Bromine in PDB 6nlh: Structure of Human Triose Phosphate Isomerase R189A

All present enzymatic activity of Structure of Human Triose Phosphate Isomerase R189A:
5.3.1.1;

The structure of Structure of Human Triose Phosphate Isomerase R189A, PDB code: 6nlh was solved by K.R.Richards, B.P.Roland, M.J.Palladino, A.P.Vandemark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.67 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	65.142, 73.661, 92.842, 90.03, 90.03, 90.00
R / Rfree (%)	17.4 / 21.6

The structure of Structure of Human Triose Phosphate Isomerase R189A also contains other interesting chemical elements:

Sodium

(Na)

20 atoms

The binding sites of Bromine atom in the Structure of Human Triose Phosphate Isomerase R189A (pdb code 6nlh). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Structure of Human Triose Phosphate Isomerase R189A, PDB code: 6nlh:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Structure of Human Triose Phosphate Isomerase R189A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range: probe atom residue distance (Å) B Occ E:Br302 b:80.9 occ:1.00 HE2 E:HIS95 2.7 33.0 1.0 HD22 E:ASN11 2.9 23.9 1.0 HB3 E:ASN11 3.1 26.9 1.0 HG E:LEU230 3.2 34.2 1.0 HE3 E:LYS13 3.3 35.1 1.0 NE2 E:HIS95 3.5 27.5 1.0 HA2 E:GLY232 3.5 31.6 1.0 O E:LEU230 3.6 29.3 1.0 ND2 E:ASN11 3.7 19.9 1.0 HE2 E:LYS13 3.7 35.1 1.0 HD23 E:LEU230 3.8 33.9 1.0 HA3 E:GLY232 3.8 31.6 1.0 HZ1 E:LYS13 3.8 36.9 1.0 CB E:ASN11 3.9 22.4 1.0 HB2 E:ASN11 3.9 26.9 1.0 CE E:LYS13 3.9 29.3 1.0 HD21 E:LEU230 4.0 33.9 1.0 CA E:GLY232 4.0 26.4 1.0 N E:GLY232 4.0 27.5 1.0 CG E:LEU230 4.0 28.5 1.0 O2 E:PO4303 4.0 83.1 1.0 C E:VAL231 4.1 26.7 1.0 CD2 E:LEU230 4.1 28.2 1.0 O E:VAL231 4.1 24.7 1.0 HD2 E:HIS95 4.1 31.4 1.0 CD2 E:HIS95 4.2 26.2 1.0 HD21 E:ASN11 4.3 23.9 1.0 H E:GLY232 4.3 33.0 1.0 CG E:ASN11 4.3 22.1 1.0 C E:LEU230 4.3 29.5 1.0 NZ E:LYS13 4.4 30.7 1.0 O E:GLY209 4.4 52.4 1.0 OE2 E:GLU165 4.4 42.5 1.0 CE1 E:HIS95 4.5 27.4 1.0 HB3 E:LEU230 4.6 36.6 1.0 HE1 E:HIS95 4.7 32.9 1.0 O E:HOH417 4.7 39.7 1.0 H E:ASN11 4.8 27.3 1.0 HZ2 E:LYS13 4.8 36.9 1.0 N E:VAL231 4.8 28.7 1.0 CB E:LEU230 4.8 30.5 1.0 HD11 E:LEU230 4.9 31.5 1.0 HG2 E:GLU165 4.9 49.3 1.0 CA E:VAL231 4.9 29.1 1.0 HA E:VAL231 4.9 34.9 1.0

