Zinc in PDB 7rww: Crystal Structure of A Zn-Bound RIDC1 Variant

The structure of Crystal Structure of A Zn-Bound RIDC1 Variant, PDB code: 7rww was solved by A.Kakkis, E.Golub, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.96 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.791, 86.913, 49.176, 90, 109.16, 90
R / Rfree (%)	17.5 / 20.8

The structure of Crystal Structure of A Zn-Bound RIDC1 Variant also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of A Zn-Bound RIDC1 Variant (pdb code 7rww). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of A Zn-Bound RIDC1 Variant, PDB code: 7rww:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of A Zn-Bound RIDC1 Variant


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 A Zn-Bound RIDC1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:24.6 occ:0.47 ZN A:ZN201 0.0 24.6 0.5 ZN A:ZN201 1.4 29.7 0.5 HE1 A:HIS77 1.7 31.4 1.0 NE2 A:HIS77 1.8 26.6 1.0 CE1 A:HIS77 1.9 26.2 1.0 OE1 A:GLU81 2.0 33.4 0.6 OE1 D:GLU81 2.2 30.0 0.4 O D:HOH302 2.3 29.9 1.0 HE2 D:HIS77 2.6 35.0 1.0 HD2 D:HIS77 2.7 36.5 1.0 CD A:GLU81 2.7 24.7 0.6 OE2 A:GLU81 3.1 27.4 0.6 NE2 D:HIS77 3.1 29.2 1.0 CD2 A:HIS77 3.1 24.8 1.0 CD2 D:HIS77 3.2 30.4 1.0 ND1 A:HIS77 3.2 40.3 1.0 CD D:GLU81 3.5 42.2 0.4 HG3 D:GLU81 3.6 47.7 0.6 HD2 A:HIS77 3.7 29.8 1.0 CG A:HIS77 3.8 27.5 1.0 HD1 A:HIS77 3.9 48.4 1.0 CG A:GLU81 3.9 26.4 0.6 HG3 A:GLU81 4.0 31.7 0.6 HG2 A:GLU81 4.0 49.2 0.4 HG2 A:GLU81 4.1 31.7 0.6 OE1 A:GLU81 4.2 39.6 0.4 OE2 D:GLU81 4.2 48.2 0.4 HD23 D:LEU78 4.2 55.3 1.0 HB2 A:GLU81 4.4 36.7 0.4 HG2 D:GLU81 4.4 43.4 0.4 CE1 D:HIS77 4.4 52.5 1.0 CG D:HIS77 4.5 29.1 1.0 CD A:GLU81 4.6 31.1 0.4 CG D:GLU81 4.6 39.8 0.6 CG D:GLU81 4.6 36.2 0.4 CG A:GLU81 4.7 41.0 0.4 HZ2 D:LYS83 4.9 98.9 1.0 HG2 D:GLU81 4.9 47.7 0.6 HE1 D:HIS77 4.9 63.0 1.0 HA D:LEU78 4.9 30.1 1.0 HD2 D:LYS83 5.0 79.0 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of A Zn-Bound RIDC1 Variant


