Chlorine in PDB 4eml: Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate

All present enzymatic activity of Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate:
4.1.3.36;

The structure of Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate, PDB code: 4eml was solved by H.G.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.62 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	244.623, 140.063, 73.458, 90.00, 95.63, 90.00
R / Rfree (%)	16.5 / 19.6

The binding sites of Chlorine atom in the Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate (pdb code 4eml). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate, PDB code: 4eml:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:52.6 occ:1.00 O A:HOH411 2.8 28.7 1.0 O A:ASP198 3.0 33.2 1.0 N A:GLU202 3.0 28.7 1.0 N A:GLU201 3.3 27.1 1.0 C A:ARG199 3.3 34.0 1.0 CA A:ARG199 3.4 30.8 1.0 CG A:GLU202 3.5 49.8 1.0 OE1 A:GLU202 3.5 74.8 1.0 C A:ASP198 3.6 32.0 1.0 CB A:GLU202 3.6 32.2 1.0 CB A:GLU201 3.7 26.9 1.0 N A:LEU200 3.7 28.6 1.0 O A:ARG199 3.7 31.6 1.0 CA A:GLU201 3.7 28.9 1.0 N A:ARG199 3.8 33.8 1.0 CD A:GLU202 3.8 68.2 1.0 C A:GLU201 3.8 26.9 1.0 CA A:GLU202 3.9 28.9 1.0 C A:LEU200 4.2 26.6 1.0 CA A:LEU200 4.5 26.9 1.0 CA A:ASP198 4.8 28.3 1.0 CB A:ARG199 4.8 32.9 1.0 OE2 A:GLU202 4.9 65.1 1.0 CG A:GLU201 4.9 27.5 1.0 O A:VAL197 4.9 28.8 1.0 OE1 A:GLU201 5.0 51.7 1.0

Chlorine binding site 2 out of 3 in the Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:78.7 occ:1.00 O D:HOH477 2.5 64.5 1.0 O A:HOH518 2.9 66.7 1.0 O A:HOH554 3.0 72.3 1.0 O D:ASN192 3.1 29.3 1.0 OE2 A:GLU172 3.1 32.1 1.0 NZ A:LYS169 3.3 34.5 1.0 O A:HOH448 3.5 45.0 1.0 CD A:GLU172 3.9 31.8 1.0 OE1 A:GLU172 3.9 31.7 1.0 CB D:THR193 4.2 36.0 1.0 C D:ASN192 4.2 35.3 1.0 O A:HOH451 4.3 36.5 1.0 OG1 D:THR193 4.4 42.1 1.0 CH2 D:TRP207 4.4 30.2 1.0 CZ2 D:TRP207 4.5 35.5 1.0 CE1 A:TYR180 4.7 35.4 1.0 CE A:LYS169 4.8 34.5 1.0 CA D:THR193 4.9 34.0 1.0 OE2 D:GLU186 4.9 57.7 1.0 N D:THR193 5.0 32.7 1.0

Chlorine binding site 3 out of 3 in the Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Synechocystis Sp. Pcc 6803 1,4-Dihydroxy-2-Naphthoyl-Coenzyme A Synthase (Menb) in Complex with Bicarbonate within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl303 b:76.8 occ:1.00 O B:HOH510 3.7 38.6 1.0 O E:ALA162 4.0 27.3 1.0 N E:GLY166 4.0 24.0 1.0 CA E:GLY166 4.1 20.9 1.0 O E:ARG163 4.2 23.8 1.0 O B:ARG163 4.4 26.7 1.0 O E:HOH419 4.4 29.1 1.0 C E:ARG163 4.4 23.3 1.0 CA F:GLY166 4.4 22.8 1.0 O E:ILE164 4.5 23.2 1.0 O F:HOH426 4.5 28.4 1.0 N F:GLY166 4.6 21.7 1.0 C E:ILE164 4.7 26.5 1.0 O F:ALA162 4.7 21.6 1.0 O E:HOH512 4.7 49.4 1.0 C E:VAL165 4.8 27.9 1.0 CA E:ARG163 4.8 22.5 1.0 C B:ARG163 4.8 28.9 1.0 N E:ILE164 4.8 21.3 1.0 O B:ALA162 4.9 26.6 1.0 O B:HOH496 4.9 28.1 1.0 N B:GLY166 5.0 24.8 1.0 N E:VAL165 5.0 21.7 1.0

Y.R.Sun, H.G.Song, J.Li, M.Jiang, Y.Li, J.H.Zhou, Z.H.Guo. Active Site Binding and Catalytic Role of Bicarbonate in 1,4-Dihydroxy-2-Naphthoyl Coenzyme A Synthases From Vitamin K Biosynthetic Pathways Biochemistry V. 51 4580 2012.
ISSN: ISSN 0006-2960
PubMed: 22606952
DOI: 10.1021/BI300486J