Zinc in PDB 5zhv: Crystal Structure of the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion

The structure of Crystal Structure of the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion, PDB code: 5zhv was solved by K.Meera, R.K.Pal, A.Arora, B.K.Biswal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.19 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	30.468, 49.208, 128.388, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 26.7

The binding sites of Zinc atom in the Crystal Structure of the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion (pdb code 5zhv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion, PDB code: 5zhv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion


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 the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:70.0 occ:1.00 NE2 A:HIS16 2.3 45.9 1.0 NE2 A:HIS34 2.4 52.8 1.0 OE1 A:GLU30 2.4 53.9 1.0 CD2 A:HIS16 3.2 43.4 1.0 CE1 A:HIS16 3.3 45.0 1.0 CD2 A:HIS34 3.3 52.8 1.0 CD A:GLU30 3.3 50.0 1.0 CE1 A:HIS34 3.4 53.4 1.0 OE2 A:GLU30 4.0 50.7 1.0 CG A:GLU30 4.2 46.8 1.0 ND1 A:HIS16 4.4 43.2 1.0 CG A:HIS16 4.4 43.2 1.0 CG A:HIS34 4.5 52.3 1.0 ND1 A:HIS34 4.5 52.9 1.0 CB A:GLU30 4.9 43.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion


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 the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:96.4 occ:1.00 OE1 B:GLU94 2.0 59.4 1.0 OE2 B:GLU94 2.5 57.6 1.0 NE2 A:HIS12 2.5 37.8 1.0 CD B:GLU94 2.5 58.6 1.0 ND1 A:HIS34 2.7 52.9 1.0 CE1 A:HIS12 3.0 36.0 1.0 CG A:HIS34 3.2 52.3 1.0 CB A:HIS34 3.3 49.9 1.0 CD2 A:HIS12 3.6 36.1 1.0 CE1 A:HIS34 3.6 53.4 1.0 O A:HIS34 3.9 51.5 1.0 CG B:GLU94 3.9 58.0 1.0 CE2 A:TYR36 4.0 43.4 1.0 CA A:HIS34 4.1 50.1 1.0 ND1 A:HIS12 4.2 35.7 1.0 OH A:TYR36 4.2 42.9 1.0 CD2 A:HIS34 4.3 52.8 1.0 NE2 A:HIS34 4.5 52.8 1.0 CG A:HIS12 4.5 35.3 1.0 C A:HIS34 4.5 50.2 1.0 CZ A:TYR36 4.7 42.4 1.0 CB B:GLU94 4.9 56.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:99.5 occ:1.00 ND1 A:HIS15 2.0 42.7 1.0 CG A:HIS15 2.9 41.5 1.0 CE1 A:HIS15 2.9 44.7 1.0 CB A:HIS15 3.3 38.5 1.0 CG1 B:VAL95 3.3 59.4 1.0 CD2 A:HIS15 3.9 43.5 1.0 NE2 A:HIS15 4.0 45.1 1.0 NH1 A:ARG85 4.2 51.0 1.0 CB B:VAL95 4.4 57.5 1.0 CD2 A:HIS12 4.4 36.1 1.0 NE2 A:HIS12 4.6 37.8 1.0 CA A:HIS15 4.7 37.1 1.0 OE1 B:GLU94 4.9 59.4 1.0 CG A:HIS12 4.9 35.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Padr-Family Transcriptional Regulator RV3488 of Mycobacterium Tuberculosis H37RV in Complex with Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:42.0 occ:1.00 OE2 B:GLU30 1.9 29.8 1.0 NE2 B:HIS34 2.0 34.5 1.0 O B:HOH317 2.1 26.2 1.0 NE2 B:HIS16 2.1 35.9 1.0 CD2 B:HIS34 2.9 34.7 1.0 CE1 B:HIS16 3.0 34.6 1.0 CD B:GLU30 3.0 30.5 1.0 CE1 B:HIS34 3.0 34.6 1.0 CD2 B:HIS16 3.2 34.4 1.0 CG B:GLU30 3.5 29.9 1.0 O B:HOH309 3.8 37.6 1.0 OE1 B:GLU30 4.1 31.4 1.0 CG B:HIS34 4.1 34.4 1.0 ND1 B:HIS34 4.1 34.8 1.0 ND1 B:HIS16 4.2 33.9 1.0 CG B:HIS16 4.3 34.3 1.0 O B:GLU30 4.9 29.5 1.0 CB B:GLU30 4.9 29.6 1.0

M.Kumari, R.K.Pal, A.K.Mishra, S.Tripathi, B.K.Biswal, K.K.Srivastava, A.Arora. Structural and Functional Characterization of the Transcriptional Regulator RV3488 Ofmycobacterium TUBERCULOSISH37RV. Biochem. J. V. 475 3393 2018.
ISSN: ESSN 1470-8728
PubMed: 30266832
DOI: 10.1042/BCJ20180356