Zinc in PDB 1rmd: RAG1 Dimerization Domain

The structure of RAG1 Dimerization Domain, PDB code: 1rmd was solved by S.F.Bellon, K.K.Rodgers, D.G.Schatz, J.E.Coleman, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.580, 57.580, 98.430, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 25.7

The binding sites of Zinc atom in the RAG1 Dimerization Domain (pdb code 1rmd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the RAG1 Dimerization Domain, PDB code: 1rmd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the RAG1 Dimerization Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RAG1 Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn117 b:23.3 occ:1.00 ND1 A:HIS6 1.9 16.5 1.0 ND1 A:HIS31 2.1 21.4 1.0 SG A:CYS2 2.3 21.1 1.0 SG A:CYS29 2.4 19.3 1.0 CE1 A:HIS6 2.8 20.8 1.0 CG A:HIS6 2.9 20.1 1.0 CE1 A:HIS31 2.9 20.6 1.0 CB A:CYS2 3.1 26.2 1.0 CB A:CYS29 3.1 20.1 1.0 CG A:HIS31 3.2 17.3 1.0 CB A:HIS6 3.3 19.9 1.0 CB A:HIS31 3.6 17.4 1.0 O A:CYS2 3.8 27.8 1.0 ZN A:ZN118 3.9 24.1 1.0 C A:CYS2 4.0 26.4 1.0 NE2 A:HIS6 4.0 21.5 1.0 CD2 A:HIS6 4.0 20.8 1.0 NE2 A:HIS31 4.1 15.5 1.0 CA A:CYS2 4.2 28.2 1.0 CD2 A:HIS31 4.3 16.1 1.0 SG A:CYS49 4.4 18.5 1.0 SG A:CYS46 4.5 20.1 1.0 CA A:CYS29 4.5 19.7 1.0 N A:SER3 4.6 25.3 1.0 N A:HIS31 4.8 18.3 1.0 CA A:HIS6 4.8 22.4 1.0 O A:CYS29 4.8 28.4 1.0 C A:CYS29 4.8 22.7 1.0 CA A:HIS31 4.9 20.6 1.0

Zinc binding site 2 out of 4 in the RAG1 Dimerization Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RAG1 Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn118 b:24.1 occ:1.00 SG A:CYS46 2.2 20.1 1.0 SG A:CYS49 2.3 18.5 1.0 SG A:CYS29 2.3 19.3 1.0 SG A:CYS26 2.3 17.5 1.0 CB A:CYS26 3.0 16.3 1.0 CB A:CYS49 3.2 21.3 1.0 CB A:CYS46 3.2 19.2 1.0 CB A:CYS29 3.3 20.1 1.0 N A:CYS46 3.8 21.0 1.0 ZN A:ZN117 3.9 23.3 1.0 N A:CYS29 4.0 19.2 1.0 CE1 A:HIS6 4.0 20.8 1.0 CA A:CYS46 4.1 20.1 1.0 ND1 A:HIS6 4.2 16.5 1.0 CA A:CYS29 4.2 19.7 1.0 CA A:CYS26 4.5 17.9 1.0 CA A:CYS49 4.5 25.3 1.0 N A:CYS49 4.8 26.9 1.0 O A:CYS46 4.8 20.6 1.0 C A:CYS46 5.0 20.8 1.0 CB A:ILE28 5.0 18.2 1.0 C A:CYS29 5.0 22.7 1.0 SG A:CYS2 5.0 21.1 1.0

Zinc binding site 3 out of 4 in the RAG1 Dimerization Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RAG1 Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn119 b:23.3 occ:1.00 ND1 A:HIS43 2.1 24.2 1.0 SG A:CYS64 2.3 18.6 1.0 SG A:CYS61 2.3 23.5 1.0 SG A:CYS41 2.4 15.4 1.0 CE1 A:HIS43 2.8 24.8 1.0 CB A:CYS61 3.1 22.5 1.0 CG A:HIS43 3.3 18.7 1.0 CB A:CYS41 3.4 17.9 1.0 CB A:CYS64 3.5 18.2 1.0 N A:CYS64 3.5 23.2 1.0 CB A:HIS43 3.8 16.4 1.0 NE2 A:HIS43 4.0 14.3 1.0 CB A:SER63 4.0 23.3 1.0 CA A:CYS64 4.0 21.6 1.0 OG1 A:THR39 4.1 18.9 1.0 CD2 A:HIS43 4.2 19.7 1.0 O A:CYS41 4.5 20.4 1.0 C A:SER63 4.5 25.3 1.0 CA A:CYS61 4.5 19.8 1.0 CA A:CYS41 4.6 19.7 1.0 CA A:SER63 4.7 21.6 1.0 C A:CYS41 4.7 19.3 1.0 N A:SER63 4.8 22.3 1.0 C A:CYS64 4.8 23.1 1.0 N A:ARG65 4.8 30.0 1.0 C A:CYS61 4.9 18.3 1.0 OG A:SER63 4.9 32.2 1.0

Zinc binding site 4 out of 4 in the RAG1 Dimerization Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RAG1 Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn120 b:34.8 occ:1.00 NE2 A:HIS112 2.0 37.1 1.0 NE2 A:HIS108 2.0 27.5 1.0 SG A:CYS91 2.3 29.8 1.0 SG A:CYS96 2.4 29.2 1.0 CE1 A:HIS112 2.8 43.6 1.0 CE1 A:HIS108 2.9 28.5 1.0 CD2 A:HIS112 3.1 40.5 1.0 CD2 A:HIS108 3.1 31.2 1.0 CB A:CYS96 3.2 37.2 1.0 CB A:CYS91 3.2 21.8 1.0 CB A:ALA93 4.0 23.3 1.0 ND1 A:HIS112 4.0 48.6 1.0 ND1 A:HIS108 4.0 30.1 1.0 CG A:HIS112 4.2 45.6 1.0 CG A:HIS108 4.2 31.7 1.0 CA A:CYS91 4.7 22.8 1.0 CA A:CYS96 4.7 39.2 1.0 CB A:GLU98 4.7 41.6 1.0 N A:ALA93 5.0 20.1 1.0 C A:CYS91 5.0 17.4 1.0

S.F.Bellon, K.K.Rodgers, D.G.Schatz, J.E.Coleman, T.A.Steitz. Crystal Structure of the RAG1 Dimerization Domain Reveals Multiple Zinc-Binding Motifs Including A Novel Zinc Binuclear Cluster. Nat.Struct.Biol. V. 4 586 1997.
ISSN: ISSN 1072-8368
PubMed: 9228952
DOI: 10.1038/NSB0797-586