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Chlorine in PDB 6brd: Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad

Protein crystallography data

The structure of Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad, PDB code: 6brd was solved by G.Cox, J.Kelso, P.J.Stogios, A.Savchenko, W.F.Anderson, G.D.Wright, Centerfor Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.42 / 3.32
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 202.026, 129.402, 74.342, 90.00, 105.45, 90.00
R / Rfree (%) 18.5 / 23.4

Other elements in 6brd:

The structure of Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad (pdb code 6brd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad, PDB code: 6brd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 6brd

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Chlorine binding site 1 out of 10 in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad


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 Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:44.9
occ:1.00
 O A:GLU357 3.4 33.2 1.0
CB A:GLU360 3.9 53.7 1.0
OH B:TYR367 4.2 20.5 1.0
CE1 B:TYR367 4.2 22.4 1.0
CZ B:TYR367 4.3 21.5 1.0
CG A:GLU360 4.4 62.6 1.0
C A:GLU357 4.4 35.2 1.0
CZ A:PHE361 4.5 32.3 1.0
CE2 A:PHE361 4.6 39.3 1.0
CA A:GLU357 4.7 39.8 1.0
CB A:GLU357 4.9 43.2 1.0
CD1 B:TYR367 5.0 23.8 1.0
CE1 A:PHE361 5.0 33.0 1.0

Chlorine binding site 2 out of 10 in 6brd

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Chlorine binding site 2 out of 10 in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad


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 Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:48.9
occ:1.00
 NZ A:LYS159 3.2 44.5 1.0
NH2 A:ARG158 3.2 15.9 1.0
NE A:ARG158 3.3 20.3 1.0
CG A:LYS159 3.4 40.0 1.0
CZ A:ARG158 3.7 17.7 1.0
CE A:LYS159 4.1 43.6 1.0
CD A:LYS159 4.2 43.9 1.0
O A:VAL163 4.3 31.0 1.0
CB A:PHE165 4.4 36.0 1.0
CB A:LYS159 4.4 36.6 1.0
CA A:LYS159 4.5 34.4 1.0
CD A:ARG158 4.5 23.0 1.0
N A:LYS159 4.8 32.5 1.0
CD2 A:PHE165 4.8 40.0 1.0
CG A:ARG158 4.8 29.5 1.0

Chlorine binding site 3 out of 10 in 6brd

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Chlorine binding site 3 out of 10 in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad


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 Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:46.7
occ:1.00
 ND1 A:HIS108 3.5 32.6 1.0
CE1 A:HIS108 4.0 32.9 1.0
CB A:ALA111 4.2 46.9 1.0
NH1 A:ARG61 4.3 55.7 1.0
NH2 A:ARG61 4.4 55.5 1.0
CG A:HIS108 4.6 30.2 1.0
O C:HOH624 4.7 35.5 1.0
O A:HIS108 4.8 43.3 1.0
CZ A:ARG61 4.8 54.7 1.0
CA A:HIS108 4.8 41.0 1.0
N C:GLY400 4.9 77.3 1.0
CA C:GLY400 5.0 73.1 1.0

Chlorine binding site 4 out of 10 in 6brd

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Chlorine binding site 4 out of 10 in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad


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 Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:63.8
occ:1.00
 NH2 B:ARG336 3.6 78.2 1.0
NH2 A:ARG353 4.5 35.9 1.0
CZ A:ARG353 4.6 40.2 1.0
OD1 B:ASP333 4.7 56.5 1.0
CZ B:ARG336 4.8 69.8 1.0
NE A:ARG353 4.9 39.6 1.0
NH1 A:ARG353 4.9 42.0 1.0

Chlorine binding site 5 out of 10 in 6brd

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Chlorine binding site 5 out of 10 in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad


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 Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:82.7
occ:0.50
 O B:GLY119 3.2 55.9 1.0
CG B:ARG120 3.8 51.4 1.0
NE B:ARG120 3.8 67.2 1.0
OD2 B:ASP138 4.1 73.8 1.0
CD B:ARG120 4.1 57.6 1.0
C B:GLY119 4.2 48.9 1.0
CA B:ARG120 4.7 40.8 1.0
CB B:ARG120 4.7 43.8 1.0
N B:ARG120 4.8 42.8 1.0
CZ B:ARG120 4.9 71.1 1.0

Chlorine binding site 6 out of 10 in 6brd

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Chlorine binding site 6 out of 10 in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad


