Zinc in PDB 1y23: Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis

The structure of Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis, PDB code: 1y23 was solved by K.R.Rajashankar, C.D.Lima, S.K.Burley, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.444, 86.444, 180.046, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 24.9

The structure of Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis (pdb code 1y23). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis, PDB code: 1y23:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis


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 A Member of Hit Family of Proteins From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:29.5 occ:1.00 ND1 A:HIS49 1.9 26.0 1.0 SG A:CYS10 2.1 30.0 1.0 ND1 A:HIS100 2.2 30.0 1.0 SG A:CYS7 2.3 37.4 1.0 CE1 A:HIS49 2.7 26.9 1.0 CB A:CYS7 3.0 36.6 1.0 CG A:HIS49 3.0 28.3 1.0 CE1 A:HIS100 3.0 28.6 1.0 CG A:HIS100 3.1 29.1 1.0 CB A:CYS10 3.4 29.9 1.0 CB A:HIS100 3.5 28.1 1.0 CB A:HIS49 3.6 28.8 1.0 N A:CYS10 3.8 30.4 1.0 NE2 A:HIS49 3.9 28.3 1.0 CA A:CYS10 4.0 30.8 1.0 CD2 A:HIS49 4.1 28.2 1.0 NE2 A:HIS100 4.1 26.6 1.0 CD2 A:HIS100 4.2 29.2 1.0 CA A:HIS49 4.2 26.9 1.0 CA A:CYS7 4.5 36.5 1.0 CA A:HIS100 4.6 26.6 1.0 CB A:PHE9 4.6 27.4 1.0 C A:PHE9 4.6 29.3 1.0 C A:CYS7 5.0 35.5 1.0 O A:PHE99 5.0 29.0 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis


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 A Member of Hit Family of Proteins From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:30.1 occ:1.00 ND1 B:HIS100 2.1 29.0 1.0 ND1 B:HIS49 2.2 38.4 1.0 SG B:CYS7 2.3 27.3 1.0 SG B:CYS10 2.5 30.4 1.0 CE1 B:HIS49 2.7 36.0 1.0 CE1 B:HIS100 3.0 28.2 1.0 CG B:HIS100 3.0 30.4 1.0 CB B:CYS7 3.2 31.6 1.0 CG B:HIS49 3.3 39.0 1.0 CB B:HIS100 3.4 28.2 1.0 CB B:CYS10 3.5 31.0 1.0 N B:CYS10 3.7 31.4 1.0 NE2 B:HIS49 3.9 38.8 1.0 CB B:HIS49 4.0 36.2 1.0 CA B:CYS10 4.0 31.7 1.0 NE2 B:HIS100 4.0 28.0 1.0 CD2 B:HIS100 4.1 30.2 1.0 CD2 B:HIS49 4.2 40.0 1.0 OE2 B:GLU5 4.3 48.8 1.0 CA B:HIS49 4.5 33.0 1.0 CB B:PHE9 4.5 29.6 1.0 C B:PHE9 4.6 30.6 1.0 CA B:HIS100 4.6 28.1 1.0 CA B:CYS7 4.6 32.7 1.0 CD B:GLU5 4.9 49.2 1.0 CA B:PHE9 4.9 31.2 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis


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 A Member of Hit Family of Proteins From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:15.8 occ:1.00 ND1 C:HIS49 2.1 30.1 1.0 ND1 C:HIS100 2.1 21.3 1.0 SG C:CYS7 2.3 25.7 1.0 SG C:CYS10 2.3 27.4 1.0 CE1 C:HIS49 2.9 31.6 1.0 CE1 C:HIS100 3.0 19.3 1.0 CG C:HIS49 3.1 29.9 1.0 CB C:CYS7 3.2 27.3 1.0 CG C:HIS100 3.2 20.4 1.0 CB C:CYS10 3.4 27.9 1.0 CB C:HIS49 3.6 29.6 1.0 CB C:HIS100 3.6 21.0 1.0 N C:CYS10 3.6 24.5 1.0 CA C:CYS10 4.0 27.7 1.0 NE2 C:HIS49 4.0 31.9 1.0 CD2 C:HIS49 4.1 30.4 1.0 NE2 C:HIS100 4.2 19.7 1.0 CD2 C:HIS100 4.3 19.8 1.0 CA C:HIS49 4.3 29.6 1.0 CB C:PHE9 4.5 24.2 1.0 C C:PHE9 4.6 24.3 1.0 CA C:CYS7 4.6 27.0 1.0 CA C:HIS100 4.7 22.8 1.0 O C:CYS7 4.8 25.9 1.0 OE2 C:GLU5 4.8 34.4 1.0 CD C:GLU5 4.8 37.8 1.0 C C:CYS7 4.9 26.1 1.0 CA C:PHE9 4.9 23.0 1.0 OE1 C:GLU5 5.0 36.2 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis