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 A Zn-Bound RIDC1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:29.7 occ:0.53 ZN A:ZN201 0.0 29.7 0.5 HE2 D:HIS77 1.3 35.0 1.0 ZN A:ZN201 1.4 24.6 0.5 NE2 D:HIS77 2.0 29.2 1.0 NE2 A:HIS77 2.0 26.6 1.0 OE1 A:GLU81 2.2 33.4 0.6 OE2 A:GLU81 2.2 27.4 0.6 CD A:GLU81 2.4 24.7 0.6 HD2 D:HIS77 2.5 36.5 1.0 CD2 D:HIS77 2.5 30.4 1.0 OE1 D:GLU81 2.6 30.0 0.4 CE1 A:HIS77 2.9 26.2 1.0 HE1 A:HIS77 3.0 31.4 1.0 HG3 D:GLU81 3.0 47.7 0.6 CD2 A:HIS77 3.1 24.8 1.0 CE1 D:HIS77 3.2 52.5 1.0 HD2 A:HIS77 3.3 29.8 1.0 HG2 A:GLU81 3.4 49.2 0.4 O D:HOH302 3.5 29.9 1.0 HE1 D:HIS77 3.6 63.0 1.0 CD D:GLU81 3.7 42.2 0.4 CG D:HIS77 3.8 29.1 1.0 HZ3 A:LYS83 3.8 59.4 1.0 CG A:GLU81 3.9 26.4 0.6 CG D:GLU81 3.9 39.8 0.6 ND1 A:HIS77 4.0 40.3 1.0 HG3 A:GLU81 4.1 31.7 0.6 ND1 D:HIS77 4.1 41.1 1.0 HB2 A:GLU81 4.1 36.7 0.4 CG A:HIS77 4.1 27.5 1.0 CG A:GLU81 4.2 41.0 0.4 HG2 D:GLU81 4.2 47.7 0.6 HG2 A:GLU81 4.3 31.7 0.6 CD D:GLU81 4.4 36.5 0.6 HG2 D:GLU81 4.4 43.4 0.4 OE2 D:GLU81 4.4 48.2 0.4 OE1 A:GLU81 4.5 39.6 0.4 HB3 D:GLU81 4.5 46.9 0.4 CD A:GLU81 4.6 31.1 0.4 CG D:GLU81 4.6 36.2 0.4 CB A:GLU81 4.6 30.6 0.4 NZ A:LYS83 4.7 49.5 1.0 HB2 A:GLU81 4.7 37.5 0.6 OE1 D:GLU81 4.7 37.9 0.6 HB3 A:GLU81 4.7 36.7 0.4 CB A:GLU81 4.8 31.2 0.6 HZ1 A:LYS83 4.8 59.4 1.0 HD1 A:HIS77 4.8 48.4 1.0 HB3 A:GLU81 4.8 37.5 0.6 HZ2 A:LYS83 4.9 59.4 1.0 OE2 D:GLU81 4.9 34.4 0.6 HG3 A:GLU81 5.0 49.2 0.4 HB2 D:GLU81 5.0 47.9 0.6

Zinc binding site 3 out of 7 in the Crystal Structure of A Zn-Bound RIDC1 Variant


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 A Zn-Bound RIDC1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:23.6 occ:0.32 H2 A:ALA1 1.6 39.9 1.0 OD2 A:ASP39 2.0 32.8 1.0 O A:ALA1 2.2 30.3 1.0 OD1 A:ASP39 2.2 54.5 1.0 CG A:ASP39 2.4 36.0 1.0 N A:ALA1 2.5 33.3 1.0 H3 A:ALA1 2.8 39.9 1.0 H1 A:ALA1 3.0 39.9 1.0 C A:ALA1 3.1 25.4 1.0 CA A:ALA1 3.3 25.4 1.0 HB3 A:ALA1 3.7 33.5 1.0 HD21 A:ASN6 3.9 35.4 1.0 O A:HOH339 3.9 39.0 1.0 CB A:ASP39 4.0 27.0 1.0 CB A:ALA1 4.1 27.9 1.0 HA A:ALA1 4.1 30.5 1.0 HB2 A:ASP39 4.3 32.4 1.0 N A:ASP2 4.3 33.1 1.0 HB3 A:ASP39 4.4 32.4 1.0 HA A:ASP2 4.5 36.2 1.0 HB2 A:ALA1 4.5 33.5 1.0 OD1 A:ASN6 4.6 25.0 1.0 ND2 A:ASN6 4.7 29.5 1.0 HA A:ASP39 4.7 34.4 1.0 HB1 A:ALA1 4.9 33.5 1.0 CA A:ASP39 4.9 28.7 1.0 CA A:ASP2 4.9 30.2 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of A Zn-Bound RIDC1 Variant


