Zinc in PDB 3ddt: Crystal Structure of the B2 Box From MURF1 in Dimeric State

The structure of Crystal Structure of the B2 Box From MURF1 in Dimeric State, PDB code: 3ddt was solved by O.Mayans, M.Mrosek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.69 / 1.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	76.220, 76.220, 146.930, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 25.2

The binding sites of Zinc atom in the Crystal Structure of the B2 Box From MURF1 in Dimeric State (pdb code 3ddt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the B2 Box From MURF1 in Dimeric State, PDB code: 3ddt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the B2 Box From MURF1 in Dimeric State


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 the B2 Box From MURF1 in Dimeric State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn46 b:27.8 occ:1.00 ND1 A:HIS9 2.2 28.1 1.0 SG A:CYS26 2.2 25.1 1.0 SG A:CYS29 2.3 29.4 1.0 SG A:CYS6 2.4 27.8 1.0 CE1 A:HIS9 3.0 32.4 1.0 CG A:HIS9 3.3 30.5 1.0 CB A:CYS6 3.3 26.0 1.0 CB A:CYS26 3.4 20.2 1.0 CB A:CYS29 3.4 24.0 1.0 N A:CYS29 3.6 25.8 1.0 CB A:HIS9 3.7 29.3 1.0 N A:HIS9 4.0 30.9 1.0 CA A:CYS29 4.0 25.1 1.0 NE2 A:HIS9 4.2 31.3 1.0 CB A:GLU8 4.2 35.4 1.0 CA A:CYS26 4.2 20.1 1.0 N A:CYS26 4.2 17.8 1.0 CD2 A:HIS9 4.3 29.1 1.0 CA A:HIS9 4.5 32.4 1.0 O A:CYS26 4.5 18.6 1.0 C A:MET28 4.5 22.8 1.0 C A:CYS26 4.5 20.5 1.0 CB A:MET28 4.6 22.2 1.0 C A:GLU8 4.7 40.2 1.0 OG1 A:THR25 4.7 19.8 1.0 CG A:GLU8 4.7 45.0 1.0 CA A:CYS6 4.8 24.3 1.0 O A:HOH60 4.8 36.0 1.0 O A:HOH79 4.8 40.6 1.0 CA A:GLU8 4.9 34.8 1.0 N A:MET28 4.9 21.4 1.0 CA A:MET28 4.9 24.9 1.0 N A:GLU8 4.9 35.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the B2 Box From MURF1 in Dimeric State


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 the B2 Box From MURF1 in Dimeric State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn47 b:21.8 occ:1.00 ND1 A:HIS35 2.0 20.0 1.0 SG A:CYS18 2.2 20.6 1.0 SG A:CYS38 2.4 21.2 1.0 SG A:CYS21 2.4 24.5 1.0 CE1 A:HIS35 2.9 23.9 1.0 CG A:HIS35 3.1 20.7 1.0 CB A:CYS38 3.1 23.0 1.0 CB A:CYS21 3.3 22.7 1.0 CB A:CYS18 3.4 18.1 1.0 CB A:HIS35 3.6 22.2 1.0 N A:CYS21 3.9 24.1 1.0 NE2 A:HIS35 4.0 24.6 1.0 CA A:HIS35 4.1 20.0 1.0 CD2 A:HIS35 4.2 22.8 1.0 CA A:CYS21 4.2 22.3 1.0 CB A:THR20 4.4 29.1 1.0 CA A:CYS38 4.6 21.5 1.0 CA A:CYS18 4.7 17.0 1.0 C A:THR20 4.8 30.0 1.0 O A:HIS35 4.9 18.9 1.0 O A:HOH74 4.9 34.9 1.0 C A:HIS35 5.0 17.9 1.0 O A:ILE34 5.0 28.9 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the B2 Box From MURF1 in Dimeric State


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 the B2 Box From MURF1 in Dimeric State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn46 b:28.3 occ:1.00 ND1 B:HIS9 2.0 24.5 1.0 SG B:CYS26 2.3 24.8 1.0 SG B:CYS29 2.3 31.6 1.0 SG B:CYS6 2.4 27.5 1.0 CE1 B:HIS9 2.8 34.4 1.0 CG B:HIS9 3.1 25.7 1.0 CB B:CYS6 3.2 24.5 1.0 CB B:CYS26 3.5 21.2 1.0 CB B:CYS29 3.5 25.4 1.0 CB B:HIS9 3.6 24.6 1.0 N B:CYS29 3.6 27.4 1.0 N B:HIS9 3.9 30.1 1.0 CA B:CYS29 4.0 28.7 1.0 NE2 B:HIS9 4.0 29.0 1.0 CD2 B:HIS9 4.2 30.5 1.0 N B:CYS26 4.3 20.9 1.0 CA B:CYS26 4.3 23.7 1.0 CB B:GLU8 4.4 41.6 1.0 CA B:HIS9 4.4 29.7 1.0 O B:CYS26 4.4 22.6 1.0 C B:MET28 4.4 25.3 1.0 O B:HOH62 4.5 40.5 1.0 O B:HOH86 4.5 47.9 1.0 C B:CYS26 4.6 23.3 1.0 CB B:MET28 4.6 22.0 1.0 CA B:CYS6 4.7 23.9 1.0 OG1 B:THR25 4.8 22.5 1.0 C B:GLU8 4.8 37.7 1.0 O B:HOH58 4.8 36.6 1.0 CA B:MET28 4.9 21.2 1.0 N B:MET28 4.9 21.5 1.0 CA B:GLU8 5.0 36.9 1.0 CG B:GLU8 5.0 52.5 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the B2 Box From MURF1 in Dimeric State


