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Chlorine in PDB 5eeh: Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol

Enzymatic activity of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol

All present enzymatic activity of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol:
2.1.1.292;

Protein crystallography data

The structure of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol, PDB code: 5eeh was solved by F.Wang, S.Singh, J.S.Thorson, G.N.Phillips Jr., Enzyme Discovery Fornatural Product Biosynthesis (Natpro), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.50 / 1.82
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.347, 110.678, 116.869, 90.00, 120.24, 90.00
R / Rfree (%) 15.4 / 18.6

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol (pdb code 5eeh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 15 binding sites of Chlorine where determined in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol, PDB code: 5eeh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 15 in 5eeh

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Chlorine binding site 1 out of 15 in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:23.3
occ:0.82
 CL1 A:P9P402 0.0 23.3 0.8
C02 A:P9P402 1.7 21.4 0.8
C10 A:P9P402 2.7 13.9 0.8
C03 A:P9P402 2.7 17.5 0.8
O11 A:P9P402 2.9 22.8 0.8
CE2 A:PHE142 3.4 14.8 1.0
CZ A:PHE142 3.5 17.2 1.0
CE1 A:PHE156 3.5 19.3 1.0
CD1 A:LEU308 3.6 13.3 1.0
CZ A:PHE156 3.6 14.5 1.0
CE A:MET304 3.8 16.7 1.0
C04 A:P9P402 4.0 17.0 0.8
C09 A:P9P402 4.0 17.9 0.8
CD2 A:PHE307 4.1 11.0 1.0
OH A:TYR143 4.2 15.8 1.0
CD2 A:PHE142 4.2 14.6 1.0
ND2 A:ASN257 4.2 14.8 1.0
CE1 A:PHE142 4.3 18.0 1.0
C08 A:P9P402 4.5 18.4 0.8
SD A:MET304 4.6 14.4 1.0
CD1 A:PHE156 4.7 16.1 1.0
CG A:LEU308 4.8 10.3 1.0
CZ A:TYR143 4.8 16.8 1.0
CE2 A:PHE307 4.9 13.7 1.0
CG A:ASN257 4.9 15.4 1.0
CE2 A:PHE156 4.9 19.1 1.0
CG A:PHE142 4.9 14.2 1.0
CD1 A:PHE142 4.9 17.3 1.0
OD1 A:ASN257 4.9 18.2 1.0

Chlorine binding site 2 out of 15 in 5eeh

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Chlorine binding site 2 out of 15 in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:26.3
occ:0.84
 CL1 A:P9P403 0.0 26.3 0.8
C02 A:P9P403 1.7 21.6 0.8
C10 A:P9P403 2.7 23.7 0.8
C03 A:P9P403 2.7 23.3 0.8
O11 A:P9P403 2.9 21.5 0.8
C08 A:P9P405 3.7 22.2 0.8
CG A:TYR342 3.7 25.9 1.0
C09 A:P9P405 3.8 23.3 0.8
CD2 A:TYR342 3.8 25.7 1.0
CD1 A:TYR342 3.9 26.1 1.0
C04 A:P9P403 4.0 26.5 0.8
C09 A:P9P403 4.0 23.6 0.8
CG1 A:VAL166 4.1 24.1 1.0
CD1 A:ILE340 4.1 32.0 1.0
CE2 A:TYR342 4.1 26.9 1.0
CB A:TYR342 4.2 25.6 1.0
CE1 A:TYR342 4.3 24.6 1.0
CZ A:TYR342 4.4 28.3 1.0
C08 A:P9P403 4.5 23.8 0.8
CL1 A:P9P406 4.5 44.2 0.9
CG1 A:ILE340 4.7 24.3 1.0
CB A:VAL166 4.7 23.0 1.0
CG2 A:VAL166 4.8 28.0 1.0
C04 A:P9P405 4.8 26.3 0.8

