Zinc in PDB 4jlw: Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa

The structure of Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa, PDB code: 4jlw was solved by S.Chen, Y.P.Liao, D.L.Wang, S.Wang, J.F.Ding, Y.M.Wang, L.J.Cai, X.Y.Ran, H.X.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.226, 98.305, 99.623, 90.00, 91.29, 90.00
R / Rfree (%)	20.9 / 25.9

The binding sites of Zinc atom in the Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa (pdb code 4jlw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa, PDB code: 4jlw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa


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 Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.4 occ:1.00 SG A:CYS104 2.3 22.5 1.0 SG A:CYS101 2.3 23.3 1.0 SG A:CYS112 2.3 22.1 1.0 SG A:CYS98 2.4 24.3 1.0 CB A:CYS112 3.3 20.4 1.0 CB A:CYS104 3.3 21.7 1.0 CB A:CYS98 3.4 23.3 1.0 N A:CYS98 3.4 21.2 1.0 CB A:CYS101 3.4 23.6 1.0 CA A:CYS112 3.7 19.4 1.0 CA A:CYS98 3.8 21.5 1.0 N A:LEU113 3.8 20.1 1.0 N A:GLY99 3.9 21.0 1.0 OG1 A:THR114 3.9 20.8 1.0 N A:CYS101 3.9 21.8 1.0 C A:CYS112 4.2 19.9 1.0 CA A:CYS101 4.2 22.8 1.0 C A:CYS98 4.3 21.5 1.0 N A:CYS104 4.4 21.0 1.0 N A:THR114 4.4 20.4 1.0 CA A:CYS104 4.4 20.9 1.0 N A:HIS100 4.5 20.6 1.0 C A:ALA97 4.5 20.2 1.0 OG1 A:THR103 4.7 20.6 1.0 CA A:ALA97 4.8 20.2 1.0 C A:CYS101 4.8 23.0 1.0 CB A:THR114 4.9 21.0 1.0 CG2 A:THR114 4.9 21.0 1.0 CA A:LEU113 4.9 20.8 1.0 O A:CYS101 4.9 22.6 1.0 CA A:GLY99 5.0 20.3 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa


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 Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:41.6 occ:1.00 OD1 A:ASP170 2.0 33.1 1.0 NE2 A:HIS68 2.0 32.8 1.0 SG A:CYS47 2.3 36.9 1.0 CE1 A:HIS68 2.3 34.2 1.0 CB A:CYS47 3.0 33.9 1.0 O A:HOH501 3.1 33.6 1.0 CG A:ASP170 3.2 27.5 1.0 CD2 A:HIS68 3.3 29.0 1.0 OG A:SER49 3.5 31.4 1.0 C5N A:NAD403 3.6 47.4 1.0 ND1 A:HIS68 3.6 30.9 1.0 CB A:SER49 3.7 30.4 1.0 OD2 A:ASP170 3.8 25.8 1.0 CG A:HIS68 4.1 28.9 1.0 C4N A:NAD403 4.2 46.3 1.0 C6N A:NAD403 4.2 47.1 1.0 CB A:ASP170 4.3 26.0 1.0 CD A:GLU69 4.3 29.4 1.0 OE1 A:GLU69 4.3 31.5 1.0 CG A:GLU69 4.4 27.2 1.0 CA A:CYS47 4.5 32.2 1.0 N A:SER49 4.6 29.3 1.0 CE1 A:TYR126 4.7 28.3 1.0 CA A:SER49 4.8 30.0 1.0 OE2 A:GLU69 4.8 30.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa


