Zinc in PDB 3byw: Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae

The structure of Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae, PDB code: 3byw was solved by K.Tan, C.Hatzos, J.Abdullah, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.25 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.885, 80.619, 115.826, 90.00, 110.91, 90.00
R / Rfree (%)	20.9 / 26.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae (pdb code 3byw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 19 binding sites of Zinc where determined in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae, PDB code: 3byw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 19 in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae


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 An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7 b:42.6 occ:1.00 NE2 A:HIS114 2.2 34.2 1.0 O B:HOH217 2.3 27.7 1.0 O B:HOH218 2.4 27.1 1.0 O A:HOH209 2.7 32.1 1.0 CD2 A:HIS114 3.1 34.0 1.0 CE1 A:HIS114 3.2 33.1 1.0 ND1 A:HIS114 4.3 34.1 1.0 CG A:HIS114 4.3 33.9 1.0 NH2 B:ARG195 4.3 50.5 1.0 CG A:ARG98 4.5 39.1 1.0 O A:ALA97 4.8 40.3 1.0

Zinc binding site 2 out of 19 in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae


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 An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn14 b:61.1 occ:0.80 OE2 A:GLU156 2.2 42.4 1.0 O A:HOH226 2.4 41.2 1.0 CD A:GLU156 3.2 42.7 1.0 OE1 A:GLU156 3.6 43.9 1.0 CG A:GLU156 4.4 42.4 1.0

Zinc binding site 3 out of 19 in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae


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 An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn6 b:34.7 occ:1.00 OE2 C:GLU149 1.9 45.6 1.0 O B:HOH216 2.0 24.8 1.0 ND1 B:HIS189 2.1 32.4 1.0 OD2 B:ASP66 2.2 38.9 1.0 CD C:GLU149 2.6 45.0 1.0 OE1 C:GLU149 2.7 47.5 1.0 OD1 B:ASP66 2.7 38.4 1.0 CG B:ASP66 2.8 37.7 1.0 CG B:HIS189 3.0 32.2 1.0 CE1 B:HIS189 3.1 31.2 1.0 CB B:HIS189 3.3 31.8 1.0 NZ C:LYS68 3.8 35.4 1.0 CG C:GLU149 4.1 42.8 1.0 NE2 B:HIS189 4.1 31.4 1.0 CD2 B:HIS189 4.2 32.1 1.0 CB B:ASP66 4.3 36.5 1.0 O B:HIS189 4.7 32.9 1.0 CA B:HIS189 4.7 32.5 1.0 C B:HIS189 4.9 33.4 1.0 CB C:GLU149 4.9 41.0 1.0

Zinc binding site 4 out of 19 in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae


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 An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8 b:65.1 occ:0.90 ND1 B:HIS114 2.3 32.9 1.0 O B:HIS114 2.4 33.0 1.0 CG B:HIS114 3.1 31.7 1.0 CB B:HIS114 3.3 30.3 1.0 C B:HIS114 3.4 32.2 1.0 CE1 B:HIS114 3.4 32.9 1.0 CA B:HIS114 3.8 31.1 1.0 O B:ALA97 3.8 36.3 1.0 CD2 B:HIS114 4.3 32.3 1.0 NE2 B:HIS114 4.4 33.0 1.0 N B:GLY115 4.5 34.3 1.0 CA B:GLY115 5.0 35.9 1.0

Zinc binding site 5 out of 19 in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae


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 An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn15 b:71.9 occ:0.90 O B:HOH220 2.8 36.7 1.0 OE2 B:GLU116 2.9 41.7 1.0 O B:HOH221 3.4 50.0 1.0 CD B:GLU116 3.8 41.6 1.0 OE1 B:GLU116 4.0 41.8 1.0 NH2 B:ARG160 4.3 41.2 1.0 O B:GLY115 4.8 37.2 1.0 CA B:GLU116 4.9 37.3 1.0