Chlorine binding site 3 out of 15 in 5eeh

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Chlorine binding site 3 out of 15 in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:25.5
occ:0.80
 CL1 A:P9P404 0.0 25.5 0.8
C02 A:P9P404 1.7 20.1 0.8
C03 A:P9P404 2.7 19.9 0.8
C10 A:P9P404 2.8 19.3 0.8
O11 A:P9P404 3.1 20.6 0.8
O A:HOH588 3.5 21.2 1.0
CA A:ALA167 3.5 21.1 1.0
O11 A:P9P403 3.5 21.5 0.8
CB A:ALA167 3.5 21.3 1.0
CG1 A:VAL166 3.7 24.1 1.0
C10 A:P9P403 3.7 23.7 0.8
CE1 A:PHE253 3.8 27.1 1.0
N A:ALA167 3.8 19.2 1.0
C09 A:P9P403 3.9 23.6 0.8
C04 A:P9P404 4.0 19.6 0.8
O A:LEU160 4.0 23.1 0.4
O A:HOH532 4.0 36.4 1.0
C09 A:P9P404 4.0 13.8 0.8
O A:LEU160 4.1 22.6 0.6
C A:VAL166 4.2 20.3 1.0
CZ A:PHE253 4.3 27.0 1.0
C02 A:P9P403 4.4 21.6 0.8
O A:VAL166 4.4 25.0 1.0
CD1 A:PHE253 4.5 22.7 1.0
CB A:VAL166 4.5 23.0 1.0
C08 A:P9P404 4.5 20.9 0.8
C08 A:P9P403 4.7 23.8 0.8
O A:ASP163 4.8 18.6 1.0
C A:ALA167 4.9 22.9 1.0
CE1 A:HIS283 5.0 18.9 1.0

Chlorine binding site 4 out of 15 in 5eeh

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Chlorine binding site 4 out of 15 in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:27.1
occ:0.84
 CL1 A:P9P405 0.0 27.1 0.8
C02 A:P9P405 1.7 22.4 0.8
C10 A:P9P405 2.7 19.8 0.8
C03 A:P9P405 2.7 20.4 0.8
O11 A:P9P405 2.9 19.9 0.8
CG2 A:ILE340 3.5 30.6 1.0
CB A:ALA101 3.5 20.6 1.0
C04 B:P9P401 3.5 27.0 0.8
CA A:ALA101 3.7 14.8 1.0
N05 B:P9P401 3.7 33.8 0.8
C03 B:P9P401 3.8 26.9 0.8
C08 B:P9P401 3.9 25.8 0.8
C09 A:P9P405 4.0 23.3 0.8
O06 B:P9P401 4.0 33.6 0.8
C04 A:P9P405 4.0 26.3 0.8
N A:ALA101 4.3 15.5 1.0
O07 B:P9P401 4.3 37.2 0.8
C02 B:P9P401 4.4 30.7 0.8
C09 B:P9P401 4.4 31.4 0.8
C08 A:P9P405 4.5 22.2 0.8
C10 B:P9P401 4.6 30.3 0.8
C A:PRO100 4.8 16.5 1.0
O A:PRO100 4.8 18.4 1.0
CB A:ILE340 4.8 27.2 1.0
CD1 A:ILE340 4.9 32.0 1.0
O A:HOH807 4.9 51.7 1.0
CG1 A:ILE340 4.9 24.3 1.0
C A:ALA101 5.0 17.6 1.0

Chlorine binding site 5 out of 15 in 5eeh

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Chlorine binding site 5 out of 15 in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:44.2
occ:0.87
 CL1 A:P9P406 0.0 44.2 0.9
C02 A:P9P406 1.7 30.5 0.9
C10 A:P9P406 2.7 26.2 0.9
C03 A:P9P406 2.7 33.7 0.9
O11 A:P9P406 2.9 36.0 0.9
O07 A:P9P405 3.3 33.8 0.8
N05 A:P9P405 3.3 33.6 0.8
CD1 A:ILE340 3.5 32.0 1.0
O06 A:P9P405 3.6 35.4 0.8
CD1 A:TYR342 3.8 26.1 1.0
C04 A:P9P405 3.8 26.3 0.8
CE1 A:TYR342 3.9 24.6 1.0
C09 A:P9P406 4.0 23.7 0.9
C04 A:P9P406 4.0 35.5 0.9
C08 A:P9P405 4.1 22.2 0.8
C03 A:P9P403 4.5 23.3 0.8
C08 A:P9P406 4.5 31.4 0.9
CL1 A:P9P403 4.5 26.3 0.8
O4 A:SO4409 4.5 32.2 0.6
C03 A:P9P405 4.6 20.4 0.8
C02 A:P9P403 4.8 21.6 0.8
O3 A:SO4409 4.8 22.6 0.6
CG A:TYR342 4.9 25.9 1.0
CG1 A:ILE340 5.0 24.3 1.0
NE2 A:GLN296 5.0 28.5 1.0

