Bromine in PDB 6o5t: Crystal Structure of Vim-2 with Compound 16

Protein crystallography data

The structure of Crystal Structure of Vim-2 with Compound 16, PDB code: 6o5t was solved by A.Akhtar, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.59 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.389, 79.185, 67.501, 90.00, 130.60, 90.00
R / Rfree (%) 17.9 / 23.6

Other elements in 6o5t:

The structure of Crystal Structure of Vim-2 with Compound 16 also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Vim-2 with Compound 16 (pdb code 6o5t). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Crystal Structure of Vim-2 with Compound 16, PDB code: 6o5t:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 6o5t

Go back to Bromine Binding Sites List in 6o5t
Bromine binding site 1 out of 6 in the Crystal Structure of Vim-2 with Compound 16


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 Vim-2 with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br503

b:84.9
occ:0.76
BR01 A:L8J503 0.0 84.9 0.8
C02 A:L8J503 1.9 55.1 0.8
C03 A:L8J503 2.9 45.3 0.8
C06 A:L8J503 2.9 52.9 0.8
O B:ASP63 3.2 57.7 1.0
CE2 A:TYR67 4.0 51.3 1.0
OH B:TYR67 4.0 64.5 1.0
CB B:ALA65 4.0 48.4 1.0
C04 A:L8J503 4.2 54.9 0.8
CB B:ASP63 4.2 57.8 1.0
C07 A:L8J503 4.2 59.0 0.8
C B:ASP63 4.3 51.3 1.0
N B:ALA65 4.5 48.8 1.0
CD2 A:TYR67 4.6 46.0 1.0
NE A:ARG205 4.7 42.7 1.0
CD A:ARG205 4.8 27.7 1.0
C08 A:L8J503 4.8 54.4 0.8
CA B:ASP63 4.9 46.9 1.0
CA B:ALA65 4.9 48.2 1.0
CZ A:TYR67 5.0 55.3 1.0

Bromine binding site 2 out of 6 in 6o5t

Go back to Bromine Binding Sites List in 6o5t
Bromine binding site 2 out of 6 in the Crystal Structure of Vim-2 with Compound 16


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 Vim-2 with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br503

b:68.0
occ:0.76
BR05 A:L8J503 0.0 68.0 0.8
C04 A:L8J503 1.9 54.9 0.8
C08 A:L8J503 2.9 54.4 0.8
C03 A:L8J503 2.9 45.3 0.8
O12 A:L8J503 3.0 45.6 0.8
C10 A:L8J503 3.1 47.3 0.8
NH2 A:ARG205 3.2 44.3 1.0
C09 A:L8J503 3.2 58.0 0.8
CD2 A:HIS240 3.3 20.4 1.0
NE2 A:HIS240 3.4 24.9 1.0
CG A:HIS240 3.4 22.0 1.0
ND1 A:HIS240 3.4 16.6 1.0
CE1 A:HIS240 3.4 28.1 1.0
P11 A:L8J503 3.6 39.9 0.8
CB A:HIS240 4.1 18.0 1.0
C07 A:L8J503 4.1 59.0 0.8
C02 A:L8J503 4.2 55.1 0.8
CZ A:ARG205 4.2 49.0 1.0
CD2 A:TYR67 4.4 46.0 1.0
O13 A:L8J503 4.5 27.9 0.8
NH1 A:ARG205 4.6 49.0 1.0
CB A:TYR67 4.6 36.5 1.0
CG A:TYR67 4.6 43.5 1.0
C15 A:L8J503 4.6 58.4 0.8
C06 A:L8J503 4.7 52.9 0.8
O14 A:L8J503 4.7 29.9 0.8
ZN A:ZN502 4.8 22.9 1.0
O A:PRO68 4.9 22.8 1.0

Bromine binding site 3 out of 6 in 6o5t

Go back to Bromine Binding Sites List in 6o5t
Bromine binding site 3 out of 6 in the Crystal Structure of Vim-2 with Compound 16


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 Vim-2 with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br503

b:82.7
occ:0.48
BR01 B:L8J503 0.0 82.7 0.5
C02 B:L8J503 1.9 61.5 0.5
C06 B:L8J503 2.9 59.7 0.5
C03 B:L8J503 2.9 61.6 0.5
O17 B:L8J503 3.1 65.8 0.5
OD1 B:ASP63 3.4 66.7 1.0
C04 B:L8J503 4.2 58.1 0.5
C07 B:L8J503 4.2 50.5 0.5
C16 B:L8J503 4.3 65.5 0.5
OG A:SER207 4.4 57.0 1.0
CB A:SER207 4.4 56.1 1.0
OD1 B:ASN210 4.4 39.5 1.0
CE1 B:PHE62 4.5 62.4 1.0
CG B:ASP63 4.7 62.6 1.0
CG B:ASN210 4.8 63.6 1.0
C08 B:L8J503 4.8 53.0 0.5

Bromine binding site 4 out of 6 in 6o5t

Go back to Bromine Binding Sites List in 6o5t
Bromine binding site 4 out of 6 in the Crystal Structure of Vim-2 with Compound 16


