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Bromine in PDB 6gl4: Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution

Protein crystallography data

The structure of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution, PDB code: 6gl4 was solved by R.Venskutonyte, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.62 / 1.95
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 46.717, 47.715, 116.713, 90.00, 93.79, 90.00
R / Rfree (%) 16.3 / 19.9

Other elements in 6gl4:

The structure of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution (pdb code 6gl4). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution, PDB code: 6gl4:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 6gl4

Go back to Bromine Binding Sites List in 6gl4
Bromine binding site 1 out of 6 in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:28.7
occ:0.42
O A:HOH465 2.9 37.2 1.0
CD A:PRO105 3.8 22.6 1.0
CG A:PRO105 3.9 24.7 1.0
O A:HOH420 4.0 24.3 1.0
CB A:LYS104 4.2 21.7 1.0
N A:PRO105 4.6 15.5 1.0
CD A:LYS104 4.7 24.6 1.0
CG A:LYS104 4.7 26.7 1.0
O A:PRO105 4.7 14.6 1.0
CD2 A:LEU239 4.9 22.3 1.0

Bromine binding site 2 out of 6 in 6gl4

Go back to Bromine Binding Sites List in 6gl4
Bromine binding site 2 out of 6 in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br303

b:35.0
occ:0.52
O A:HOH574 2.9 35.7 1.0
OG1 A:THR93 3.3 17.6 1.0
CG2 A:VAL95 3.6 23.9 0.5
CG1 A:VAL95 3.6 23.9 0.5
CG2 A:THR93 3.7 17.1 1.0
NE A:ARG96 3.8 14.9 1.0
CB A:THR93 3.9 18.9 1.0
CG A:GLU145 4.0 35.3 1.0
CZ A:ARG96 4.1 17.7 1.0
CA A:SER142 4.2 20.4 1.0
CB A:GLU145 4.2 30.1 1.0
NH2 A:ARG96 4.2 15.4 1.0
CB A:SER142 4.3 20.9 1.0
CD A:ARG96 4.3 17.1 1.0
CG A:ARG96 4.5 16.6 1.0
O A:HOH564 4.6 22.1 1.0
N A:SER142 4.8 21.1 1.0
NH1 A:ARG96 4.8 18.9 1.0
O A:GLY62 4.8 25.5 1.0
O A:GLY141 4.9 24.4 0.6
O A:GLY141 4.9 24.2 0.4

Bromine binding site 3 out of 6 in 6gl4

Go back to Bromine Binding Sites List in 6gl4
Bromine binding site 3 out of 6 in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br304

b:57.1
occ:0.61
O A:GLN244 4.0 25.2 1.0
CB A:LEU246 4.1 25.8 1.0
CA A:LEU246 4.2 23.9 1.0
CD2 A:LEU246 4.2 32.8 1.0
N A:LEU246 4.4 21.4 1.0
CG A:LEU246 4.6 28.3 1.0
CB A:GLN244 4.6 34.4 1.0
OE1 A:GLN244 4.7 44.5 1.0
C A:GLN244 4.8 22.2 1.0
C A:GLY245 4.8 24.3 1.0

Bromine binding site 4 out of 6 in 6gl4

Go back to Bromine Binding Sites List in 6gl4
Bromine binding site 4 out of 6 in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br302

b:26.4
occ:0.43
CD B:PRO105 3.9 17.9 1.0
CG B:PRO105 4.1 20.4 1.0
CB B:LYS104 4.2 20.5 1.0
N B:PRO105 4.6 14.8 1.0
O B:PRO105 4.7 14.7 1.0
CG B:LYS104 4.7 24.1 1.0
CD B:LYS104 4.9 23.6 1.0
CD2 B:LEU239 4.9 17.4 1.0

Bromine binding site 5 out of 6 in 6gl4

Go back to Bromine Binding Sites List in 6gl4
Bromine binding site 5 out of 6 in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br303

b:29.5
occ:0.47
O B:HOH608 2.7 30.1 1.0
O B:HOH471 3.0 24.9 1.0
OG1 B:THR93 3.5 14.2 1.0
CG2 B:THR93 3.7 20.5 1.0
CB B:THR93 3.9 14.1 1.0
NE B:ARG96 3.9 17.0 1.0
CG2 B:VAL95 4.0 21.0 1.0
CA B:SER142 4.0 18.1 1.0
CZ B:ARG96 4.1 16.4 1.0
CG B:GLU145 4.1 42.3 1.0
CB B:SER142 4.2 17.8 1.0
NH2 B:ARG96 4.2 15.3 1.0
CB B:GLU145 4.3 31.2 1.0
O B:HOH438 4.3 15.2 0.5
CD B:ARG96 4.5 15.6 1.0
N B:SER142 4.5 19.0 1.0
CG B:ARG96 4.7 13.0 1.0
O B:GLY141 4.7 20.3 0.4
C B:GLY141 4.8 20.1 0.4
NH1 B:ARG96 4.8 12.5 1.0
O B:GLY62 4.8 27.2 1.0
C B:GLY141 4.9 20.0 0.6
O B:HOH560 4.9 22.6 1.0
O B:GLY141 4.9 20.1 0.6

Bromine binding site 6 out of 6 in 6gl4

Go back to Bromine Binding Sites List in 6gl4
Bromine binding site 6 out of 6 in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br304

b:38.0
occ:0.44
O B:HOH489 3.0 22.1 1.0
N B:SER108 3.2 13.9 1.0
O B:HOH486 3.4 32.7 1.0
CA B:MET107 3.9 17.1 1.0
CG B:MET107 3.9 21.7 1.0
CB B:SER108 4.0 25.1 1.0
C B:MET107 4.1 17.7 1.0
CA B:SER108 4.1 17.1 1.0
OG B:SER108 4.1 27.5 1.0
O B:HOH573 4.2 15.6 0.3
O B:SER108 4.4 20.9 1.0
CB B:MET107 4.5 16.0 1.0
O B:HOH573 4.6 30.8 0.7
C B:SER108 4.7 19.2 1.0
O B:HOH424 4.8 31.4 1.0
O B:HOH432 4.8 24.3 1.0
O B:PHE106 4.9 15.3 1.0
N B:MET107 5.0 17.4 1.0

Reference:

G.B.Dawe, M.F.Kadir, R.Venskutonyte, A.M.Perozzo, Y.Yan, R.P.D.Alexander, C.Navarrete, E.A.Santander, M.Arsenault, C.Fuentes, M.R.P.Aurousseau, K.Frydenvang, N.P.Barrera, J.S.Kastrup, J.M.Edwardson, D.Bowie. Nanoscale Mobility of the Apo State and Tarp Stoichiometry Dictate the Gating Behavior of Alternatively Spliced Ampa Receptors. Neuron V. 102 976 2019.
ISSN: ISSN 0896-6273
PubMed: 31053408
DOI: 10.1016/J.NEURON.2019.03.046
Page generated: Thu Jul 11 01:59:18 2024

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