Chlorine binding site 6 out of 15 in 5eeh

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Chlorine binding site 6 out of 15 in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:37.6
occ:0.70
 CL1 A:P9P407 0.0 37.6 0.7
C02 A:P9P407 1.7 37.0 0.7
C03 A:P9P407 2.7 32.6 0.7
C10 A:P9P407 2.7 32.1 0.7
O11 A:P9P407 3.0 27.2 0.7
O A:HOH625 3.2 40.0 1.0
C B:THR339 3.8 30.5 1.0
CA B:THR339 3.9 25.3 1.0
O B:THR339 4.0 30.9 1.0
CB A:ALA173 4.0 24.2 1.0
C04 A:P9P407 4.0 28.3 0.7
C09 A:P9P407 4.0 31.5 0.7
CB B:THR339 4.1 26.6 1.0
N B:ILE340 4.3 27.0 1.0
C08 A:P9P407 4.5 27.2 0.7
O B:HOH573 4.6 42.0 1.0
O B:HOH744 4.6 48.1 1.0
CG2 B:ILE340 4.6 35.7 1.0
CG2 B:THR339 4.7 27.9 1.0
O A:HOH689 4.7 34.4 1.0
CA B:ILE340 5.0 27.5 1.0

Chlorine binding site 7 out of 15 in 5eeh

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Chlorine binding site 7 out of 15 in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:38.6
occ:0.75
 CL1 B:P9P401 0.0 38.6 0.8
C02 B:P9P401 1.8 30.7 0.8
C03 B:P9P401 2.7 26.9 0.8
C10 B:P9P401 2.7 30.3 0.8
O11 B:P9P401 3.0 27.2 0.8
O B:HOH638 3.2 41.2 1.0
O A:HOH836 3.6 56.2 1.0
C A:THR339 3.8 32.2 1.0
O A:THR339 3.8 28.2 1.0
CA A:THR339 3.9 25.8 1.0
C04 B:P9P401 4.0 27.0 0.8
CB B:ALA173 4.0 24.3 1.0
C09 B:P9P401 4.0 31.4 0.8
CB A:THR339 4.2 34.5 1.0
N A:ILE340 4.3 27.5 1.0
O A:HOH533 4.3 44.3 1.0
O A:HOH637 4.4 50.2 1.0
C08 B:P9P401 4.5 25.8 0.8
CG2 A:ILE340 4.7 30.6 1.0
CG2 A:THR339 4.8 35.7 1.0
CA A:ILE340 4.9 27.9 1.0

Chlorine binding site 8 out of 15 in 5eeh

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Chlorine binding site 8 out of 15 in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:24.0
occ:0.83
 CL1 B:P9P403 0.0 24.0 0.8
C02 B:P9P403 1.7 21.0 0.8
C03 B:P9P403 2.7 17.4 0.8
C10 B:P9P403 2.7 19.9 0.8
O11 B:P9P403 3.0 24.1 0.8
CE1 B:PHE156 3.5 17.8 1.0
CD1 B:LEU308 3.6 18.9 1.0
CZ B:PHE156 3.6 16.5 1.0
CE2 B:PHE142 3.6 17.9 1.0
CZ B:PHE142 3.7 19.5 1.0
CE B:MET304 3.8 17.0 1.0
C04 B:P9P403 4.0 19.4 0.8
C09 B:P9P403 4.0 19.3 0.8
OH B:TYR143 4.1 18.2 1.0
CD2 B:PHE307 4.1 16.8 1.0
ND2 B:ASN257 4.1 17.2 1.0
CD2 B:PHE142 4.3 15.5 1.0
CE1 B:PHE142 4.5 23.5 1.0
C08 B:P9P403 4.5 21.9 0.8
SD B:MET304 4.6 17.4 1.0
CD1 B:PHE156 4.7 19.1 1.0
CZ B:TYR143 4.7 17.2 1.0
CG B:LEU308 4.8 14.8 1.0
CG B:ASN257 4.8 15.6 1.0
CE2 B:PHE307 4.8 19.6 1.0
OD1 B:ASN257 4.8 19.3 1.0
CE2 B:PHE156 4.9 21.5 1.0

