Bromine in PDB 5jvl: C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue

All present enzymatic activity of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue:
2.7.9.1;

The structure of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue, PDB code: 5jvl was solved by A.Minges, A.Hoeppner, G.Groth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.79 / 2.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	69.980, 108.450, 152.760, 106.22, 101.81, 98.32
R / Rfree (%)	21.2 / 23.2

The structure of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Bromine atom in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue (pdb code 5jvl). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue, PDB code: 5jvl:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Br901 b:55.3 occ:1.00 BR A:6NQ901 0.0 55.3 1.0 C2' A:6NQ901 2.0 31.1 1.0 O3' A:6NQ901 2.8 30.8 1.0 C1' A:6NQ901 2.9 27.0 1.0 C3' A:6NQ901 2.9 30.6 1.0 N9 A:6NQ901 3.6 22.0 1.0 OG1 A:THR326 3.7 50.3 1.0 CB A:LEU335 3.9 44.3 1.0 N3 A:6NQ901 4.0 20.7 1.0 CB A:GLU324 4.0 34.5 1.0 C4 A:6NQ901 4.0 19.9 1.0 O4' A:6NQ901 4.0 27.3 1.0 C4' A:6NQ901 4.1 30.1 1.0 OG1 A:THR254 4.2 40.2 1.0 CD1 A:LEU335 4.2 46.4 1.0 CD A:GLU324 4.4 35.2 1.0 CG A:LEU335 4.4 45.8 1.0 CD2 A:LEU335 4.4 47.9 1.0 OE1 A:GLU324 4.5 34.9 1.0 N A:PHE325 4.5 36.1 1.0 C8 A:6NQ901 4.6 22.1 1.0 OE2 A:GLU324 4.6 36.2 1.0 O A:PHE325 4.6 38.4 1.0 C A:GLU324 4.7 35.0 1.0 C A:PHE325 4.7 37.7 1.0 CG A:GLU324 4.8 34.6 1.0 CA A:GLU324 4.9 34.8 1.0

Bromine binding site 2 out of 3 in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue within 5.0Å range: probe atom residue distance (Å) B Occ C:Br901 b:63.4 occ:1.00 BR C:6NQ901 0.0 63.4 1.0 C2' C:6NQ901 2.0 39.4 1.0 O3' C:6NQ901 2.9 33.1 1.0 C3' C:6NQ901 3.0 38.8 1.0 C1' C:6NQ901 3.0 37.5 1.0 N9 C:6NQ901 3.6 30.6 1.0 OE2 C:GLU324 3.8 38.6 1.0 CB C:LEU335 3.9 38.0 1.0 C4 C:6NQ901 4.1 30.0 1.0 CD C:GLU324 4.1 38.4 1.0 N3 C:6NQ901 4.1 28.6 1.0 O4' C:6NQ901 4.1 36.5 1.0 OG1 C:THR326 4.1 35.5 1.0 CD2 C:LEU335 4.2 39.3 1.0 C4' C:6NQ901 4.2 38.4 1.0 CA C:GLY279 4.2 43.8 1.0 OE1 C:GLU324 4.2 39.6 1.0 CB C:GLU324 4.3 36.2 1.0 CG C:LEU335 4.4 38.2 1.0 C8 C:6NQ901 4.5 31.4 1.0 CD1 C:LEU335 4.5 37.5 1.0 OG1 C:THR254 4.6 34.3 1.0 N C:GLY279 4.8 42.8 1.0 CG C:GLU324 4.9 36.9 1.0

Bromine binding site 3 out of 3 in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue within 5.0Å range: probe atom residue distance (Å) B Occ D:Br901 b:63.1 occ:1.00 BR D:6NQ901 0.0 63.1 1.0 C2' D:6NQ901 2.0 32.2 1.0 C1' D:6NQ901 2.9 28.7 1.0 C3' D:6NQ901 3.0 31.4 1.0 O3' D:6NQ901 3.1 33.1 1.0 N9 D:6NQ901 3.6 24.0 1.0 CB D:LEU335 3.8 29.7 1.0 OG1 D:THR326 3.8 29.1 1.0 CB D:GLU324 4.0 29.6 1.0 OE2 D:GLU324 4.0 30.6 1.0 O4' D:6NQ901 4.1 27.5 1.0 C4 D:6NQ901 4.1 24.1 1.0 N3 D:6NQ901 4.2 23.7 1.0 C4' D:6NQ901 4.2 30.0 1.0 CD2 D:LEU335 4.2 31.1 1.0 CD D:GLU324 4.2 30.8 1.0 OG1 D:THR254 4.2 28.8 1.0 CG D:LEU335 4.3 30.4 1.0 CD1 D:LEU335 4.4 29.9 1.0 C8 D:6NQ901 4.5 24.7 1.0 OE1 D:GLU324 4.5 31.9 1.0 N D:PHE325 4.7 28.1 1.0 CA D:GLY279 4.7 44.0 1.0 CG D:GLU324 4.8 29.9 1.0 C D:GLU324 4.8 28.6 1.0 O D:PHE325 4.8 27.6 1.0 C D:PHE325 4.9 28.0 1.0 CA D:GLU324 5.0 28.9 1.0

A.Minges, D.Ciupka, C.Winkler, A.Hoppner, H.Gohlke, G.Groth. Structural Intermediates and Directionality of the Swiveling Motion of Pyruvate Phosphate Dikinase. Sci Rep V. 7 45389 2017.
ISSN: ESSN 2045-2322
PubMed: 28358005
DOI: 10.1038/SREP45389