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Chlorine in PDB 4els: Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate

Enzymatic activity of Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate

All present enzymatic activity of Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate:
4.1.3.36;

Protein crystallography data

The structure of Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate, PDB code: 4els was solved by Y.R.Sun, H.G.Song, J.Li, M.Jiang, Y.Li, J.H.Zhou, Z.H.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.85 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.367, 133.888, 153.250, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate (pdb code 4els). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate, PDB code: 4els:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4els

Go back to Chlorine Binding Sites List in 4els
Chlorine binding site 1 out of 5 in the Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (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 Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:44.5
occ:1.00
 O C:HOH452 3.0 37.2 1.0
O A:HOH477 3.1 33.1 1.0
O D:HOH426 3.2 37.7 1.0
O1 A:EDO303 3.2 49.3 1.0
C1 A:EDO303 4.1 42.6 1.0
CA D:ARG173 4.3 30.3 1.0
CA A:ARG173 4.4 25.3 1.0
O A:ALA172 4.4 28.5 1.0
CD A:ARG173 4.4 27.2 1.0
CA C:ARG173 4.4 22.8 1.0
CD D:ARG173 4.4 24.9 1.0
CD C:ARG173 4.4 23.3 1.0
O C:ALA172 4.5 29.0 1.0
O D:ALA172 4.5 26.2 1.0
O D:ARG173 4.5 31.4 1.0
O A:ARG173 4.6 29.5 1.0
O C:ARG173 4.6 30.2 1.0
C D:ARG173 4.8 30.0 1.0
C A:ARG173 4.8 30.2 1.0
C C:ARG173 4.8 24.1 1.0

Chlorine binding site 2 out of 5 in 4els

Go back to Chlorine Binding Sites List in 4els
Chlorine binding site 2 out of 5 in the Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (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 Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:60.7
occ:1.00
 CD B:PRO50 3.9 40.9 1.0
N B:LEU51 4.0 35.0 1.0
CD B:ARG49 4.1 27.6 1.0
CB B:PRO50 4.2 39.7 1.0
CG B:PRO50 4.3 50.3 1.0
N B:PRO50 4.3 36.4 1.0
CB B:LEU51 4.3 36.6 1.0
CG B:ARG49 4.3 38.9 1.0
CB B:ARG49 4.4 30.8 1.0
CA B:PRO50 4.7 42.9 1.0
CA B:LEU51 4.7 41.2 1.0
C B:PRO50 4.8 40.0 1.0
NE B:ARG49 4.8 37.0 1.0

Chlorine binding site 3 out of 5 in 4els

Go back to Chlorine Binding Sites List in 4els
Chlorine binding site 3 out of 5 in the Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (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 Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:60.9
occ:1.00
 CD C:ARG49 3.9 34.2 1.0
CB C:LEU51 4.0 32.7 1.0
N C:LEU51 4.2 36.7 1.0
NH1 C:ARG49 4.4 42.2 1.0
NE C:ARG49 4.4 45.9 1.0
CG C:ARG49 4.5 40.6 1.0
CZ C:ARG49 4.6 48.6 1.0
CA C:LEU51 4.7 41.8 1.0
CD C:PRO50 4.7 49.9 1.0
CB C:ARG49 4.8 37.5 1.0
CB C:PRO50 4.9 45.2 1.0
CL C:CL304 5.0 81.6 1.0
N C:PRO50 5.0 48.6 1.0

Chlorine binding site 4 out of 5 in 4els

Go back to Chlorine Binding Sites List in 4els
Chlorine binding site 4 out of 5 in the Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (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 4 of Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl304

b:81.6
occ:1.00
 OE1 C:GLU23 3.8 62.6 1.0
OE2 C:GLU23 4.5 94.1 1.0
NH1 C:ARG49 4.5 42.2 1.0
CD2 C:LEU51 4.5 41.6 1.0
CD C:GLU23 4.5 78.8 1.0
NH2 C:ARG49 4.6 51.5 1.0
CZ C:ARG49 4.8 48.6 1.0
CL C:CL303 5.0 60.9 1.0

Chlorine binding site 5 out of 5 in 4els

Go back to Chlorine Binding Sites List in 4els
Chlorine binding site 5 out of 5 in the Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (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 5 of Structure of E. Coli. 1,4-Dihydroxy-2- Naphthoyl Coenzyme A Synthases (Menb) in Complex with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:68.8
occ:1.00
 NH2 D:ARG173 2.9 22.5 1.0
O C:HOH401 3.0 45.2 1.0
O D:HOH458 3.1 26.5 1.0
O D:ASP239 3.5 26.9 1.0
O D:CYS240 3.7 29.3 1.0
CZ D:ARG173 4.0 32.4 1.0
CA D:CYS240 4.1 22.4 1.0
C D:CYS240 4.1 29.2 1.0
NH1 D:ARG173 4.3 22.4 1.0
C D:ASP239 4.4 29.8 1.0
OD1 C:ASP239 4.6 29.6 1.0
N D:CYS240 4.6 20.0 1.0
C2 A:EDO305 4.6 56.9 1.0
O1 A:EDO305 4.7 37.6 1.0
O C:HOH409 4.9 31.7 1.0
O C:ASP239 5.0 20.3 1.0
C1 A:EDO305 5.0 56.7 1.0
NH2 A:ARG173 5.0 21.0 1.0

Reference:

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
Page generated: Sun Jul 21 13:03:18 2024

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