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 the B2 Box From MURF1 in Dimeric State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn47 b:35.2 occ:1.00 SG B:CYS18 1.9 28.5 1.0 ND1 B:HIS35 2.1 44.1 1.0 SG B:CYS38 2.4 36.7 1.0 SG B:CYS21 2.5 40.6 1.0 CE1 B:HIS35 2.9 42.7 1.0 CB B:CYS38 3.1 34.9 1.0 CG B:HIS35 3.1 37.3 1.0 CB B:CYS21 3.3 45.7 1.0 CB B:CYS18 3.3 27.8 1.0 CB B:HIS35 3.6 34.1 1.0 N B:CYS21 3.8 42.3 1.0 NE2 B:HIS35 4.1 39.9 1.0 CA B:HIS35 4.1 28.4 1.0 CA B:CYS21 4.1 40.3 1.0 CD2 B:HIS35 4.2 38.0 1.0 CB B:THR20 4.4 47.4 1.0 CA B:CYS38 4.6 34.2 1.0 CA B:CYS18 4.7 36.9 1.0 C B:THR20 4.8 47.2 1.0 CG2 B:THR20 4.8 45.6 1.0 O B:ILE34 4.9 41.8 1.0 O B:HIS35 4.9 29.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the B2 Box From MURF1 in Dimeric State


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 the B2 Box From MURF1 in Dimeric State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn46 b:33.1 occ:1.00 ND1 C:HIS35 2.1 29.0 1.0 SG C:CYS18 2.2 32.9 1.0 SG C:CYS38 2.4 36.5 1.0 SG C:CYS21 2.5 33.2 1.0 CE1 C:HIS35 2.9 33.6 1.0 CG C:HIS35 3.1 29.3 1.0 CB C:CYS38 3.2 32.7 1.0 CB C:CYS21 3.2 31.6 1.0 CB C:CYS18 3.4 28.0 1.0 CB C:HIS35 3.6 32.3 1.0 N C:CYS21 3.9 39.6 1.0 CA C:HIS35 4.0 28.6 1.0 NE2 C:HIS35 4.1 31.5 1.0 CA C:CYS21 4.2 37.6 1.0 CD2 C:HIS35 4.2 29.2 1.0 CB C:THR20 4.4 38.7 1.0 CA C:CYS38 4.6 33.6 1.0 O C:HOH86 4.7 49.1 1.0 CA C:CYS18 4.8 27.3 1.0 O C:HOH69 4.8 51.6 1.0 C C:THR20 4.8 45.2 1.0 O C:HIS35 4.8 30.3 1.0 C C:HIS35 4.9 27.7 1.0 O C:ILE34 4.9 33.9 1.0 CG2 C:THR20 5.0 42.8 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the B2 Box From MURF1 in Dimeric State


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 the B2 Box From MURF1 in Dimeric State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn47 b:29.1 occ:1.00 ND1 C:HIS9 2.2 29.9 1.0 SG C:CYS29 2.2 30.1 1.0 SG C:CYS6 2.3 31.2 1.0 SG C:CYS26 2.3 26.1 1.0 CE1 C:HIS9 3.2 31.6 1.0 CG C:HIS9 3.2 32.4 1.0 CB C:CYS6 3.3 27.4 1.0 CB C:CYS29 3.5 27.2 1.0 CB C:HIS9 3.5 27.6 1.0 N C:CYS29 3.5 25.9 1.0 CB C:CYS26 3.6 24.1 1.0 N C:HIS9 3.9 36.0 1.0 CA C:CYS29 3.9 24.6 1.0 CB C:GLU8 4.3 40.2 1.0 NE2 C:HIS9 4.3 29.9 1.0 N C:CYS26 4.3 26.5 1.0 CD2 C:HIS9 4.3 27.9 1.0 CA C:HIS9 4.4 33.6 1.0 CA C:CYS26 4.4 23.6 1.0 C C:MET28 4.4 26.2 1.0 O C:CYS26 4.5 19.6 1.0 C C:GLU8 4.5 43.2 1.0 CB C:MET28 4.6 27.2 1.0 C C:CYS26 4.6 21.8 1.0 O C:HOH91 4.7 41.1 1.0 CA C:CYS6 4.7 34.1 1.0 OG1 C:THR25 4.7 24.5 1.0 CA C:GLU8 4.8 38.8 1.0 N C:GLU8 4.8 43.5 1.0 CA C:MET28 4.8 25.9 1.0 N C:MET28 4.9 20.8 1.0

M.Mrosek, S.Meier, Z.Ucurum-Fotiadis, E.Von Castelmur, E.Hedbom, A.Lustig, S.Grzesiek, D.Labeit, S.Labeit, O.Mayans. Structural Analysis of B-Box 2 From MURF1: Identification of A Novel Self-Association Pattern in A Ring-Like Fold Biochemistry V. 47 10722 2008.
ISSN: ISSN 0006-2960
PubMed: 18795805
DOI: 10.1021/BI800733Z