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Bromine in PDB 5h11: Crystal Structure of Zebrafish SEC10

Protein crystallography data

The structure of Crystal Structure of Zebrafish SEC10, PDB code: 5h11 was solved by J.Chen, A.Yamagata, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.92 / 2.73
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.693, 162.652, 45.572, 90.00, 95.55, 90.00
R / Rfree (%) 23.6 / 26.7

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Zebrafish SEC10 (pdb code 5h11). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 10 binding sites of Bromine where determined in the Crystal Structure of Zebrafish SEC10, PDB code: 5h11:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 10 in 5h11

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Bromine binding site 1 out of 10 in the Crystal Structure of Zebrafish SEC10


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 Zebrafish SEC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br801

b:0.6
occ:1.00
 CB A:SER328 2.8 55.0 1.0
OG A:SER328 3.8 55.7 1.0
CA A:SER328 3.9 64.0 1.0
N A:SER328 4.5 69.1 1.0
CE A:LYS330 4.9 46.5 1.0
NZ A:LYS330 5.0 40.0 1.0

Bromine binding site 2 out of 10 in 5h11

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Bromine binding site 2 out of 10 in the Crystal Structure of Zebrafish SEC10


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Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Zebrafish SEC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br802

b:0.8
occ:1.00
 CD A:LYS432 3.7 68.0 1.0
CB A:THR315 4.0 52.8 1.0
CG2 A:THR315 4.1 66.8 1.0
OG1 A:THR315 4.2 43.5 1.0
CG A:LYS432 4.2 55.1 1.0
CE A:LYS432 4.3 76.8 1.0
OG1 A:THR312 4.4 36.2 1.0
CB A:LYS432 4.4 35.5 1.0
CA A:THR312 4.4 44.2 1.0
NZ A:LYS432 4.4 76.4 1.0
CD2 A:TYR311 4.7 38.0 1.0
CE2 A:TYR311 4.8 35.9 1.0
O A:TYR311 4.8 43.4 1.0
CB A:THR312 4.9 53.2 1.0
O A:THR312 4.9 51.1 1.0

Bromine binding site 3 out of 10 in 5h11

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Bromine binding site 3 out of 10 in the Crystal Structure of Zebrafish SEC10


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 Zebrafish SEC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br803

b:0.8
occ:1.00
 NE A:ARG429 3.3 44.3 1.0
CG A:ARG429 3.6 35.9 1.0
CD A:ARG429 3.8 36.1 1.0
CG A:LYS305 4.1 37.4 1.0
CZ A:ARG429 4.3 52.2 1.0
CD2 A:TYR308 4.3 36.2 1.0
O A:HIS425 4.4 64.8 1.0
NH1 A:ARG429 4.5 63.8 1.0
CA A:LYS305 4.5 59.1 1.0
CB A:LYS305 4.6 37.5 1.0
CG A:TYR308 4.6 36.0 1.0
CB A:HIS425 4.7 45.3 1.0
CE2 A:TYR308 4.8 36.1 1.0
CB A:TYR308 4.8 42.1 1.0
CE A:LYS305 4.9 56.2 1.0
CD A:LYS305 4.9 49.1 1.0

Bromine binding site 4 out of 10 in 5h11

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Bromine binding site 4 out of 10 in the Crystal Structure of Zebrafish SEC10


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 Zebrafish SEC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br804

b:0.3
occ:1.00
 CB A:GLN499 2.8 57.2 1.0
NE2 A:GLN499 3.2 55.7 1.0
CA A:GLN499 3.7 58.8 1.0
CD A:ARG424 4.0 46.0 1.0
CG A:GLN499 4.0 56.2 1.0
CD A:GLN499 4.1 51.4 1.0
NH1 A:ARG424 4.3 82.8 1.0
NE A:ARG424 4.4 67.5 1.0
CE1 A:HIS503 4.4 46.3 1.0
N A:GLN499 4.4 61.7 1.0
CB A:ARG424 4.4 39.6 1.0
ND1 A:HIS503 4.5 47.5 1.0
CZ A:ARG424 4.5 80.4 1.0
CG A:ARG424 4.6 37.8 1.0
CB A:LEU420 4.7 43.7 1.0
O A:LEU420 4.7 56.6 1.0
NE2 A:HIS503 4.8 57.5 1.0
C A:GLN499 5.0 62.2 1.0
CG A:HIS503 5.0 45.0 1.0

Bromine binding site 5 out of 10 in 5h11

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Bromine binding site 5 out of 10 in the Crystal Structure of Zebrafish SEC10


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 Zebrafish SEC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br805

b:0.0
occ:1.00
 N A:ASP595 3.6 69.5 1.0
CB A:ASN598 3.7 86.4 1.0
CA A:GLN487 3.7 51.9 1.0
CG A:GLN487 4.0 52.4 1.0
CB A:ASP595 4.1 83.5 1.0
CB A:MET594 4.1 48.3 1.0
CB A:GLN487 4.2 53.8 1.0
ND2 A:ASN598 4.3 77.2 1.0
CB A:ASN490 4.3 43.4 1.0
CA A:ASP595 4.3 71.7 1.0
CA A:MET594 4.3 55.4 1.0
O A:GLN487 4.3 57.5 1.0
O A:ASP595 4.4 74.5 1.0
CG A:MET594 4.4 49.5 1.0
C A:MET594 4.5 66.6 1.0
N A:GLN487 4.5 50.1 1.0
CG A:ASN490 4.6 52.4 1.0
C A:GLN487 4.6 55.9 1.0
CG A:ASN598 4.6 83.8 1.0
SD A:MET594 4.6 0.0 1.0
OD2 A:ASP595 4.6 88.6 1.0
CG A:ASP595 4.7 90.5 1.0
ND2 A:ASN490 4.7 53.3 1.0
O A:VAL486 4.7 63.9 1.0
CA A:ASN598 4.8 81.8 1.0
C A:ASP595 4.8 68.4 1.0
N A:ASN598 4.8 73.5 1.0
C A:VAL486 4.9 57.4 1.0