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 A Zn-Bound RIDC1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:19.1 occ:0.42 HD1 A:HIS59 1.5 46.5 1.0 ND1 A:HIS59 2.0 38.7 1.0 NE2 B:HIS73 2.1 17.2 0.6 O B:HOH348 2.2 25.0 1.0 O B:HOH349 2.4 20.1 1.0 CE1 A:HIS59 2.7 37.1 1.0 HB3 A:HIS59 2.8 27.9 1.0 CG A:HIS59 2.8 31.7 1.0 CD2 B:HIS73 2.9 25.9 0.6 HD2 B:HIS73 3.0 31.1 0.6 HE1 A:HIS59 3.0 44.5 1.0 CE1 B:HIS73 3.2 24.2 0.6 CB A:HIS59 3.3 23.2 1.0 HE1 B:HIS73 3.5 29.0 0.6 HD1 B:HIS77 3.5 33.8 1.0 NE2 A:HIS59 3.7 33.3 1.0 CD2 A:HIS59 3.7 40.1 1.0 HB2 A:HIS59 3.8 27.9 1.0 HB2 B:HIS77 3.9 26.4 1.0 CG B:HIS73 4.1 21.6 0.6 ND1 B:HIS73 4.2 20.4 0.6 ND1 B:HIS77 4.3 28.2 1.0 O B:HOH359 4.4 54.5 1.0 HA B:HIS77 4.4 26.3 1.0 HE2 A:HIS59 4.4 39.9 1.0 HA A:HIS59 4.4 26.5 1.0 CA A:HIS59 4.5 22.1 1.0 HD22 B:ASN80 4.5 43.0 1.0 HD2 A:HIS59 4.5 48.1 1.0 HD23 B:LEU76 4.6 38.6 1.0 CB B:HIS77 4.6 22.0 1.0 O B:HIS73 4.7 24.4 0.5 HB3 B:HIS73 4.7 30.8 0.5 CA B:HIS77 4.9 21.9 1.0 HH21 A:ARG62 4.9 42.2 1.0 O B:HIS73 4.9 23.1 0.6 H B:HIS77 4.9 25.9 1.0 HG B:LEU76 4.9 39.0 1.0 HB3 B:LEU76 5.0 30.9 1.0 CG B:HIS77 5.0 25.9 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of A Zn-Bound RIDC1 Variant


