Zinc in PDB 4mgr: The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent Transcriptional Activator of Gabt

Protein crystallography data

The structure of The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent Transcriptional Activator of Gabt, PDB code: 4mgr was solved by R.Wu, R.Edayathumangalam, 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) 49.30 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.930, 101.360, 213.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent Transcriptional Activator of Gabt (pdb code 4mgr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent Transcriptional Activator of Gabt, PDB code: 4mgr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4mgr

Go back to Zinc Binding Sites List in 4mgr
Zinc binding site 1 out of 4 in the The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent 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 The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent Transcriptional Activator of Gabt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:63.5
occ:1.00
O A:HOH610 2.4 15.0 1.0
O A:HOH611 2.4 43.2 1.0
OD1 A:ASN303 2.4 49.8 1.0
O A:HOH619 2.6 28.3 1.0
CG A:ASN303 3.4 19.3 1.0
ND2 A:ASN303 3.8 47.4 1.0
O A:PHE301 4.2 37.2 1.0
CB A:ASN303 4.7 22.5 1.0
N A:ARG273 4.8 34.7 1.0
O A:ARG274 4.8 33.7 1.0

Zinc binding site 2 out of 4 in 4mgr

Go back to Zinc Binding Sites List in 4mgr
Zinc binding site 2 out of 4 in the The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent 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 The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent Transcriptional Activator of Gabt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:88.7
occ:1.00
ND2 B:ASN303 2.1 28.4 1.0
O B:HOH685 2.2 55.5 1.0
CG B:ASN303 3.3 32.5 1.0
OD1 B:ASN303 3.7 38.0 1.0
OE1 B:GLU328 4.2 81.0 1.0
O B:ARG274 4.3 33.2 1.0
O B:PHE301 4.4 44.3 1.0
N B:ARG273 4.4 45.0 1.0
CB B:ASN303 4.6 28.2 1.0
O B:ALA268 4.6 29.1 1.0
O B:GLU271 4.7 48.3 1.0
N B:ARG274 4.8 41.6 1.0
CA B:ASN303 4.9 19.5 1.0

Zinc binding site 3 out of 4 in 4mgr

Go back to Zinc Binding Sites List in 4mgr
Zinc binding site 3 out of 4 in the The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent 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 The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent Transcriptional Activator of Gabt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:78.5
occ:1.00
O C:HOH722 2.2 45.3 1.0
OD1 C:ASN303 2.5 49.0 1.0
CG C:ASN303 3.6 38.2 1.0
O C:HOH726 3.7 47.8 1.0
ND2 C:ASN303 4.1 39.7 1.0
N C:ARG273 4.3 35.5 1.0
O C:PHE301 4.5 30.9 1.0
O C:ARG274 4.6 33.6 1.0
CA C:PRO272 4.8 44.8 1.0
CB C:ASN303 4.9 33.6 1.0
OE2 C:GLU328 4.9 56.1 1.0
C C:PRO272 5.0 42.2 1.0

Zinc binding site 4 out of 4 in 4mgr

Go back to Zinc Binding Sites List in 4mgr
Zinc binding site 4 out of 4 in the The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent 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 The Crystal Structure of Bacillus Subtilis Gabr, An Autorepressor and Plp- and Gaba-Dependent Transcriptional Activator of Gabt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:81.9
occ:1.00
O D:HOH701 2.1 51.1 1.0
O D:HOH657 2.1 45.0 1.0
O D:HOH714 2.4 48.0 1.0
OD1 D:ASN303 2.6 34.8 1.0
CG D:ASN303 3.7 33.2 1.0
N D:ARG273 4.0 31.1 1.0
ND2 D:ASN303 4.2 34.1 1.0
CA D:PRO272 4.3 48.3 1.0
O D:GLU271 4.4 40.0 1.0
O D:PHE301 4.5 24.0 1.0
C D:PRO272 4.5 44.3 1.0
N D:ARG274 4.6 35.5 1.0
O D:ARG274 4.7 36.8 1.0
OE1 D:GLU328 4.8 63.2 1.0
CA D:ARG273 4.8 43.2 1.0
CB D:ASN303 4.9 19.0 1.0
O D:ALA268 4.9 42.3 1.0

Reference:

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
Page generated: Wed Dec 16 05:35:23 2020

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