Zinc in PDB 4gbd: Crystal Structure of Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin

The structure of Crystal Structure of Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin, PDB code: 4gbd was solved by M.Ho, R.Guan, S.C.Almo, V.L.Schramm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.10 / 1.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.814, 120.310, 77.298, 90.00, 108.00, 90.00
R / Rfree (%)	19 / 23.1

The binding sites of Zinc atom in the Crystal Structure of Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin (pdb code 4gbd). 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 Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin, PDB code: 4gbd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin


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 Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:40.1 occ:1.00 NE2 A:HIS72 1.8 28.9 1.0 NE2 A:HIS74 2.1 38.2 1.0 NE2 A:HIS221 2.1 41.6 1.0 O8 A:MCF501 2.2 38.6 1.0 OD1 A:ASP309 2.3 35.3 1.0 CE1 A:HIS72 2.7 31.8 1.0 CD2 A:HIS74 2.9 38.8 1.0 CD2 A:HIS72 2.9 29.7 1.0 CD2 A:HIS221 3.1 38.2 1.0 CE1 A:HIS221 3.1 40.3 1.0 CE1 A:HIS74 3.2 37.2 1.0 CG A:ASP309 3.2 35.4 1.0 C9 A:MCF501 3.3 40.1 1.0 C8 A:MCF501 3.3 35.2 1.0 OD2 A:ASP309 3.5 31.4 1.0 N1 A:MCF501 3.6 42.9 1.0 C10 A:MCF501 3.8 39.3 1.0 ND1 A:HIS72 3.9 31.6 1.0 CG A:HIS72 4.0 32.8 1.0 NE2 A:HIS258 4.2 45.0 1.0 CG A:HIS74 4.2 39.1 1.0 C2 A:MCF501 4.2 41.0 1.0 ND1 A:HIS74 4.2 39.5 1.0 ND1 A:HIS221 4.2 36.4 1.0 CG A:HIS221 4.3 42.4 1.0 N3 A:MCF501 4.4 42.1 1.0 N4 A:MCF501 4.4 41.9 1.0 N6 A:MCF501 4.5 37.4 1.0 CB A:ASP309 4.5 29.2 1.0 C7 A:MCF501 4.5 36.7 1.0 O A:HOH614 4.6 34.4 1.0 CE1 A:HIS258 4.7 39.3 1.0 C5 A:MCF501 4.7 41.1 1.0 CA A:ASP309 4.7 31.1 1.0 CG1 A:VAL257 4.9 35.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin


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 Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:41.8 occ:1.00 O A:HOH726 2.0 37.7 1.0 O A:HOH724 2.0 41.7 1.0 OE1 A:GLU282 2.1 34.4 1.0 OD1 A:ASP316 2.2 33.8 1.0 OD1 A:ASN314 2.3 29.8 1.0 O A:HOH725 2.3 37.7 1.0 CG A:ASP316 3.0 34.1 1.0 CD A:GLU282 3.1 37.1 1.0 CG A:ASN314 3.1 31.2 1.0 ND2 A:ASN314 3.3 29.2 1.0 OD2 A:ASP316 3.3 42.7 1.0 OE2 A:GLU282 3.4 33.3 1.0 O A:HOH643 3.7 46.2 1.0 OE1 A:GLU322 3.8 42.1 1.0 O A:ASP316 4.1 34.6 1.0 O A:ASP318 4.3 36.7 1.0 N A:ASP316 4.3 36.0 1.0 CB A:ASP316 4.4 30.3 1.0 CG A:GLU282 4.4 28.5 1.0 CB A:ASP318 4.5 32.4 1.0 C A:ASP316 4.5 36.8 1.0 CB A:ASN314 4.5 31.8 1.0 CA A:ASP316 4.6 36.3 1.0 N A:ASP318 4.6 36.6 1.0 CB A:GLU282 4.6 30.0 1.0 C A:ASN314 4.6 33.1 1.0 O A:ASN314 4.6 34.9 1.0 N A:ASN315 4.9 33.9 1.0 CD A:GLU322 5.0 38.1 1.0 CA A:ASP318 5.0 34.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin


