Zinc in PDB 2yvr: Crystal Structure of MS1043

The structure of Crystal Structure of MS1043, PDB code: 2yvr was solved by H.Wang, S.Kishishita, K.Murayama, C.Takemoto, T.Terada, M.Shirouzu, Riken Structural Genomics/Proteomics Initiative(Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.12 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	38.950, 38.950, 125.835, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.8

The binding sites of Zinc atom in the Crystal Structure of MS1043 (pdb code 2yvr). 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 MS1043, PDB code: 2yvr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of MS1043


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 MS1043 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:16.8 occ:1.00 ND1 A:HIS12 2.1 14.5 1.0 SG A:CYS32 2.3 24.7 1.0 SG A:CYS29 2.3 12.5 1.0 SG A:CYS9 2.4 16.7 1.0 CE1 A:HIS12 3.0 24.1 1.0 CG A:HIS12 3.2 15.6 1.0 CB A:CYS9 3.3 15.5 1.0 CB A:CYS32 3.4 16.9 1.0 CB A:CYS29 3.4 9.2 1.0 CB A:HIS12 3.6 16.3 1.0 N A:CYS32 3.7 17.4 1.0 CA A:CYS32 4.0 18.5 1.0 N A:HIS12 4.0 22.0 1.0 N A:CYS29 4.1 9.8 1.0 NE2 A:HIS12 4.1 17.1 1.0 CD2 A:HIS12 4.3 19.3 1.0 CA A:CYS29 4.3 10.8 1.0 CB A:VAL11 4.4 34.4 1.0 CA A:HIS12 4.5 18.6 1.0 CB A:ASP31 4.7 12.4 1.0 C A:ASP31 4.7 18.2 1.0 CA A:CYS9 4.7 15.4 1.0 C A:CYS29 4.8 12.2 1.0 O A:CYS29 4.8 9.9 1.0 C A:VAL11 4.9 31.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of MS1043


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 MS1043 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:20.3 occ:1.00 ND1 A:HIS37 2.1 19.7 1.0 ND1 A:HIS40 2.2 18.9 1.0 SG A:CYS21 2.2 18.9 1.0 SG A:CYS24 2.4 22.7 1.0 CE1 A:HIS37 3.0 25.6 1.0 CE1 A:HIS40 3.1 23.3 1.0 CG A:HIS37 3.1 20.5 1.0 CG A:HIS40 3.2 17.5 1.0 CB A:CYS24 3.3 25.8 1.0 CB A:CYS21 3.4 12.9 1.0 CB A:HIS37 3.5 16.6 1.0 CB A:HIS40 3.6 18.6 1.0 N A:CYS24 3.9 21.3 1.0 NE2 A:HIS37 4.2 19.5 1.0 CB A:SER23 4.2 27.8 1.0 CA A:CYS24 4.2 21.2 1.0 NE2 A:HIS40 4.2 18.8 1.0 CD2 A:HIS37 4.2 24.3 1.0 CA A:HIS37 4.2 17.9 1.0 CD2 A:HIS40 4.3 17.0 1.0 C A:SER23 4.6 32.6 1.0 O A:HOH1032 4.6 27.8 1.0 CA A:CYS21 4.7 18.7 1.0 OE1 A:GLN33 4.8 17.5 1.0 CA A:SER23 4.8 26.4 1.0 OG1 A:THR26 4.8 40.5 1.0 O A:HIS37 4.9 18.8 1.0 N A:SER23 4.9 27.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of MS1043


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 MS1043 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:13.8 occ:1.00 ND1 B:HIS12 2.0 10.3 1.0 SG B:CYS29 2.3 10.9 1.0 SG B:CYS32 2.4 15.7 1.0 SG B:CYS9 2.4 14.5 1.0 CE1 B:HIS12 2.9 13.8 1.0 CG B:HIS12 3.1 13.4 1.0 CB B:CYS9 3.3 17.1 1.0 CB B:CYS32 3.5 15.3 1.0 CB B:CYS29 3.5 9.0 1.0 CB B:HIS12 3.6 13.0 1.0 N B:CYS32 3.8 11.1 1.0 N B:CYS29 3.9 10.6 1.0 N B:HIS12 3.9 15.5 1.0 CA B:CYS32 4.0 11.4 1.0 NE2 B:HIS12 4.0 16.1 1.0 CD2 B:HIS12 4.2 15.3 1.0 CA B:CYS29 4.2 12.4 1.0 CA B:HIS12 4.4 12.8 1.0 CB B:VAL11 4.5 21.4 1.0 C B:CYS29 4.7 10.8 1.0 CA B:CYS9 4.8 13.0 1.0 O B:CYS29 4.8 9.9 1.0 C B:ASP31 4.8 10.6 1.0 CB B:ASP31 4.8 12.6 1.0 C B:VAL11 4.9 20.3 1.0 O B:HOH1027 4.9 26.6 1.0 CG1 B:VAL11 5.0 21.7 1.0 O B:HIS12 5.0 12.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of MS1043


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 MS1043 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:18.0 occ:1.00 ND1 B:HIS40 2.0 15.5 1.0 ND1 B:HIS37 2.1 16.8 1.0 SG B:CYS21 2.3 15.6 1.0 SG B:CYS24 2.4 19.5 1.0 CE1 B:HIS40 2.9 21.3 1.0 CE1 B:HIS37 2.9 18.2 1.0 CG B:HIS40 3.1 21.9 1.0 CG B:HIS37 3.2 18.8 1.0 CB B:CYS24 3.3 20.5 1.0 CB B:CYS21 3.4 12.1 1.0 CB B:HIS40 3.5 18.0 1.0 CB B:HIS37 3.6 12.0 1.0 N B:CYS24 4.0 19.4 1.0 NE2 B:HIS40 4.1 23.0 1.0 NE2 B:HIS37 4.1 14.5 1.0 CD2 B:HIS40 4.2 26.6 1.0 CB B:SER23 4.2 24.2 1.0 CD2 B:HIS37 4.3 12.6 1.0 CA B:HIS37 4.3 12.4 1.0 CA B:CYS24 4.3 18.3 1.0 C B:SER23 4.6 25.4 1.0 O B:HOH1037 4.7 53.6 1.0 CA B:CYS21 4.8 14.1 1.0 CA B:SER23 4.9 23.9 1.0 O B:HIS37 4.9 16.5 1.0 O B:HOH1024 4.9 32.8 1.0 NE2 B:GLN33 4.9 11.4 1.0 N B:SER23 5.0 21.7 1.0

H.Wang, S.Kishishita, C.Takemoto, T.Terada, M.Shirouzu, S.Yokoyama. Crystal Structure of MS1043 To Be Published.