4 0.8 O A:HOH415 3.6 25.4 0.8 OG1 A:THR102 3.7 39.0 0.2 CD1 A:TRP99 3.7 28.1 0.8 NZ A:LYS235 3.7 26.0 0.2 CD1 A:TRP99 3.7 28.1 0.2 N A:TRP99 3.8 28.8 0.2 CG2 A:THR102 3.8 29.4 0.2 CE A:LYS235 3.8 30.5 0.8 NE1 A:TRP99 4.0 25.7 0.8 CB A:ALA61 4.0 21.1 1.0 CB A:THR102 4.0 24.1 0.8 CA A:ALA61 4.1 29.6 1.0 CG A:ASN98 4.2 49.2 0.8 C15 A:RET301 4.2 25.9 0.2 CE A:LYS235 4.2 30.5 0.2 C15 A:RET301 4.2 25.9 0.8 NE1 A:TRP99 4.3 25.7 0.2 CB A:ASN98 4.3 29.3 0.8 CB A:THR102 4.4 24.1 0.2 CA A:TRP99 4.5 30.2 0.2 CD A:LYS235 4.5 23.0 0.8 C14 A:RET301 4.5 28.7 0.8 CG2 A:ILE64 4.5 39.3 0.8 N A:ASN98 4.7 28.0 0.2 N A:ALA61 4.7 21.2 1.0 OD1 A:ASP231 4.8 25.6 0.2 C A:ASN98 4.8 28.1 0.8 CG A:TRP99 4.8 22.0 0.2 N A:TRP99 4.8 28.8 0.8 O A:HOH444 4.8 33.7 0.2 O A:ASN98 4.9 29.6 0.8 CG A:TRP99 4.9 22.0 0.8 O A:ARG95 4.9 29.7 0.2

Bromine binding site 2 out of 3 in the Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3 : Structure Obtained 1 Msec After Photoexcitation with Bromide Ion


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3 : Structure Obtained 1 Msec After Photoexcitation with Bromide Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br310 b:55.1 occ:0.66 N A:LYS46 3.3 32.2 1.0 CD A:PRO45 3.5 33.6 1.0 CB A:LYS46 3.7 38.0 1.0 N A:PRO45 3.8 34.9 1.0 CB A:PRO45 3.9 32.2 1.0 CB A:ALA44 4.1 34.2 1.0 CG A:PRO45 4.1 34.8 1.0 CA A:LYS46 4.1 39.4 1.0 NZ A:LYS46 4.1 64.0 1.0 C A:PRO45 4.2 37.5 1.0 CA A:PRO45 4.2 38.6 1.0 C A:ALA44 4.4 37.5 1.0 CE A:LYS46 4.6 50.1 1.0 CA A:ALA44 4.8 32.7 1.0 CG A:LYS46 5.0 50.1 1.0

Bromine binding site 3 out of 3 in the Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3 : Structure Obtained 1 Msec After Photoexcitation with Bromide Ion


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3 : Structure Obtained 1 Msec After Photoexcitation with Bromide Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br311 b:149.4 occ:1.00 C10 A:D10308 3.6 44.8 1.0 CG A:LYS177 4.3 30.6 1.0 CE A:LYS177 4.5 37.1 1.0 CB A:PHE176 4.7 29.6 1.0 C9 A:D10308 4.8 55.4 1.0 O A:PHE176 4.9 30.7 1.0

T.Hosaka, T.Nomura, M.Kubo, T.Nakane, L.Fangjia, S.I.Sekine, T.Ito, K.Murayama, K.Ihara, H.Ehara, K.Kashiwagi, K.Katsura, R.Akasaka, T.Hisano, T.Tanaka, R.Tanaka, T.Arima, A.Yamashita, M.Sugahara, H.Naitow, Y.Matsuura, S.Yoshizawa, K.Tono, S.Owada, O.Nureki, T.Kimura-Someya, S.Iwata, E.Nango, M.Shirouzu. Conformational Alterations in Unidirectional Ion Transport of A Light-Driven Chloride Pump Revealed Using X-Ray Free Electron Lasers. Proc.Natl.Acad.Sci.Usa V. 119 2022.
ISSN: ESSN 1091-6490
PubMed: 35197289
DOI: 10.1073/PNAS.2117433119