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 Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:41.7 occ:1.00 NE2 B:HIS74 2.1 31.1 1.0 NE2 B:HIS72 2.1 33.8 1.0 NE2 B:HIS221 2.2 39.2 1.0 OD1 B:ASP309 2.3 37.1 1.0 O8 B:MCF501 2.3 43.4 1.0 CE1 B:HIS72 3.0 31.4 1.0 CD2 B:HIS74 3.1 35.4 1.0 CE1 B:HIS74 3.1 35.0 1.0 CD2 B:HIS221 3.1 32.8 1.0 CG B:ASP309 3.2 35.6 1.0 CD2 B:HIS72 3.2 35.4 1.0 C9 B:MCF501 3.3 37.2 1.0 CE1 B:HIS221 3.3 33.9 1.0 C8 B:MCF501 3.3 38.5 1.0 OD2 B:ASP309 3.4 37.6 1.0 N1 B:MCF501 3.5 38.2 1.0 C10 B:MCF501 3.9 35.0 1.0 NE2 B:HIS258 4.1 35.9 1.0 ND1 B:HIS72 4.2 36.1 1.0 C2 B:MCF501 4.2 37.2 1.0 ND1 B:HIS74 4.2 31.0 1.0 CG B:HIS74 4.2 35.7 1.0 CG B:HIS72 4.3 34.6 1.0 CG B:HIS221 4.3 36.1 1.0 N3 B:MCF501 4.4 36.8 1.0 ND1 B:HIS221 4.4 37.5 1.0 N4 B:MCF501 4.5 36.0 1.0 N6 B:MCF501 4.5 40.5 1.0 CB B:ASP309 4.5 34.1 1.0 C7 B:MCF501 4.6 36.6 1.0 O B:HOH610 4.7 32.3 1.0 CE1 B:HIS258 4.7 33.0 1.0 C5 B:MCF501 4.7 37.2 1.0 CA B:ASP309 4.8 34.5 1.0 CG1 B:VAL257 5.0 34.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin


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 Adenosine Deaminase From Pseudomonas Aeruginosa PAO1 with Bound Zn and Methylthio-Coformycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:48.3 occ:1.00 OE1 B:GLU282 2.1 40.8 1.0 OD1 B:ASN314 2.2 34.3 1.0 OD1 B:ASP316 2.2 35.7 1.0 O B:HOH715 2.3 37.6 1.0 O B:HOH716 2.3 46.8 1.0 O B:HOH714 2.3 50.5 1.0 CD B:GLU282 3.0 38.5 1.0 CG B:ASP316 3.0 39.6 1.0 CG B:ASN314 3.1 32.8 1.0 OE2 B:GLU282 3.3 37.0 1.0 ND2 B:ASN314 3.3 31.8 1.0 OD2 B:ASP316 3.3 43.6 1.0 OE1 B:GLU322 3.7 35.4 1.0 O B:HOH605 3.8 44.4 1.0 O B:ASP316 4.2 38.1 1.0 N B:ASP316 4.2 35.0 1.0 O B:ASP318 4.3 33.7 1.0 CG B:GLU282 4.3 34.8 1.0 CB B:ASP316 4.4 36.2 1.0 CB B:ASN314 4.5 33.1 1.0 C B:ASP316 4.5 35.9 1.0 CB B:ASP318 4.5 33.3 1.0 CB B:GLU282 4.6 32.7 1.0 CA B:ASP316 4.6 34.9 1.0 O B:ASN314 4.6 35.3 1.0 C B:ASN314 4.6 32.5 1.0 N B:ASP318 4.7 36.1 1.0 CD B:GLU322 4.8 34.2 1.0 N B:ASN315 4.9 30.5 1.0 N B:GLU322 5.0 29.9 1.0

R.Guan, M.C.Ho, R.F.Frohlich, P.C.Tyler, S.C.Almo, V.L.Schramm. Methylthioadenosine Deaminase in An Alternative Quorum Sensing Pathway in Pseudomonas Aeruginosa. Biochemistry V. 51 9094 2012.
ISSN: ISSN 0006-2960
PubMed: 23050701
DOI: 10.1021/BI301062Y