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 A Zn-Bound RIDC1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:23.6 occ:0.64 ZN C:ZN201 0.0 23.6 0.6 ZN C:ZN201 1.6 35.8 0.4 NE2 B:HIS77 1.9 25.7 1.0 HZ2 C:LYS83 2.0 27.9 1.0 OE1 B:GLU81 2.0 31.1 0.8 OE1 C:GLU81 2.1 29.9 0.5 NE2 C:HIS77 2.2 37.8 1.0 HZ1 C:LYS83 2.3 27.9 1.0 NZ C:LYS83 2.5 23.2 1.0 OE1 B:GLU81 2.6 30.4 0.2 CD B:GLU81 2.7 27.2 0.8 HZ3 C:LYS83 2.7 27.9 1.0 OE2 B:GLU81 2.7 32.5 0.8 CD2 B:HIS77 2.8 30.5 1.0 CD C:GLU81 2.9 31.7 0.5 HD2 B:HIS77 3.0 36.6 1.0 CE1 B:HIS77 3.0 32.9 1.0 OE2 C:GLU81 3.1 28.9 0.5 CD2 C:HIS77 3.1 21.8 1.0 CE1 C:HIS77 3.2 32.6 1.0 HG3 C:GLU81 3.3 39.1 0.5 HD2 C:HIS77 3.3 26.2 1.0 HE1 B:HIS77 3.3 39.5 1.0 CD B:GLU81 3.4 34.7 0.2 HE1 C:HIS77 3.4 39.2 1.0 OE2 B:GLU81 3.8 35.1 0.2 CE C:LYS83 3.9 55.2 1.0 HD23 C:LEU78 3.9 36.6 1.0 HE3 C:LYS83 4.0 66.2 1.0 CG B:HIS77 4.0 25.9 1.0 ND1 B:HIS77 4.0 28.2 1.0 CG B:GLU81 4.1 31.7 0.8 CG C:GLU81 4.2 32.6 0.5 CG C:HIS77 4.3 23.5 1.0 ND1 C:HIS77 4.3 35.2 1.0 CG C:GLU81 4.3 32.7 0.5 HE2 C:LYS83 4.4 66.2 1.0 HG2 B:GLU81 4.4 38.1 0.8 HG3 B:GLU81 4.5 38.1 0.8 HB3 B:GLU81 4.5 47.0 0.2 HB2 C:GLU81 4.5 40.7 0.5 HZ1 B:LYS83 4.5 52.2 1.0 HB2 C:GLU81 4.6 40.7 0.5 HG2 C:GLU81 4.6 39.1 0.5 CG B:GLU81 4.6 38.2 0.2 HA C:LEU78 4.7 23.6 1.0 HG2 B:GLU81 4.7 45.8 0.2 HG3 C:GLU81 4.7 39.2 0.5 HD3 C:LYS83 4.8 46.9 1.0 CD2 C:LEU78 4.8 30.5 1.0 O B:HOH354 4.8 43.0 1.0 HB3 C:GLU81 4.8 40.7 0.5 HB3 C:GLU81 4.8 40.7 0.5 CB C:GLU81 4.8 33.9 0.5 HD1 B:HIS77 4.8 33.8 1.0 CD C:LYS83 4.8 39.0 1.0 CB C:GLU81 4.8 33.9 0.5 HD23 B:LEU78 4.9 43.4 1.0 HD2 C:LYS83 4.9 46.9 1.0 HG2 C:GLU81 4.9 39.2 0.5 HD21 C:LEU78 4.9 36.6 1.0 HB2 B:GLU81 4.9 47.3 0.8 OE1 C:GLU81 5.0 35.6 0.5

Zinc binding site 6 out of 7 in the Crystal Structure of A Zn-Bound RIDC1 Variant


