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

Protein crystallography data

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

Zinc Binding Sites:

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 5zhv

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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 5zhv

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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 5zhv

Go back to Zinc Binding Sites List in 5zhv
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 5zhv

Go back to Zinc Binding Sites List in 5zhv
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

Reference:

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
Page generated: Wed Dec 16 11:26:50 2020

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