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 Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:23.5 occ:1.00 SG B:CYS101 2.3 23.7 1.0 SG B:CYS98 2.3 23.6 1.0 SG B:CYS104 2.3 25.6 1.0 SG B:CYS112 2.3 23.4 1.0 CB B:CYS98 3.2 22.6 1.0 N B:CYS98 3.2 20.1 1.0 CB B:CYS112 3.4 21.7 1.0 CB B:CYS104 3.4 23.9 1.0 CB B:CYS101 3.5 24.3 1.0 CA B:CYS98 3.6 20.9 1.0 N B:GLY99 3.7 21.0 1.0 N B:CYS101 3.8 22.8 1.0 CA B:CYS112 3.8 21.1 1.0 OG1 B:THR114 3.9 22.1 1.0 N B:LEU113 3.9 21.5 1.0 C B:CYS98 4.1 20.9 1.0 CA B:CYS101 4.2 23.7 1.0 C B:CYS112 4.3 21.1 1.0 N B:HIS100 4.4 21.5 1.0 C B:ALA97 4.4 19.5 1.0 N B:THR114 4.5 21.5 1.0 N B:CYS104 4.5 22.6 1.0 CA B:CYS104 4.6 22.8 1.0 CA B:ALA97 4.8 18.8 1.0 CA B:GLY99 4.8 21.1 1.0 CB B:THR114 4.9 22.6 1.0 CG2 B:THR114 4.9 23.2 1.0 C B:CYS101 4.9 24.2 1.0 C B:HIS100 4.9 22.9 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa


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 Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:34.3 occ:1.00 OD1 B:ASP170 2.0 30.6 1.0 NE2 B:HIS68 2.1 25.8 1.0 SG B:CYS47 2.3 27.5 1.0 CG B:ASP170 2.9 26.7 1.0 CD2 B:HIS68 3.0 22.5 1.0 O B:HOH501 3.1 35.6 1.0 CE1 B:HIS68 3.1 23.9 1.0 OD2 B:ASP170 3.2 25.8 1.0 CB B:CYS47 3.4 25.3 1.0 C5N B:NAD403 3.5 36.7 1.0 OG B:SER49 3.7 23.2 1.0 CB B:SER49 4.1 22.2 1.0 C4N B:NAD403 4.1 35.3 1.0 CB B:ASP170 4.1 25.5 1.0 CG B:HIS68 4.2 21.6 1.0 ND1 B:HIS68 4.2 22.4 1.0 C6N B:NAD403 4.4 34.0 1.0 CD B:GLU69 4.5 21.8 1.0 CG B:GLU69 4.6 21.4 1.0 OE1 B:GLU69 4.6 22.2 1.0 CE1 B:TYR126 4.8 25.1 1.0 CA B:CYS47 4.8 23.5 1.0 N B:SER49 4.9 22.9 1.0 OE2 B:GLU69 5.0 22.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa


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 Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:19.5 occ:1.00 SG C:CYS101 2.2 21.0 1.0 SG C:CYS98 2.3 21.2 1.0 SG C:CYS112 2.3 20.5 1.0 SG C:CYS104 2.4 19.9 1.0 CB C:CYS98 3.3 20.4 1.0 N C:CYS98 3.3 17.7 1.0 CB C:CYS112 3.3 19.1 1.0 CB C:CYS104 3.4 18.9 1.0 CB C:CYS101 3.5 22.0 1.0 CA C:CYS98 3.7 18.5 1.0 N C:GLY99 3.7 17.9 1.0 CA C:CYS112 3.7 18.4 1.0 N C:CYS101 3.9 20.7 1.0 N C:LEU113 3.9 19.2 1.0 C C:CYS98 4.1 18.5 1.0 OG1 C:THR114 4.2 21.0 1.0 C C:CYS112 4.2 19.0 1.0 CA C:CYS101 4.3 21.4 1.0 N C:CYS104 4.3 18.4 1.0 N C:HIS100 4.4 19.9 1.0 CA C:CYS104 4.4 18.1 1.0 C C:ALA97 4.5 16.7 1.0 N C:THR114 4.5 20.7 1.0 CA C:ALA97 4.8 16.2 1.0 CA C:GLY99 4.8 18.3 1.0 CG2 C:THR114 4.8 22.1 1.0 OG1 C:THR103 5.0 19.4 1.0 C C:CYS101 5.0 20.8 1.0 C C:HIS100 5.0 21.2 1.0 CA C:LEU113 5.0 20.3 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa


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 Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:37.7 occ:1.00 OD1 C:ASP170 1.9 30.8 1.0 NE2 C:HIS68 2.1 28.1 1.0 SG C:CYS47 2.3 31.6 1.0 CG C:ASP170 3.0 25.9 1.0 CE1 C:HIS68 3.1 25.1 1.0 CD2 C:HIS68 3.1 24.3 1.0 CB C:CYS47 3.1 26.8 1.0 O C:HOH501 3.4 33.7 1.0 OD2 C:ASP170 3.4 24.2 1.0 C5N C:NAD403 3.5 32.4 1.0 OG C:SER49 4.0 20.8 1.0 CB C:SER49 4.1 20.4 1.0 CB C:ASP170 4.2 23.8 1.0 C4N C:NAD403 4.2 32.2 1.0 ND1 C:HIS68 4.2 24.2 1.0 CG C:HIS68 4.3 23.2 1.0 C6N C:NAD403 4.4 31.1 1.0 OE1 C:GLU69 4.5 27.2 1.0 CD C:GLU69 4.5 26.1 1.0 CA C:CYS47 4.5 25.1 1.0 CG C:GLU69 4.5 24.5 1.0 N C:SER49 4.8 22.1 1.0 OE2 C:GLU69 5.0 26.5 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa


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 Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:19.7 occ:1.00 SG D:CYS101 2.3 19.9 1.0 SG D:CYS104 2.3 19.9 1.0 SG D:CYS112 2.4 22.4 1.0 SG D:CYS98 2.4 22.2 1.0 CB D:CYS98 3.3 20.8 1.0 N D:CYS98 3.4 18.7 1.0 CB D:CYS112 3.4 19.3 1.0 CB D:CYS104 3.4 19.0 1.0 CB D:CYS101 3.5 20.5 1.0 CA D:CYS112 3.7 17.8 1.0 CA D:CYS98 3.7 19.1 1.0 N D:CYS101 3.8 19.7 1.0 N D:GLY99 3.9 19.1 1.0 N D:LEU113 3.9 17.9 1.0 OG1 D:THR114 4.0 18.8 1.0 CA D:CYS101 4.2 20.3 1.0 C D:CYS112 4.2 17.9 1.0 C D:CYS98 4.2 19.3 1.0 N D:CYS104 4.4 18.4 1.0 N D:THR114 4.4 18.3 1.0 CA D:CYS104 4.5 18.1 1.0 N D:HIS100 4.5 18.7 1.0 C D:ALA97 4.5 18.0 1.0 OG1 D:THR103 4.7 17.7 1.0 CA D:ALA97 4.8 17.8 1.0 C D:CYS101 4.8 20.5 1.0 O D:CYS101 4.9 20.0 1.0 CB D:THR114 5.0 19.0 1.0 C D:HIS100 5.0 19.7 1.0 CA D:LEU113 5.0 18.4 1.0 CA D:GLY99 5.0 18.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa


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 Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:41.4 occ:1.00 OD1 D:ASP170 2.0 30.6 1.0 NE2 D:HIS68 2.1 31.2 1.0 SG D:CYS47 2.2 30.5 1.0 O D:HOH501 2.9 32.1 1.0 CE1 D:HIS68 3.0 30.1 1.0 CG D:ASP170 3.0 25.9 1.0 CB D:CYS47 3.1 29.9 1.0 CD2 D:HIS68 3.1 27.2 1.0 C5N D:NAD403 3.3 34.0 1.0 OD2 D:ASP170 3.6 25.7 1.0 OG D:SER49 3.7 29.9 1.0 CB D:SER49 4.0 27.9 1.0 C4N D:NAD403 4.0 33.8 1.0 C6N D:NAD403 4.1 34.6 1.0 ND1 D:HIS68 4.2 28.1 1.0 CB D:ASP170 4.2 23.5 1.0 OE1 D:GLU69 4.2 25.7 1.0 CD D:GLU69 4.3 23.9 1.0 CG D:HIS68 4.3 26.8 1.0 CG D:GLU69 4.4 23.2 1.0 CA D:CYS47 4.5 27.8 1.0 OE2 D:GLU69 4.7 24.4 1.0 N D:SER49 4.8 28.6 1.0

Y.P.Liao, S.Chen, D.L.Wang, W.Zhang, S.Wang, J.F.Ding, Y.M.Wang, L.J.Cai, X.Y.Ran, X.Wang, H.X.Zhu. Structure of Formaldehyde Dehydrogenase From Pseudomonas Aeruginosa: the Binary Complex with the Cofactor Nad+. Acta Crystallogr.,Sect.F V. 69 967 2013.
ISSN: ESSN 1744-3091
PubMed: 23989142
DOI: 10.1107/S174430911302160X