Bromine binding site 6 out of 10 in 5h11

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Bromine binding site 6 out of 10 in the Crystal Structure of Zebrafish SEC10


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 Zebrafish SEC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br806

b:0.1
occ:1.00
 CD1 A:ILE449 3.1 64.1 1.0
NE2 A:GLN358 3.3 48.9 1.0
CB A:GLU452 3.8 50.9 1.0
CG A:GLU452 3.9 63.9 1.0
CE2 A:TYR453 4.1 46.2 1.0
CG A:GLN358 4.2 38.5 1.0
CD A:GLN358 4.2 46.6 1.0
CA A:ILE449 4.3 50.6 1.0
CG1 A:ILE449 4.5 57.1 1.0
CG2 A:ILE449 4.6 52.6 1.0
CB A:ILE449 4.7 52.8 1.0
CD2 A:TYR453 4.7 44.6 1.0
O A:LEU448 4.7 58.2 1.0
CD A:GLU452 4.9 81.5 1.0
CZ A:TYR453 5.0 52.2 1.0
O A:ILE449 5.0 64.4 1.0

Bromine binding site 7 out of 10 in 5h11

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Bromine binding site 7 out of 10 in the Crystal Structure of Zebrafish SEC10


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 Zebrafish SEC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br807

b:0.3
occ:1.00
 NZ A:LYS274 3.8 57.9 1.0
CG1 A:VAL229 3.9 74.5 1.0
CE2 A:TYR225 3.9 39.2 1.0
CD2 A:TYR225 4.1 39.1 1.0
OG1 A:THR270 4.5 64.6 1.0
CB A:THR270 4.6 57.5 1.0
CB A:VAL229 4.7 63.5 1.0
CE A:LYS274 4.8 66.3 1.0
CG2 A:VAL229 4.9 55.4 1.0
O A:TYR225 4.9 56.9 1.0
CA A:ALA226 4.9 49.2 1.0

Bromine binding site 8 out of 10 in 5h11

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Bromine binding site 8 out of 10 in the Crystal Structure of Zebrafish SEC10


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 Zebrafish SEC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br808

b:0.9
occ:1.00
 NH1 A:ARG205 2.5 92.7 1.0
CZ A:ARG205 3.8 93.4 1.0
CA A:ALA202 3.9 48.4 1.0
N A:ALA202 4.1 44.6 1.0
CG2 A:THR201 4.1 50.3 1.0
CB A:ALA202 4.2 55.7 1.0
CD A:ARG205 4.3 72.7 1.0
C A:THR201 4.4 46.8 1.0
NE A:ARG205 4.5 84.1 1.0
O A:THR201 4.5 45.5 1.0
NH2 A:ARG205 4.7 91.4 1.0
CB A:THR201 4.7 40.8 1.0
CB A:ARG205 4.8 70.2 1.0
O A:GLN198 5.0 63.1 1.0

Bromine binding site 9 out of 10 in 5h11

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Bromine binding site 9 out of 10 in the Crystal Structure of Zebrafish SEC10


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 Zebrafish SEC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br809

b:0.8
occ:1.00
 CG2 A:VAL415 3.8 45.9 1.0
CA A:VAL415 3.8 50.5 1.0
CG2 A:ILE364 3.9 42.0 1.0
N A:VAL415 3.9 55.4 1.0
O A:GLU414 4.0 66.2 1.0
C A:GLU414 4.0 58.9 1.0
CB A:ASN418 4.1 52.6 1.0
CB A:VAL415 4.4 47.9 1.0
CG A:ASN418 4.4 57.0 1.0
CB A:GLU414 4.5 72.3 1.0
OD1 A:ASN418 4.5 49.4 1.0
OE2 A:GLU414 4.5 90.3 1.0
CA A:GLU414 4.9 63.2 1.0
C A:VAL415 4.9 57.6 1.0

Bromine binding site 10 out of 10 in 5h11

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Bromine binding site 10 out of 10 in the Crystal Structure of Zebrafish SEC10


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 Zebrafish SEC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br810

b:0.8
occ:1.00
 CD2 A:TYR572 3.6 31.9 1.0
N A:TYR572 3.6 40.9 1.0
CA A:GLN571 3.8 36.7 1.0
CB A:CYS633 3.8 45.1 1.0
SG A:CYS633 3.9 72.9 1.0
C A:GLN571 4.1 38.2 1.0
CE2 A:TYR572 4.3 32.3 1.0
CB A:GLN571 4.3 44.2 1.0
CG A:TYR572 4.5 31.7 1.0
CB A:TYR572 4.6 40.0 1.0
CA A:CYS633 4.6 31.0 1.0
CA A:TYR572 4.7 40.2 1.0
CG A:GLN571 4.8 56.6 1.0
O A:ILE570 4.8 31.4 1.0
O A:CYS633 4.9 31.2 1.0
N A:GLN571 5.0 46.9 1.0

Reference:

J.Chen, A.Yamagata, K.Kubota, Y.Sato, S.Goto-Ito, S.Fukai. Crystal Structure of SEC10, A Subunit of the Exocyst Complex Sci Rep V. 7 40909 2017.
ISSN: ESSN 2045-2322
PubMed: 28098232
DOI: 10.1038/SREP40909
Page generated: Wed Jul 10 23:45:48 2024

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