Zinc binding site 6 out of 19 in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2 b:33.0 occ:1.00 OD1 C:ASP66 2.0 33.5 1.0 OE1 B:GLU149 2.0 41.5 1.0 ND1 C:HIS189 2.2 40.8 1.0 CG C:ASP66 2.8 35.7 1.0 CD B:GLU149 2.8 40.2 1.0 OD2 C:ASP66 2.9 39.6 1.0 OE2 B:GLU149 2.9 41.8 1.0 CG C:HIS189 3.1 38.3 1.0 CE1 C:HIS189 3.2 40.8 1.0 CB C:HIS189 3.3 36.3 1.0 CE B:LYS68 3.9 40.2 1.0 CD2 C:HIS189 4.1 39.7 1.0 NE2 C:HIS189 4.2 41.4 1.0 CG B:GLU149 4.2 40.0 1.0 CB C:ASP66 4.2 32.7 1.0 CA C:HIS189 4.8 34.5 1.0 CD B:LYS68 4.8 39.1 1.0 O C:HIS189 5.0 35.0 1.0 NZ B:LYS68 5.0 39.8 1.0

Zinc binding site 7 out of 19 in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn16 b:68.9 occ:0.70 OD2 C:ASP94 2.3 52.6 1.0 CG C:ASP94 3.0 51.9 1.0 OD1 C:ASP94 3.2 52.3 1.0 OE1 C:GLU93 4.3 53.9 1.0 CB C:ASP94 4.4 51.0 1.0 CG C:GLU93 4.5 52.6 1.0 CD C:GLU93 4.6 53.5 1.0

Zinc binding site 8 out of 19 in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1 b:29.0 occ:1.00 OE1 E:GLU149 1.9 42.7 1.0 OD1 D:ASP66 2.0 39.4 1.0 ND1 D:HIS189 2.0 35.9 1.0 CD E:GLU149 2.6 42.5 1.0 OE2 E:GLU149 2.6 40.7 1.0 CG D:ASP66 2.8 39.3 1.0 OD2 D:ASP66 2.9 42.1 1.0 CE1 D:HIS189 3.0 35.7 1.0 CG D:HIS189 3.0 35.0 1.0 CB D:HIS189 3.4 33.1 1.0 O D:HOH220 3.8 28.2 1.0 CG E:GLU149 4.1 41.9 1.0 NE2 D:HIS189 4.1 36.6 1.0 CD2 D:HIS189 4.1 35.4 1.0 CB D:ASP66 4.3 36.9 1.0 O D:HOH212 4.3 18.6 1.0 CD E:LYS68 4.5 37.0 1.0 CE E:LYS68 4.7 36.3 1.0 NZ E:LYS68 4.8 36.5 1.0 CA D:HIS189 4.8 33.1 1.0 O D:HIS189 4.9 30.6 1.0 CB E:GLU149 5.0 42.6 1.0

Zinc binding site 9 out of 19 in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn13 b:65.9 occ:0.90 O D:HOH223 1.9 36.0 1.0 ND1 D:HIS114 2.3 39.1 1.0 O D:HIS114 2.3 39.5 1.0 O D:HOH221 2.7 40.0 1.0 CE1 D:HIS114 3.1 39.9 1.0 CG D:HIS114 3.3 38.8 1.0 C D:HIS114 3.4 38.4 1.0 CB D:HIS114 3.6 37.5 1.0 OE1 D:GLU116 3.8 46.0 1.0 O D:ALA97 4.0 34.9 1.0 CA D:HIS114 4.1 37.9 1.0 NE2 D:HIS114 4.3 40.1 1.0 CD2 D:HIS114 4.4 38.4 1.0 N D:GLY115 4.4 38.2 1.0 CA D:GLY115 4.6 38.6 1.0 N D:GLU116 4.9 38.9 1.0

Zinc binding site 10 out of 19 in the Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn17 b:59.5 occ:0.80 OE2 D:GLU159 2.3 41.3 1.0 CD D:GLU159 3.1 42.2 1.0 OE1 D:GLU159 3.6 42.9 1.0 CG D:GLU159 4.2 41.1 1.0 CB D:GLU159 5.0 38.6 1.0

K.Tan, C.Hatzos, J.Abdullah, A.Joachimiak. The Structure of An Extracellular Domain of Arabinofuranosyltransferase From Corynebacterium Diphtheriae. To Be Published.