Bromine binding site 2 out of 4 in the Structure of Human Triose Phosphate Isomerase R189A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range: probe atom residue distance (Å) B Occ C:Br304 b:77.8 occ:1.00 HE2 C:HIS95 2.5 30.5 1.0 HD22 C:ASN11 2.8 25.1 1.0 O C:HOH433 2.8 24.9 1.0 HG C:LEU230 3.0 34.3 1.0 HB3 C:ASN11 3.2 27.9 1.0 NE2 C:HIS95 3.3 25.5 1.0 HD23 C:LEU230 3.5 30.9 1.0 HE2 C:LYS13 3.5 31.1 1.0 HE3 C:LYS13 3.5 31.1 1.0 ND2 C:ASN11 3.6 20.9 1.0 HA2 C:GLY232 3.7 34.6 1.0 HD21 C:LEU230 3.7 30.9 1.0 HZ3 C:LYS13 3.7 33.3 1.0 O C:LEU230 3.8 35.0 1.0 HA3 C:GLY232 3.8 34.6 1.0 CG C:LEU230 3.8 28.6 1.0 CD2 C:LEU230 3.8 25.8 1.0 CB C:ASN11 3.9 23.2 1.0 CE C:LYS13 3.9 25.9 1.0 HB2 C:ASN11 3.9 27.9 1.0 HD2 C:HIS95 4.0 29.4 1.0 CA C:GLY232 4.0 28.9 1.0 N C:GLY232 4.1 29.8 1.0 CD2 C:HIS95 4.1 24.6 1.0 HD21 C:ASN11 4.1 25.1 1.0 C C:VAL231 4.2 29.0 1.0 CG C:ASN11 4.2 22.9 1.0 O C:VAL231 4.3 28.8 1.0 NZ C:LYS13 4.3 27.8 1.0 H C:GLY232 4.3 35.7 1.0 C C:LEU230 4.4 33.4 1.0 CE1 C:HIS95 4.4 25.5 1.0 OE2 C:GLU165 4.4 38.3 1.0 HB3 C:LEU230 4.4 33.6 1.0 O C:GLY209 4.5 40.3 1.0 HE1 C:HIS95 4.6 30.5 1.0 CB C:LEU230 4.7 28.0 1.0 HD11 C:LEU230 4.8 30.0 1.0 HD22 C:LEU230 4.8 30.9 1.0 HZ2 C:LYS13 4.8 33.3 1.0 HZ1 C:LYS13 4.8 33.3 1.0 CD1 C:LEU230 4.9 25.1 1.0 N C:VAL231 4.9 31.9 1.0 H C:ASN11 4.9 28.3 1.0 HG2 C:GLU165 5.0 46.7 1.0

Bromine binding site 3 out of 4 in the Structure of Human Triose Phosphate Isomerase R189A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range: probe atom residue distance (Å) B Occ F:Br303 b:80.1 occ:1.00 HE2 F:HIS95 2.5 34.1 1.0 HD22 F:ASN11 2.8 25.4 1.0 O F:HOH433 2.9 21.8 1.0 HG F:LEU230 3.1 36.6 1.0 HB3 F:ASN11 3.1 25.2 1.0 HE2 F:LYS13 3.2 29.7 1.0 NE2 F:HIS95 3.4 28.4 1.0 HA2 F:GLY232 3.5 32.3 1.0 HD23 F:LEU230 3.6 37.6 1.0 ND2 F:ASN11 3.6 21.3 1.0 HZ3 F:LYS13 3.7 31.0 1.0 HA3 F:GLY232 3.7 32.3 1.0 HE3 F:LYS13 3.8 29.7 1.0 HD21 F:LEU230 3.8 37.6 1.0 O F:LEU230 3.9 30.9 1.0 CE F:LYS13 3.9 24.7 1.0 CB F:ASN11 3.9 21.1 1.0 CA F:GLY232 3.9 27.0 1.0 CG F:LEU230 3.9 30.5 1.0 N F:GLY232 4.0 28.0 1.0 CD2 F:LEU230 4.0 31.3 1.0 HB2 F:ASN11 4.0 25.2 1.0 HD2 F:HIS95 4.1 33.0 1.0 C F:VAL231 4.1 31.5 1.0 O F:VAL231 4.2 25.2 1.0 CD2 F:HIS95 4.2 27.4 1.0 HD21 F:ASN11 4.2 25.4 1.0 NZ F:LYS13 4.2 25.8 1.0 CG F:ASN11 4.3 25.6 1.0 H F:GLY232 4.3 33.5 1.0 CE1 F:HIS95 4.4 28.4 1.0 C F:LEU230 4.4 30.9 1.0 HB3 F:LEU230 4.5 37.8 1.0 HE1 F:HIS95 4.5 34.1 1.0 O F:GLY209 4.5 42.8 1.0 OE2 F:GLU165 4.5 38.2 1.0 HZ2 F:LYS13 4.6 31.0 1.0 CB F:LEU230 4.8 31.5 1.0 H F:ASN11 4.8 28.1 1.0 N F:VAL231 4.9 31.8 1.0 O1 F:PO4304 4.9 72.6 1.0 HD11 F:LEU230 4.9 35.4 1.0 HD22 F:LEU230 4.9 37.6 1.0 HZ1 F:LYS13 5.0 31.0 1.0 CD1 F:LEU230 5.0 29.5 1.0 CA F:VAL231 5.0 32.8 1.0

