Zinc in PDB 4n0b: Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt

The structure of Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt, PDB code: 4n0b was solved by R.Edayathumangalam, R.Wu, R.Garcia, Y.Wang, W.Wang, C.A.Kreinbring, A.Bach, J.Liao, T.Stone, T.Terwilliger, Q.Q.Hoang, B.R.Belitsky, G.A.Petsko, D.Ringe, D.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.63 / 2.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.248, 101.330, 211.215, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.8

The structure of Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt (pdb code 4n0b). 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 Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt, PDB code: 4n0b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt


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 Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.2 occ:1.00 O A:HOH616 2.7 67.5 1.0 O A:HOH617 2.8 84.8 1.0 OD1 A:ASN303 2.9 74.4 1.0 CG A:ASN303 3.7 69.3 1.0 ND2 A:ASN303 4.0 72.0 1.0 CA A:PRO272 4.2 80.8 1.0 N A:ARG273 4.4 72.2 1.0 O A:PHE301 4.7 72.9 1.0 CB A:PRO272 4.7 81.3 1.0 OE2 A:GLU328 4.7 85.5 1.0 C A:PRO272 4.8 78.3 1.0 O A:ARG274 4.9 54.1 1.0 O A:ALA268 5.0 59.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt


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 Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:0.6 occ:1.00 O B:HOH621 2.7 84.0 1.0 O B:HOH620 2.8 73.9 1.0 OD1 B:ASN303 2.9 62.7 1.0 N B:ARG273 3.7 62.6 1.0 CG B:ASN303 3.8 56.3 1.0 CA B:PRO272 4.0 67.6 1.0 ND2 B:ASN303 4.1 56.0 1.0 C B:PRO272 4.3 64.6 1.0 O B:GLU271 4.3 69.5 1.0 N B:ARG274 4.5 59.6 1.0 CA B:ARG273 4.6 64.0 1.0 O B:ARG274 4.6 61.3 1.0 O B:ALA268 4.6 54.9 1.0 O B:PHE301 4.8 60.3 1.0 CB B:PRO272 4.9 68.3 1.0 N B:PRO272 5.0 68.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt


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 Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:0.5 occ:1.00 O C:HOH608 2.7 65.9 1.0 OD1 C:ASN303 2.8 69.4 1.0 O C:HOH609 2.8 51.1 1.0 O C:HOH610 2.9 56.5 1.0 CG C:ASN303 3.7 64.2 1.0 ND2 C:ASN303 4.0 65.8 1.0 N C:ARG273 4.6 74.8 1.0 O C:PHE301 4.6 75.1 1.0 O C:ARG274 5.0 56.2 1.0 O C:ALA268 5.0 49.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt


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 Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:0.0 occ:1.00 OD1 D:ASN303 2.8 72.0 1.0 O D:HOH607 2.9 62.4 1.0 CG D:ASN303 3.8 70.5 1.0 ND2 D:ASN303 4.3 76.2 1.0 N D:ARG273 4.4 75.8 1.0 OE1 D:GLU328 4.6 83.3 1.0 O D:PHE301 4.7 73.6 1.0 CA D:PRO272 4.8 78.0 1.0 CD D:GLU328 4.8 84.3 1.0 O D:ARG274 4.8 69.7 1.0 O D:GLN302 4.9 70.5 1.0

R.Edayathumangalam, R.Wu, R.Garcia, Y.Wang, W.Wang, C.A.Kreinbring, A.Bach, J.Liao, T.A.Stone, T.C.Terwilliger, Q.Q.Hoang, B.R.Belitsky, G.A.Petsko, D.Ringe, D.Liu. Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Transcriptional Activator of Gabt. Proc.Natl.Acad.Sci.Usa V. 110 17820 2013.
ISSN: ISSN 0027-8424
PubMed: 24127574
DOI: 10.1073/PNAS.1315887110