Zinc in PDB 3a44: Crystal Structure of Hypa in the Dimeric Form

The structure of Crystal Structure of Hypa in the Dimeric Form, PDB code: 3a44 was solved by S.Watanabe, T.Arai, R.Matsumi, H.Atomi, T.Imanaka, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.16 / 3.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.830, 97.975, 136.480, 90.00, 90.00, 90.00
R / Rfree (%)	29.2 / 33.7

The binding sites of Zinc atom in the Crystal Structure of Hypa in the Dimeric Form (pdb code 3a44). 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 Hypa in the Dimeric Form, PDB code: 3a44:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Hypa in the Dimeric Form


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 Hypa in the Dimeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn140 b:0.9 occ:1.00 SG A:CYS76 2.1 83.9 1.0 SG B:CYS110 2.2 90.2 1.0 SG A:CYS73 2.2 72.7 1.0 SG B:CYS113 2.3 72.7 1.0 OG B:SER115 2.5 0.1 1.0 CB A:CYS73 3.1 84.9 1.0 CB B:CYS110 3.2 91.3 1.0 CB A:CYS76 3.3 83.2 1.0 N B:CYS113 3.6 0.4 1.0 CB B:CYS113 3.7 0.9 1.0 CB B:SER115 3.9 0.5 1.0 N A:CYS76 4.0 98.2 1.0 CA B:CYS113 4.2 0.8 1.0 CA A:CYS76 4.2 91.4 1.0 CB A:TYR78 4.2 98.3 1.0 CB B:LYS112 4.3 87.8 1.0 O B:CYS113 4.5 0.5 1.0 CA A:CYS73 4.5 98.6 1.0 C B:CYS113 4.6 0.9 1.0 CA B:CYS110 4.6 95.0 1.0 C A:CYS76 4.7 98.6 1.0 N A:TYR78 4.7 0.2 1.0 C B:LYS112 4.7 0.2 1.0 CA B:SER115 4.8 0.2 1.0 CB A:ASN75 4.8 0.2 1.0 O B:CYS110 4.8 92.7 1.0 C B:CYS110 4.9 92.1 1.0 CA B:LYS112 4.9 0.2 1.0 N B:LYS112 4.9 0.7 1.0 C A:ASN75 4.9 0.1 1.0 N A:ASN77 5.0 0.8 1.0 CD2 A:TYR78 5.0 99.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Hypa in the Dimeric Form


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 Hypa in the Dimeric Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn140 b:0.3 occ:1.00 SG B:CYS76 1.7 0.7 1.0 SG B:CYS73 2.2 0.3 1.0 SG A:CYS110 2.2 0.3 1.0 SG A:CYS113 2.7 0.3 1.0 CB B:CYS73 2.9 0.5 1.0 CB A:CYS110 3.0 0.4 1.0 CB B:CYS76 3.3 0.7 1.0 CB A:LYS112 4.0 0.8 1.0 N B:CYS76 4.0 0.3 1.0 CB A:CYS113 4.1 0.5 1.0 CB A:SER115 4.1 0.9 1.0 N A:CYS113 4.2 0.3 1.0 CA B:CYS76 4.3 0.8 1.0 CA B:CYS73 4.4 0.0 1.0 CA A:CYS110 4.4 0.8 1.0 CB B:TYR78 4.5 0.1 1.0 OG A:SER115 4.5 0.5 1.0 CA A:LYS112 4.7 0.8 1.0 C A:CYS110 4.8 0.0 1.0 O A:CYS110 4.8 0.1 1.0 C A:LYS112 4.8 0.3 1.0 CA A:CYS113 4.8 0.8 1.0 N B:TYR78 4.8 0.7 1.0 N A:LYS112 4.9 0.9 1.0 N B:ASN77 4.9 0.8 1.0 C B:CYS73 5.0 0.8 1.0 C B:CYS76 5.0 0.1 1.0 C B:ASN75 5.0 0.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Hypa in the Dimeric Form


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 Hypa in the Dimeric Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn140 b:1.0 occ:1.00 SG C:CYS76 2.1 87.0 1.0 SG D:CYS110 2.2 89.9 1.0 SG D:CYS113 2.3 86.0 1.0 SG C:CYS73 2.4 96.8 1.0 CB D:CYS110 3.1 88.5 1.0 CB C:CYS73 3.2 0.2 1.0 CB C:CYS76 3.2 0.3 1.0 CB D:CYS113 3.6 97.6 1.0 N C:CYS76 3.8 0.0 1.0 N D:CYS113 4.0 0.9 1.0 CB D:SER115 4.0 0.9 1.0 CA C:CYS76 4.0 0.0 1.0 ND2 C:ASN75 4.3 0.0 1.0 CA D:CYS113 4.3 0.3 1.0 CB C:TYR78 4.4 0.4 1.0 C C:CYS76 4.5 0.5 1.0 CA D:CYS110 4.6 95.4 1.0 OG D:SER115 4.6 0.8 1.0 CB D:LYS112 4.6 0.1 1.0 CB C:ASN75 4.7 0.6 1.0 CA C:CYS73 4.7 0.4 1.0 C D:CYS113 4.7 0.4 1.0 C C:ASN75 4.9 0.1 1.0 N C:TYR78 4.9 0.9 1.0 O C:CYS76 5.0 0.5 1.0 N C:ASN77 5.0 0.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Hypa in the Dimeric Form


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 Hypa in the Dimeric Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn141 b:0.8 occ:1.00 SG D:CYS76 2.0 0.4 1.0 SG C:CYS110 2.1 0.9 1.0 SG D:CYS73 2.5 0.2 1.0 SG C:CYS113 2.5 0.3 1.0 CB D:CYS76 2.8 0.7 1.0 CB C:CYS110 2.9 0.8 1.0 CB D:CYS73 3.5 0.1 1.0 CB C:SER115 3.7 0.4 1.0 CB C:CYS113 3.7 0.2 1.0 OG C:SER115 3.9 0.2 1.0 N D:CYS76 4.0 0.9 1.0 CA D:CYS76 4.0 0.9 1.0 O C:CYS110 4.0 0.6 1.0 CA C:CYS110 4.3 0.5 1.0 N C:CYS113 4.3 1.0 1.0 C C:CYS110 4.5 0.6 1.0 ND2 D:ASN75 4.6 0.1 1.0 CA C:CYS113 4.6 0.5 1.0 CB C:LYS112 4.7 0.1 1.0 N C:GLY114 4.7 0.2 1.0 C D:ASN75 4.7 0.6 1.0 CB D:ASN75 4.9 0.5 1.0 CA C:SER115 4.9 0.6 1.0 N C:SER115 4.9 0.7 1.0 CA D:CYS73 5.0 1.0 1.0

S.Watanabe, T.Arai, R.Matsumi, H.Atomi, T.Imanaka, K.Miki. Crystal Structure of Hypa, A Nickel-Binding Metallochaperone For [Nife] Hydrogenase Maturation. J.Mol.Biol. V. 394 448 2009.
ISSN: ISSN 0022-2836
PubMed: 19769985
DOI: 10.1016/J.JMB.2009.09.030