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Zinc in PDB 3e7l: Crystal Structure of SIGMA54 Activator NTRC4'S Dna Binding Domain

Protein crystallography data

The structure of Crystal Structure of SIGMA54 Activator NTRC4'S Dna Binding Domain, PDB code: 3e7l was solved by J.D.Batchelor, M.Doucleff, C.-J.Lee, K.Matsubara, S.De Carlo, J.Heideker, M.M.Lamers, J.G.Pelton, D.E.Wemmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.17 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.239, 55.866, 62.338, 90.00, 93.39, 90.00
R / Rfree (%) 20.3 / 24.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of SIGMA54 Activator NTRC4'S Dna Binding Domain (pdb code 3e7l). 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 SIGMA54 Activator NTRC4'S Dna Binding Domain, PDB code: 3e7l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3e7l

Go back to Zinc Binding Sites List in 3e7l
Zinc binding site 1 out of 4 in the Crystal Structure of SIGMA54 Activator NTRC4'S Dna Binding Domain


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 SIGMA54 Activator NTRC4'S Dna Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:0.8
occ:1.00
OE2 A:GLU57 2.4 73.2 1.0
OE1 A:GLU57 2.6 69.4 1.0
CD A:GLU57 2.8 66.9 1.0
CG A:GLU57 4.3 62.2 1.0
NH2 A:ARG53 4.5 67.1 1.0

Zinc binding site 2 out of 4 in 3e7l

Go back to Zinc Binding Sites List in 3e7l
Zinc binding site 2 out of 4 in the Crystal Structure of SIGMA54 Activator NTRC4'S Dna Binding Domain


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 SIGMA54 Activator NTRC4'S Dna Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:0.9
occ:1.00
OE2 B:GLU57 2.4 0.1 1.0
OE1 B:GLU57 2.7 0.9 1.0
CD B:GLU57 2.7 0.2 1.0
NZ A:LYS26 3.9 0.7 1.0
CG B:GLU57 4.0 0.3 1.0
CE A:LYS26 4.6 0.7 1.0
CB B:GLU57 4.8 96.0 1.0

Zinc binding site 3 out of 4 in 3e7l

Go back to Zinc Binding Sites List in 3e7l
Zinc binding site 3 out of 4 in the Crystal Structure of SIGMA54 Activator NTRC4'S Dna Binding Domain


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 SIGMA54 Activator NTRC4'S Dna Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:0.0
occ:1.00
OE1 B:GLU27 3.1 0.2 1.0
CD B:GLU27 3.8 0.8 1.0
OE2 B:GLU27 3.9 0.1 1.0
CG B:GLU27 4.9 91.8 1.0

Zinc binding site 4 out of 4 in 3e7l

Go back to Zinc Binding Sites List in 3e7l
Zinc binding site 4 out of 4 in the Crystal Structure of SIGMA54 Activator NTRC4'S Dna Binding Domain


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 SIGMA54 Activator NTRC4'S Dna Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:74.9
occ:1.00
OD2 A:ASP50 2.0 52.7 1.0
OE2 C:GLU30 2.1 56.1 1.0
OE1 C:GLU27 2.5 69.9 1.0
CD C:GLU30 2.8 51.7 1.0
OE1 C:GLU30 2.9 53.2 1.0
CG A:ASP50 3.0 54.1 1.0
OD1 A:ASP50 3.4 54.3 1.0
CD C:GLU27 3.7 71.6 1.0
CG C:GLU30 4.2 43.1 1.0
OE2 C:GLU27 4.3 80.2 1.0
CB A:ASP50 4.4 57.4 1.0
CB A:ARG53 4.7 63.5 1.0
CG C:GLU27 4.7 58.9 1.0
CD C:LYS26 5.0 69.0 1.0

Reference:

J.D.Batchelor, M.Doucleff, C.J.Lee, K.Matsubara, S.De Carlo, J.Heideker, M.H.Lamers, J.G.Pelton, D.E.Wemmer. Structure and Regulatory Mechanism of Aquifex Aeolicus NTRC4: Variability and Evolution in Bacterial Transcriptional Regulation. J.Mol.Biol. V. 384 1058 2008.
ISSN: ISSN 0022-2836
PubMed: 18955063
DOI: 10.1016/J.JMB.2008.10.024
Page generated: Wed Dec 16 04:15:09 2020

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