Chlorine binding site 9 out of 15 in 5eeh

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Chlorine binding site 9 out of 15 in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:30.5
occ:0.85
 CL1 B:P9P404 0.0 30.5 0.8
C02 B:P9P404 1.7 25.2 0.8
C10 B:P9P404 2.7 21.6 0.8
C03 B:P9P404 2.7 22.6 0.8
O11 B:P9P404 2.9 20.7 0.8
CG B:TYR342 3.7 26.9 1.0
C08 B:P9P406 3.8 24.8 0.8
CD2 B:TYR342 3.9 29.5 1.0
C09 B:P9P406 3.9 21.2 0.8
CD1 B:TYR342 4.0 27.6 1.0
C09 B:P9P404 4.0 23.1 0.8
C04 B:P9P404 4.0 26.1 0.8
CG1 B:VAL166 4.1 24.9 1.0
CD1 B:ILE340 4.1 34.6 1.0
CB B:TYR342 4.2 23.5 1.0
CE2 B:TYR342 4.2 24.0 1.0
CE1 B:TYR342 4.3 25.3 1.0
CL1 B:P9P407 4.4 49.6 0.8
CZ B:TYR342 4.4 27.4 1.0
C08 B:P9P404 4.5 23.4 0.8
CG1 B:ILE340 4.7 29.3 1.0
CB B:VAL166 4.7 22.5 1.0
CG2 B:VAL166 4.8 25.1 1.0
C04 B:P9P406 4.9 23.5 0.8
CL1 B:P9P405 5.0 26.6 0.8

Chlorine binding site 10 out of 15 in 5eeh

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Chlorine binding site 10 out of 15 in the Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Carminomycin-4-O-Methyltransferase Dnrk in Complex with Sah and 2-Chloro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:26.6
occ:0.80
 CL1 B:P9P405 0.0 26.6 0.8
C02 B:P9P405 1.7 25.3 0.8
C03 B:P9P405 2.7 20.3 0.8
C10 B:P9P405 2.7 27.6 0.8
O11 B:P9P405 3.0 22.6 0.8
O B:HOH587 3.5 22.4 1.0
O11 B:P9P404 3.5 20.7 0.8
CA B:ALA167 3.5 20.2 1.0
CB B:ALA167 3.5 21.6 1.0
C10 B:P9P404 3.7 21.6 0.8
CG1 B:VAL166 3.8 24.9 1.0
N B:ALA167 3.8 19.5 1.0
CE2 B:PHE253 3.8 30.0 1.0
C09 B:P9P404 3.9 23.1 0.8
O B:HOH607 4.0 43.6 1.0
C04 B:P9P405 4.0 22.7 0.8
C09 B:P9P405 4.0 22.9 0.8
O B:LEU160 4.1 29.7 1.0
C B:VAL166 4.2 23.1 1.0
C02 B:P9P404 4.3 25.2 0.8
CZ B:PHE253 4.3 23.8 1.0
O B:VAL166 4.4 23.4 1.0
CD2 B:PHE253 4.5 25.2 1.0
C08 B:P9P405 4.5 21.8 0.8
CB B:VAL166 4.5 22.5 1.0
C08 B:P9P404 4.7 23.4 0.8
O B:ASP163 4.8 19.4 1.0
C B:ALA167 4.9 30.6 1.0
CL1 B:P9P404 5.0 30.5 0.8

Reference:

T.D.Huber, F.Wang, S.Singh, B.R.Johnson, J.Zhang, M.Sunkara, S.G.Van Lanen, A.J.Morris, G.N.Phillips, J.S.Thorson. Functional Adomet Isosteres Resistant to Classical Adomet Degradation Pathways. Acs Chem.Biol. V. 11 2484 2016.
ISSN: ESSN 1554-8937
PubMed: 27351335
DOI: 10.1021/ACSCHEMBIO.6B00348
Page generated: Fri Jul 26 07:16:58 2024

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