Zinc in PDB 2dph: Crystal Structure of Formaldehyde Dismutase

All present enzymatic activity of Crystal Structure of Formaldehyde Dismutase:
1.2.99.4;

The structure of Crystal Structure of Formaldehyde Dismutase, PDB code: 2dph was solved by T.Hasegawa, A.Yamano, H.Yanase, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.92 / 2.27
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	90.229, 90.229, 226.689, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25

The binding sites of Zinc atom in the Crystal Structure of Formaldehyde Dismutase (pdb code 2dph). 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 Formaldehyde Dismutase, PDB code: 2dph:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Formaldehyde Dismutase


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 Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:31.1 occ:1.00 SG A:CYS110 2.3 27.3 1.0 SG A:CYS102 2.3 29.7 1.0 SG A:CYS99 2.3 29.1 1.0 SG A:CYS96 2.4 28.2 1.0 CB A:CYS102 3.3 29.5 1.0 CB A:CYS110 3.4 27.7 1.0 N A:CYS96 3.4 27.2 1.0 CB A:CYS99 3.4 28.7 1.0 CB A:CYS96 3.5 27.5 1.0 N A:GLY97 3.8 27.0 1.0 N A:CYS99 3.8 28.3 1.0 CA A:CYS110 3.8 27.7 1.0 CA A:CYS96 3.9 27.2 1.0 N A:GLU111 4.1 28.6 1.0 CA A:CYS99 4.2 28.7 1.0 CB A:ASN112 4.3 29.6 1.0 C A:CYS96 4.3 27.2 1.0 N A:ARG98 4.3 27.5 1.0 N A:ASN112 4.3 29.6 1.0 N A:CYS102 4.4 29.6 1.0 C A:CYS110 4.4 28.0 1.0 CA A:CYS102 4.4 29.5 1.0 C A:ALA95 4.5 27.0 1.0 CA A:ALA95 4.7 26.8 1.0 CA A:GLY97 4.7 27.2 1.0 C A:CYS99 4.8 28.8 1.0 O A:CYS99 4.9 28.7 1.0 C A:ARG98 4.9 28.1 1.0 CA A:ASN112 5.0 29.8 1.0 C A:GLY97 5.0 27.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Formaldehyde Dismutase


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 Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:37.5 occ:1.00 OD2 A:ASP169 1.9 24.4 1.0 NE2 A:HIS66 2.2 28.1 1.0 SG A:CYS45 2.3 29.3 1.0 C5N A:NAD1403 2.9 35.1 1.0 CD2 A:HIS66 3.1 27.1 1.0 CG A:ASP169 3.1 23.3 1.0 CE1 A:HIS66 3.2 28.6 1.0 CB A:CYS45 3.2 28.2 1.0 OD1 A:ASP169 3.6 25.6 1.0 C6N A:NAD1403 3.6 35.4 1.0 C4N A:NAD1403 3.8 34.9 1.0 OG A:SER47 3.8 27.8 1.0 CB A:SER47 4.0 26.5 1.0 CG A:HIS66 4.2 27.3 1.0 ND1 A:HIS66 4.3 28.4 1.0 CB A:ASP169 4.3 22.3 1.0 CG2 A:ILE170 4.3 21.2 1.0 OE2 A:GLU67 4.4 23.9 1.0 CD A:GLU67 4.5 24.5 1.0 CG A:GLU67 4.5 25.3 1.0 CA A:CYS45 4.7 27.8 1.0 CZ A:PHE126 4.8 37.2 1.0 N A:SER47 4.9 26.4 1.0 N1N A:NAD1403 4.9 34.4 1.0 O A:HOH1463 4.9 30.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Formaldehyde Dismutase


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 Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:29.6 occ:1.00 SG B:CYS102 2.3 26.7 1.0 SG B:CYS99 2.3 27.2 1.0 SG B:CYS96 2.4 27.8 1.0 SG B:CYS110 2.4 27.0 1.0 N B:CYS96 3.3 27.2 1.0 CB B:CYS110 3.4 27.0 1.0 CB B:CYS102 3.4 26.3 1.0 CB B:CYS99 3.4 27.3 1.0 CB B:CYS96 3.4 27.4 1.0 CA B:CYS110 3.7 26.8 1.0 CA B:CYS96 3.8 27.3 1.0 N B:GLY97 3.8 26.8 1.0 N B:CYS99 3.9 27.1 1.0 N B:GLU111 4.0 27.6 1.0 CB B:ASN112 4.2 29.0 1.0 CA B:CYS99 4.2 27.2 1.0 C B:CYS96 4.3 27.2 1.0 C B:CYS110 4.3 27.1 1.0 N B:ASN112 4.3 28.8 1.0 N B:CYS102 4.4 26.1 1.0 C B:ALA95 4.4 27.2 1.0 N B:ARG98 4.4 26.8 1.0 CA B:CYS102 4.5 26.3 1.0 CA B:ALA95 4.6 27.2 1.0 CB B:ALA95 4.9 27.0 1.0 CA B:GLY97 4.9 26.6 1.0 C B:CYS99 4.9 27.3 1.0 CA B:ASN112 4.9 29.0 1.0 O B:CYS99 4.9 27.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Formaldehyde Dismutase


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 Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:38.7 occ:1.00 OD2 B:ASP169 2.0 32.8 1.0 NE2 B:HIS66 2.1 34.7 1.0 SG B:CYS45 2.3 33.1 1.0 C5N B:NAD2403 2.8 41.9 1.0 CD2 B:HIS66 3.0 34.0 1.0 CE1 B:HIS66 3.1 34.8 1.0 CG B:ASP169 3.1 30.2 1.0 CB B:CYS45 3.2 32.4 1.0 C6N B:NAD2403 3.5 42.0 1.0 OD1 B:ASP169 3.6 31.6 1.0 OG B:SER47 3.7 33.4 1.0 C4N B:NAD2403 3.7 41.8 1.0 CB B:SER47 4.0 32.6 1.0 ND1 B:HIS66 4.2 33.9 1.0 CG B:HIS66 4.2 33.7 1.0 CG2 B:ILE170 4.3 27.3 1.0 CB B:ASP169 4.3 29.4 1.0 CG B:GLU67 4.5 30.9 1.0 OE2 B:GLU67 4.5 31.0 1.0 CD B:GLU67 4.5 30.4 1.0 CA B:CYS45 4.7 32.2 1.0 N1N B:NAD2403 4.8 41.5 1.0 N B:SER47 4.8 32.0 1.0 C3N B:NAD2403 4.9 42.3 1.0 O B:HOH2412 5.0 22.1 1.0

T.Hasegawa, A.Yamano, K.Miura, Y.Katsube, H.Yanase, N.Kato. The X-Ray Crystal Structure of Formaldehyde Dismutase at 2.3 A Resolution Acta Crystallogr.,Sect.A V. 58 C102 2002.
ISSN: ISSN 0108-7673