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 Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:56.4
occ:1.00
 NH2 B:ARG352 3.2 41.9 1.0
NE B:ARG352 3.4 40.9 1.0
CZ B:ARG352 3.7 37.8 1.0
O B:LYS197 3.9 84.2 1.0
O B:ARG196 4.4 82.5 1.0
C B:LYS197 4.6 85.8 1.0
CD B:ARG352 4.6 40.4 1.0
CA B:LYS197 4.7 84.8 1.0
NE2 B:GLN200 4.7 69.1 1.0

Chlorine binding site 7 out of 10 in 6brd

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Chlorine binding site 7 out of 10 in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad


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 Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:61.8
occ:1.00
 NE B:ARG158 3.3 36.8 1.0
O B:VAL163 3.6 30.4 1.0
CG B:LYS159 3.8 48.2 1.0
CD B:ARG158 4.0 30.9 1.0
CG B:ARG158 4.1 28.5 1.0
NH2 B:ARG158 4.1 26.9 1.0
CZ B:ARG158 4.2 32.2 1.0
CB B:PHE165 4.2 42.4 1.0
CA B:LYS159 4.5 43.5 1.0
CB B:LYS159 4.6 42.6 1.0
CE B:LYS159 4.6 61.3 1.0
N B:LYS159 4.6 44.0 1.0
CD B:LYS159 4.7 57.2 1.0
N B:PHE165 4.7 40.0 1.0
C B:ARG158 4.8 46.3 1.0
C B:VAL163 4.8 36.7 1.0
O B:ARG158 4.9 54.6 1.0
C B:ALA164 4.9 37.5 1.0
CB B:ARG158 4.9 32.6 1.0
CG B:PHE165 5.0 40.6 1.0

Chlorine binding site 8 out of 10 in 6brd

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Chlorine binding site 8 out of 10 in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad


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 Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:58.0
occ:1.00
 ND1 C:HIS108 3.4 48.9 1.0
NH2 C:ARG61 3.7 56.0 1.0
CB C:ALA111 3.7 32.2 1.0
CE1 C:HIS108 4.1 50.2 1.0
NH1 C:ARG61 4.5 54.0 1.0
CG C:HIS108 4.5 48.1 1.0
CZ C:ARG61 4.5 55.5 1.0
CA C:HIS108 4.7 47.7 1.0
CB C:HIS108 4.9 48.3 1.0
O C:HIS108 4.9 45.4 1.0

Chlorine binding site 9 out of 10 in 6brd

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Chlorine binding site 9 out of 10 in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad


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 Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:64.9
occ:1.00
 O C:ASN363 3.8 35.1 1.0
CD C:ARG366 4.0 48.9 1.0
N C:TYR367 4.3 47.5 1.0
CB C:TYR367 4.3 40.9 1.0
CB C:ARG366 4.4 46.2 1.0
CG C:ARG366 4.4 45.1 1.0
CA C:TYR367 4.5 47.4 1.0
NH1 C:ARG366 4.5 64.9 1.0
CA C:ASN363 4.6 31.9 1.0
C C:ASN363 4.6 33.0 1.0
CB C:ASN363 4.7 32.5 1.0
C C:ARG366 4.7 45.1 1.0
NE C:ARG366 4.7 53.5 1.0
CZ C:ARG366 4.9 58.4 1.0
OE2 C:GLU370 5.0 61.0 1.0

Chlorine binding site 10 out of 10 in 6brd

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Chlorine binding site 10 out of 10 in the Crystal Structure of Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad


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 Rifampin Monooxygenase From Streptomyces Venezuelae, Complexed with Rifampin and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl505

b:44.4
occ:1.00
 O C:HOH612 3.0 44.5 1.0
ND1 C:HIS407 3.0 49.5 1.0
CE1 C:HIS407 3.9 50.4 1.0
CG C:HIS407 3.9 46.4 1.0
CB C:HIS407 4.1 49.2 1.0

Reference:

K.Koteva, G.Cox, J.K.Kelso, M.D.Surette, H.L.Zubyk, L.Ejim, P.Stogios, A.Savchenko, D.Sorensen, G.D.Wright. Rox, A Rifamycin Resistance Enzyme with An Unprecedented Mechanism of Action. Cell Chem Biol V. 25 403 2018.
ISSN: ESSN 2451-9448
PubMed: 29398560
DOI: 10.1016/J.CHEMBIOL.2018.01.009
Page generated: Fri Jul 26 23:02:40 2024

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