Zinc in PDB 3m6i: L-Arabinitol 4-Dehydrogenase

All present enzymatic activity of L-Arabinitol 4-Dehydrogenase:
1.1.1.12;

The structure of L-Arabinitol 4-Dehydrogenase, PDB code: 3m6i was solved by B.Bae, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.60
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	134.520, 134.520, 224.340, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 26.6

The binding sites of Zinc atom in the L-Arabinitol 4-Dehydrogenase (pdb code 3m6i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the L-Arabinitol 4-Dehydrogenase, PDB code: 3m6i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the L-Arabinitol 4-Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of L-Arabinitol 4-Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:91.3 occ:1.00 SG A:CYS53 2.1 50.8 1.0 NE2 A:HIS78 2.5 43.5 1.0 CB A:CYS53 2.7 50.1 1.0 O A:HOH412 2.9 52.1 1.0 CE1 A:HIS78 3.3 42.3 1.0 OE2 A:GLU79 3.4 50.5 1.0 CD2 A:HIS78 3.5 41.1 1.0 C5N A:NAD501 3.5 40.8 1.0 O A:HOH385 3.8 60.0 1.0 OE1 A:GLU163 4.0 45.5 1.0 CB A:SER55 4.1 51.2 1.0 C6N A:NAD501 4.1 39.8 1.0 CA A:CYS53 4.1 49.8 1.0 C4N A:NAD501 4.2 41.1 1.0 OE2 A:GLU163 4.3 45.8 1.0 CD A:GLU79 4.3 46.6 1.0 CG A:GLU79 4.4 43.4 1.0 ND1 A:HIS78 4.5 42.1 1.0 OG A:SER55 4.5 53.8 1.0 CD A:GLU163 4.6 44.9 1.0 CG A:HIS78 4.6 41.2 1.0 C A:CYS53 4.9 50.4 1.0 O A:HOH369 4.9 44.2 1.0 N A:GLY54 5.0 50.9 1.0

Zinc binding site 2 out of 4 in the L-Arabinitol 4-Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of L-Arabinitol 4-Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:57.0 occ:1.00 SG A:CYS122 2.3 54.0 1.0 SG A:CYS108 2.4 55.7 1.0 SG A:CYS111 2.4 54.6 1.0 SG A:CYS114 2.5 57.6 1.0 CB A:CYS122 3.2 56.5 1.0 CB A:CYS114 3.4 58.4 1.0 CB A:CYS108 3.4 54.8 1.0 CB A:CYS111 3.5 58.4 1.0 N A:CYS108 3.6 53.7 1.0 N A:CYS111 3.7 59.4 1.0 CA A:CYS122 3.7 56.5 1.0 N A:ASN109 3.8 57.1 1.0 CA A:CYS108 3.9 54.8 1.0 N A:GLU123 4.0 58.7 1.0 CA A:CYS111 4.1 58.7 1.0 C A:CYS108 4.1 55.7 1.0 N A:ALA110 4.2 59.4 1.0 C A:CYS122 4.3 57.5 1.0 CA A:CYS114 4.5 58.4 1.0 N A:CYS114 4.5 58.8 1.0 O A:CYS111 4.7 59.8 1.0 N A:ARG124 4.7 60.0 1.0 C A:CYS111 4.7 59.7 1.0 CA A:ASN109 4.8 58.4 1.0 C A:ILE107 4.8 53.1 1.0 C A:ALA110 4.8 59.6 1.0 C A:ASN109 5.0 59.0 1.0

Zinc binding site 3 out of 4 in the L-Arabinitol 4-Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of L-Arabinitol 4-Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:0.1 occ:1.00 NE2 B:HIS78 2.4 56.2 1.0 SG B:CYS53 2.9 68.3 1.0 OE1 B:GLU163 3.1 63.1 1.0 CD2 B:HIS78 3.2 57.5 1.0 CE1 B:HIS78 3.4 56.0 1.0 OE2 B:GLU79 3.5 64.0 1.0 OE2 B:GLU163 3.5 65.8 1.0 CD B:GLU163 3.7 63.4 1.0 CB B:CYS53 3.7 68.3 1.0 CD B:GLU79 3.9 61.8 1.0 CG B:GLU79 4.1 59.5 1.0 C5N B:NAD501 4.2 61.9 1.0 CG B:HIS78 4.4 57.7 1.0 ND1 B:HIS78 4.5 56.3 1.0 C4N B:NAD501 4.8 62.9 1.0 OE1 B:GLU79 4.8 63.6 1.0

Zinc binding site 4 out of 4 in the L-Arabinitol 4-Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of L-Arabinitol 4-Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:70.8 occ:1.00 SG B:CYS108 2.3 69.2 1.0 SG B:CYS122 2.4 71.4 1.0 SG B:CYS114 2.5 71.1 1.0 SG B:CYS111 2.6 72.6 1.0 CB B:CYS122 3.3 71.7 1.0 CB B:CYS108 3.4 71.1 1.0 CB B:CYS114 3.4 69.8 1.0 CA B:CYS122 3.6 72.1 1.0 CB B:CYS111 3.7 72.4 1.0 N B:CYS108 3.7 71.2 1.0 N B:ASN109 3.8 71.5 1.0 N B:CYS111 3.9 72.6 1.0 CA B:CYS108 3.9 71.0 1.0 N B:GLU123 4.0 73.3 1.0 C B:CYS122 4.2 72.8 1.0 C B:CYS108 4.3 71.1 1.0 N B:ALA110 4.3 73.0 1.0 CA B:CYS111 4.4 72.2 1.0 CA B:CYS114 4.5 70.0 1.0 N B:CYS114 4.5 69.9 1.0 N B:ARG124 4.7 74.9 1.0 CA B:ASN109 4.8 72.2 1.0 O B:CYS111 4.8 72.2 1.0 NH2 B:ARG124 4.8 83.6 1.0 N B:CYS122 4.9 71.7 1.0 C B:CYS111 4.9 72.3 1.0 C B:ILE107 4.9 71.7 1.0 C B:ASN109 5.0 72.8 1.0

B.Bae, R.P.Sullivan, H.Zhao, S.K.Nair. Structure and Engineering of L-Arabinitol 4-Dehydrogenase From Neurospora Crassa J.Mol.Biol. V. 402 230 2010.
ISSN: ISSN 0022-2836
PubMed: 20655316
DOI: 10.1016/J.JMB.2010.07.033