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 Vim-2 with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br503

b:74.2
occ:0.52
BR01 B:L8J503 0.0 74.2 0.5
C02 B:L8J503 1.9 60.5 0.5
C03 B:L8J503 2.9 59.2 0.5
C06 B:L8J503 2.9 57.3 0.5
O A:ASP63 3.6 50.9 1.0
NE B:ARG205 3.9 43.1 1.0
CB A:ASP63 4.2 51.4 1.0
C04 B:L8J503 4.2 56.1 0.5
C07 B:L8J503 4.3 59.5 0.5
CE2 B:TYR67 4.3 52.8 1.0
CA B:GLY209 4.3 52.2 1.0
OH A:TYR67 4.4 66.0 1.0
CD B:ARG205 4.4 35.7 1.0
CZ B:ARG205 4.6 57.7 1.0
C A:ASP63 4.6 43.4 1.0
NH1 B:ARG205 4.7 54.8 1.0
CG B:ARG205 4.8 38.5 1.0
CB A:ALA65 4.8 41.2 1.0
CD2 B:TYR67 4.8 46.8 1.0
C08 B:L8J503 4.8 61.7 0.5
N B:GLY209 4.9 46.4 1.0
O B:SER207 5.0 42.4 1.0

Bromine binding site 5 out of 6 in 6o5t

Go back to Bromine Binding Sites List in 6o5t
Bromine binding site 5 out of 6 in the Crystal Structure of Vim-2 with Compound 16


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 Vim-2 with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br503

b:82.0
occ:0.48
BR05 B:L8J503 0.0 82.0 0.5
C15 B:L8J503 0.7 67.4 0.5
C09 B:L8J503 0.8 65.8 0.5
C10 B:L8J503 1.8 54.8 0.5
C16 B:L8J503 1.9 65.5 0.5
C04 B:L8J503 1.9 58.1 0.5
C08 B:L8J503 2.0 61.7 0.5
N18 B:L8J503 2.6 60.4 0.5
C07 B:L8J503 2.6 59.5 0.5
C08 B:L8J503 2.8 53.0 0.5
O17 B:L8J503 2.9 65.8 0.5
C03 B:L8J503 2.9 61.6 0.5
O14 B:L8J503 3.0 42.1 0.5
P11 B:L8J503 3.0 53.9 0.5
C10 B:L8J503 3.1 45.9 0.5
C09 B:L8J503 3.2 50.6 0.5
C04 B:L8J503 3.3 56.1 0.5
O14 B:L8J503 3.8 47.4 0.5
CB B:ASN210 3.8 53.1 1.0
P11 B:L8J503 3.9 49.6 0.5
BR05 B:L8J503 4.0 73.3 0.5
O13 B:L8J503 4.0 48.1 0.5
C06 B:L8J503 4.0 57.3 0.5
O12 B:L8J503 4.1 42.5 0.5
C07 B:L8J503 4.1 50.5 0.5
C02 B:L8J503 4.2 61.5 0.5
O12 B:L8J503 4.2 42.1 0.5
C03 B:L8J503 4.5 59.2 0.5
CD1 B:PHE62 4.6 62.2 1.0
C15 B:L8J503 4.6 40.6 0.5
C06 B:L8J503 4.7 59.7 0.5
CG B:ASN210 4.7 63.6 1.0
ND2 B:ASN210 4.7 51.8 1.0
C02 B:L8J503 4.8 60.5 0.5
CE1 B:PHE62 4.8 62.4 1.0
N B:ASN210 4.8 57.0 1.0
O B:HOH607 4.9 40.5 1.0
CZ B:TYR67 4.9 50.7 1.0
CA B:ASN210 5.0 51.4 1.0
CE1 B:TYR67 5.0 51.2 1.0

Bromine binding site 6 out of 6 in 6o5t

Go back to Bromine Binding Sites List in 6o5t
Bromine binding site 6 out of 6 in the Crystal Structure of Vim-2 with Compound 16


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 Vim-2 with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br503

b:73.3
occ:0.52
BR05 B:L8J503 0.0 73.3 0.5
C04 B:L8J503 1.9 56.1 0.5
C08 B:L8J503 2.9 61.7 0.5
C03 B:L8J503 2.9 59.2 0.5
O12 B:L8J503 3.0 42.5 0.5
C10 B:L8J503 3.1 54.8 0.5
C09 B:L8J503 3.3 65.8 0.5
NE2 B:HIS240 3.3 28.8 1.0
O B:HOH607 3.4 40.5 1.0
CD2 B:HIS240 3.4 24.0 1.0
CE1 B:HIS240 3.5 29.8 1.0
P11 B:L8J503 3.6 53.9 0.5
CG B:HIS240 3.6 25.1 1.0
ND1 B:HIS240 3.7 22.5 1.0
O12 B:L8J503 3.8 42.1 0.5
NH2 B:ARG205 4.0 43.6 1.0
BR05 B:L8J503 4.0 82.0 0.5
C07 B:L8J503 4.1 59.5 0.5
C02 B:L8J503 4.2 60.5 0.5
NH1 B:ARG205 4.2 54.8 1.0
CZ B:ARG205 4.2 57.7 1.0
ZN B:ZN502 4.3 27.0 1.0
CD2 B:TYR67 4.3 46.8 1.0
O14 B:L8J503 4.4 42.1 0.5
CB B:HIS240 4.5 27.9 1.0
CG B:TYR67 4.5 43.5 1.0
CB B:TYR67 4.6 33.6 1.0
C15 B:L8J503 4.6 67.4 0.5
C06 B:L8J503 4.7 57.3 0.5
O B:HOH652 4.8 25.1 1.0
O13 B:L8J503 4.8 48.1 0.5
P11 B:L8J503 4.9 49.6 0.5
C10 B:L8J503 4.9 45.9 0.5
CE2 B:TYR67 4.9 52.8 1.0

Reference:

O.A.Pemberton, P.Jaishankar, A.Akhtar, J.L.Adams, L.N.Shaw, A.R.Renslo, Y.Chen. Heteroaryl Phosphonates As Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J.Med.Chem. V. 62 8480 2019.
ISSN: ISSN 0022-2623
PubMed: 31483651
DOI: 10.1021/ACS.JMEDCHEM.9B00728
Page generated: Sat Dec 12 02:35:18 2020

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