Bromine binding site 4 out of 4 in the Structure of Human Triose Phosphate Isomerase R189A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range: probe atom residue distance (Å) B Occ H:Br303 b:74.0 occ:1.00 HE2 H:HIS95 2.4 33.9 1.0 HD22 H:ASN11 2.7 23.7 1.0 HG H:LEU230 3.2 40.1 1.0 HB3 H:ASN11 3.2 25.2 1.0 HE2 H:LYS13 3.3 32.8 1.0 NE2 H:HIS95 3.3 28.2 1.0 HA2 H:GLY232 3.6 39.5 1.0 HE3 H:LYS13 3.6 32.8 1.0 ND2 H:ASN11 3.7 19.8 1.0 O H:LEU230 3.7 36.2 1.0 HD23 H:LEU230 3.7 39.2 1.0 HZ3 H:LYS13 3.8 34.1 1.0 HA3 H:GLY232 3.8 39.5 1.0 CE H:LYS13 3.8 27.3 1.0 HB2 H:ASN11 3.9 25.2 1.0 CB H:ASN11 3.9 21.0 1.0 CA H:GLY232 4.0 33.0 1.0 HD21 H:LEU230 4.0 39.2 1.0 N H:GLY232 4.0 33.9 1.0 CG H:LEU230 4.0 33.4 1.0 HD2 H:HIS95 4.1 32.4 1.0 CD2 H:LEU230 4.1 32.6 1.0 CD2 H:HIS95 4.1 27.0 1.0 C H:VAL231 4.2 33.0 1.0 OE2 H:GLU165 4.2 36.7 1.0 O H:VAL231 4.2 31.3 1.0 NZ H:LYS13 4.3 28.4 1.0 H H:GLY232 4.3 40.6 1.0 CG H:ASN11 4.3 20.8 1.0 CE1 H:HIS95 4.3 28.2 1.0 HD21 H:ASN11 4.3 23.7 1.0 C H:LEU230 4.4 35.4 1.0 HE1 H:HIS95 4.4 33.9 1.0 O H:GLY209 4.5 40.6 1.0 HB3 H:LEU230 4.5 42.5 1.0 HZ2 H:LYS13 4.7 34.1 1.0 CB H:LEU230 4.8 35.4 1.0 O4 H:PO4304 4.8 92.1 1.0 H H:ASN11 4.8 26.9 1.0 N H:VAL231 4.9 34.1 1.0 HZ1 H:LYS13 5.0 34.1 1.0 HD13 H:LEU230 5.0 37.5 1.0

B.P.Roland, K.R.Richards, S.L.Hrizo, S.Eicher, Z.J.Barile, T.C.Chang, G.Savon, P.Bianchi, E.Fermo, B.M.Ricerca, L.Tortorolo, J.Vockley, A.P.Vandemark, M.J.Palladino. Missense Variant in TPI1 (ARG189GLN) Causes Neurologic Deficits Through Structural Changes in the Triosephosphate Isomerase Catalytic Site and Reduced Enzyme Levels in Vivo. Biochim Biophys Acta Mol V.1865 2257 2019BASIS Dis.
ISSN: ISSN 1879-260X
PubMed: 31075491
DOI: 10.1016/J.BBADIS.2019.05.002