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Zinc in PDB 6dcf: Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A

Enzymatic activity of Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A

All present enzymatic activity of Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A, PDB code: 6dcf was solved by M.Lilic, S.A.Darst, E.A.Campbell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.89 / 3.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 129.250, 160.909, 136.864, 90.00, 110.75, 90.00
R / Rfree (%) 25.2 / 29

Other elements in 6dcf:

The structure of Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A (pdb code 6dcf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A, PDB code: 6dcf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6dcf

Go back to Zinc Binding Sites List in 6dcf
Zinc binding site 1 out of 2 in the Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:89.3
occ:1.00
SG D:CYS977 2.3 91.4 1.0
SG D:CYS890 2.3 98.0 1.0
SG D:CYS974 2.3 87.0 1.0
SG D:CYS967 2.3 0.9 1.0
CB D:CYS977 3.0 80.5 1.0
CB D:CYS967 3.1 91.2 1.0
CA D:CYS967 3.4 95.4 1.0
CB D:CYS890 3.6 100.0 1.0
CB D:CYS974 3.7 84.1 1.0
NH1 D:ARG962 3.9 84.5 1.0
OG D:SER969 4.0 0.0 1.0
N D:THR968 4.1 0.6 1.0
CA D:CYS977 4.2 76.2 1.0
C D:CYS967 4.2 0.0 1.0
N D:CYS974 4.3 70.0 1.0
N D:CYS977 4.3 74.9 1.0
N D:CYS890 4.4 0.2 1.0
CG2 D:THR892 4.4 0.6 1.0
CA D:CYS974 4.5 78.8 1.0
CA D:CYS890 4.6 0.6 1.0
N D:CYS967 4.6 97.5 1.0
N D:SER969 4.8 93.7 1.0
O D:CYS974 5.0 74.2 1.0

Zinc binding site 2 out of 2 in 6dcf

Go back to Zinc Binding Sites List in 6dcf
Zinc binding site 2 out of 2 in the Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Bound to Kanglemycin A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.0
occ:1.00
SG D:CYS75 2.3 89.2 1.0
SG D:CYS62 2.3 0.9 1.0
SG D:CYS78 2.3 0.4 1.0
SG D:CYS60 2.3 0.0 1.0
N D:CYS62 3.0 95.8 1.0
CB D:CYS62 3.1 0.2 1.0
CB D:CYS75 3.4 0.0 1.0
CB D:CYS60 3.5 0.9 1.0
CA D:CYS62 3.5 95.9 1.0
CB D:CYS78 3.6 92.0 1.0
N D:GLY63 3.8 0.7 1.0
N D:TYR61 3.9 0.8 1.0
N D:CYS78 4.0 0.3 1.0
C D:CYS62 4.1 0.0 1.0
C D:TYR61 4.2 0.4 1.0
CA D:CYS78 4.4 96.7 1.0
N D:LYS64 4.4 0.8 1.0
CA D:TYR61 4.5 0.9 1.0
C D:CYS60 4.5 93.0 1.0
CB D:ARG77 4.6 0.4 1.0
CA D:CYS60 4.7 96.2 1.0
CA D:CYS75 4.8 0.6 1.0
CB D:TYR61 4.8 0.9 1.0
CB D:LYS64 4.9 0.2 1.0
C D:ARG77 5.0 0.9 1.0
CA D:GLY63 5.0 0.8 1.0

Reference:

J.Peek, M.Lilic, D.Montiel, A.Milshteyn, I.Woodworth, J.B.Biggins, M.A.Ternei, P.Y.Calle, M.Danziger, T.Warrier, K.Saito, N.Braffman, A.Fay, M.S.Glickman, S.A.Darst, E.A.Campbell, S.F.Brady. Rifamycin Congeners Kanglemycins Are Active Against Rifampicin-Resistant Bacteria Via A Distinct Mechanism. Nat Commun V. 9 4147 2018.
ISSN: ESSN 2041-1723
PubMed: 30297823
DOI: 10.1038/S41467-018-06587-2
Page generated: Wed Dec 16 11:39:44 2020

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