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 A Member of Hit Family of Proteins From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1004 b:26.1 occ:1.00 ND1 D:HIS49 2.1 27.0 1.0 ND1 D:HIS100 2.1 32.5 1.0 SG D:CYS7 2.2 22.5 1.0 SG D:CYS10 2.3 31.1 1.0 CE1 D:HIS49 2.9 25.1 1.0 CE1 D:HIS100 3.0 32.4 1.0 CG D:HIS100 3.0 30.5 1.0 CG D:HIS49 3.2 27.1 1.0 CB D:CYS7 3.2 28.1 1.0 CB D:CYS10 3.4 28.4 1.0 CB D:HIS100 3.4 28.7 1.0 N D:CYS10 3.6 26.5 1.0 CB D:HIS49 3.7 29.9 1.0 CA D:CYS10 3.9 28.8 1.0 NE2 D:HIS100 4.0 30.7 1.0 CD2 D:HIS100 4.1 32.2 1.0 NE2 D:HIS49 4.1 24.7 1.0 CD2 D:HIS49 4.2 25.5 1.0 CA D:HIS49 4.3 30.7 1.0 CB D:PHE9 4.5 24.5 1.0 C D:PHE9 4.5 24.7 1.0 CA D:HIS100 4.6 25.5 1.0 CA D:CYS7 4.6 29.2 1.0 OE2 D:GLU5 4.8 37.8 1.0 O D:CYS7 4.8 30.8 1.0 CD D:GLU5 4.8 39.8 1.0 CA D:PHE9 4.9 24.9 1.0 C D:CYS7 5.0 29.6 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1005 b:18.5 occ:1.00 ND1 E:HIS49 2.0 27.8 1.0 ND1 E:HIS100 2.1 16.3 1.0 SG E:CYS7 2.3 23.2 1.0 SG E:CYS10 2.4 21.8 1.0 CE1 E:HIS49 2.8 26.2 1.0 CE1 E:HIS100 2.9 17.1 1.0 CB E:CYS7 3.1 26.8 1.0 CG E:HIS100 3.2 19.4 1.0 CG E:HIS49 3.2 29.2 1.0 CB E:CYS10 3.4 24.0 1.0 CB E:HIS100 3.6 19.6 1.0 N E:CYS10 3.7 24.1 1.0 CB E:HIS49 3.8 27.0 1.0 NE2 E:HIS49 4.0 26.7 1.0 CA E:CYS10 4.0 24.5 1.0 NE2 E:HIS100 4.1 20.3 1.0 CD2 E:HIS49 4.2 26.9 1.0 CD2 E:HIS100 4.2 19.0 1.0 CA E:HIS49 4.4 27.4 1.0 CA E:CYS7 4.5 27.9 1.0 CB E:PHE9 4.6 21.4 1.0 C E:PHE9 4.6 22.3 1.0 CD E:GLU5 4.7 43.4 1.0 CA E:HIS100 4.7 19.8 1.0 OE1 E:GLU5 4.8 41.7 1.0 O E:HOH1027 4.9 20.5 1.0 OE2 E:GLU5 4.9 42.2 1.0 O E:CYS7 4.9 26.0 1.0 C E:CYS7 4.9 27.0 1.0 CG E:GLU5 5.0 40.3 1.0

K.R.Rajashankar, C.D.Lima. Crystal Structure of A Member of Hit Family of Proteins From Bacillus Subtilis To Be Published.