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Bromine in PDB 7vgt: Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3: Resting State Structure with Bromide Ion

Protein crystallography data

The structure of Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3: Resting State Structure with Bromide Ion, PDB code: 7vgt 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 (%) 17.6 / 20.8

Bromine Binding Sites:

The binding sites of Bromine atom in the Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3: Resting State Structure with Bromide Ion (pdb code 7vgt). 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: Resting State Structure with Bromide Ion, PDB code: 7vgt:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in 7vgt

Go back to Bromine Binding Sites List in 7vgt
Bromine binding site 1 out of 3 in the Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3: Resting State Structure 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: Resting State Structure with Bromide Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br309

b:34.4
occ:0.88
ND2 A:ASN98 3.1 37.1 1.0
NZ A:LYS235 3.2 26.0 1.0
OG1 A:THR102 3.5 39.0 1.0
CG2 A:THR102 3.6 29.4 1.0
O A:HOH413 3.6 25.4 1.0
CD1 A:TRP99 3.7 28.1 1.0
CE A:LYS235 3.8 30.5 1.0
NE1 A:TRP99 4.0 25.7 1.0
CB A:ALA61 4.0 21.1 1.0
CB A:THR102 4.0 24.1 1.0
CA A:ALA61 4.1 29.6 1.0
CG A:ASN98 4.2 49.2 1.0
C15 A:RET301 4.2 25.9 1.0
CB A:ASN98 4.3 29.3 1.0
CD A:LYS235 4.5 23.0 1.0
C14 A:RET301 4.5 28.7 1.0
CG2 A:ILE64 4.5 39.3 1.0
N A:ALA61 4.7 21.2 1.0
C A:ASN98 4.8 28.1 1.0
N A:TRP99 4.8 28.8 1.0
O A:ASN98 4.9 29.6 1.0
CG A:TRP99 4.9 22.0 1.0

Bromine binding site 2 out of 3 in 7vgt

Go back to Bromine Binding Sites List in 7vgt
Bromine binding site 2 out of 3 in the Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3: Resting State Structure 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: Resting State Structure with Bromide Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br310

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

Bromine binding site 3 out of 3 in 7vgt

Go back to Bromine Binding Sites List in 7vgt
Bromine binding site 3 out of 3 in the Time-Resolved Serial Femtosecond Crystallography Structure of Light- Driven Chloride Ion-Pumping Rhodopsin, Nm-R3: Resting State Structure 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: Resting State Structure with Bromide Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br311

b:55.1
occ:0.69
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

Reference:

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
Page generated: Thu Jul 11 04:39:23 2024

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