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 A Zn-Bound RIDC1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:35.8 occ:0.36 ZN C:ZN201 0.0 35.8 0.4 NE2 C:HIS77 1.6 37.8 1.0 ZN C:ZN201 1.6 23.6 0.6 HE1 C:HIS77 1.9 39.2 1.0 CE1 C:HIS77 2.0 32.6 1.0 OE1 B:GLU81 2.0 30.4 0.2 OE2 B:GLU81 2.1 32.5 0.8 OE2 C:GLU81 2.2 28.9 0.5 OE2 B:GLU81 2.4 35.1 0.2 CD B:GLU81 2.5 34.7 0.2 OE1 C:GLU81 2.5 29.9 0.5 CD C:GLU81 2.6 31.7 0.5 CD B:GLU81 2.8 27.2 0.8 HD2 B:HIS77 2.8 36.6 1.0 OE1 B:GLU81 2.8 31.1 0.8 NE2 B:HIS77 2.9 25.7 1.0 CD2 C:HIS77 3.0 21.8 1.0 HG3 C:GLU81 3.0 39.1 0.5 CD2 B:HIS77 3.2 30.5 1.0 HZ1 B:LYS83 3.2 52.2 1.0 ND1 C:HIS77 3.3 35.2 1.0 HZ2 C:LYS83 3.3 27.9 1.0 HZ2 B:LYS83 3.4 52.2 1.0 HD2 C:HIS77 3.5 26.2 1.0 HD23 B:LEU78 3.7 43.4 1.0 CG C:HIS77 3.7 23.5 1.0 NZ B:LYS83 3.8 43.5 1.0 HZ1 C:LYS83 3.8 27.9 1.0 NZ C:LYS83 3.9 23.2 1.0 HD1 C:HIS77 3.9 42.2 1.0 HZ3 C:LYS83 3.9 27.9 1.0 CG C:GLU81 4.0 32.6 0.5 CG B:GLU81 4.0 38.2 0.2 OE1 C:GLU81 4.0 35.6 0.5 CG C:GLU81 4.1 32.7 0.5 HG2 B:GLU81 4.2 45.8 0.2 CG B:GLU81 4.2 31.7 0.8 CE1 B:HIS77 4.2 32.9 1.0 HG2 C:GLU81 4.2 39.1 0.5 HE3 B:LYS83 4.3 54.8 1.0 HG3 C:GLU81 4.3 39.2 0.5 HB2 B:GLU81 4.4 47.3 0.8 HZ3 B:LYS83 4.4 52.2 1.0 CD C:GLU81 4.4 29.9 0.5 HB3 B:GLU81 4.5 47.0 0.2 HG2 C:GLU81 4.5 39.2 0.5 CG B:HIS77 4.5 25.9 1.0 CD2 B:LEU78 4.5 36.2 1.0 HG3 B:GLU81 4.5 45.8 0.2 HA B:LEU78 4.6 28.2 1.0 CE B:LYS83 4.6 45.7 1.0 HG2 B:GLU81 4.6 38.1 0.8 HD22 B:LEU78 4.7 43.4 1.0 HE1 B:HIS77 4.7 39.5 1.0 HD21 B:LEU78 4.7 43.4 1.0 CB B:GLU81 4.7 39.2 0.2 CB B:GLU81 4.8 39.5 0.8 HG3 B:GLU81 4.8 38.1 0.8 O B:HOH310 4.9 49.7 1.0 HB3 B:GLU81 4.9 47.3 0.8 HB2 B:GLU81 4.9 47.0 0.2 HD2 B:LYS83 4.9 57.9 1.0 HB2 C:GLU81 4.9 40.7 0.5 HD23 C:LEU78 5.0 36.6 1.0 HB2 C:GLU81 5.0 40.7 0.5 ND1 B:HIS77 5.0 28.2 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of A Zn-Bound RIDC1 Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Zn-Bound RIDC1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:29.1 occ:0.26 HD1 D:HIS59 2.0 58.3 1.0 ND1 D:HIS59 2.1 48.5 1.0 O C:HOH356 2.2 38.2 1.0 NE2 C:HIS73 2.3 25.1 0.5 O C:HOH337 2.4 38.2 1.0 CE1 D:HIS59 2.6 51.6 1.0 HE1 D:HIS59 2.8 61.9 1.0 CG D:HIS59 2.9 40.3 1.0 CD2 C:HIS73 3.1 32.4 0.5 HB3 D:HIS59 3.2 48.3 1.0 HD2 C:HIS73 3.2 38.9 0.5 CE1 C:HIS73 3.3 39.0 0.5 NE2 D:HIS59 3.4 43.9 1.0 HE1 C:HIS73 3.5 46.8 0.5 CB D:HIS59 3.6 40.3 1.0 CD2 D:HIS59 3.6 53.4 1.0 HB2 D:HIS59 4.1 48.3 1.0 HE2 D:HIS59 4.1 52.6 1.0 HB2 C:HIS77 4.1 31.2 1.0 CG C:HIS73 4.3 27.0 0.5 ND1 C:HIS73 4.3 29.0 0.5 HD22 C:ASN80 4.3 60.9 1.0 HD2 D:HIS59 4.4 64.1 1.0 HA C:HIS77 4.6 30.2 1.0 HH21 D:ARG62 4.6 41.6 1.0 O C:HIS73 4.7 21.4 0.6 HA D:HIS59 4.7 43.0 1.0 HB3 C:HIS73 4.8 30.7 0.6 HD21 C:ASN80 4.8 60.9 1.0 CA D:HIS59 4.8 35.9 1.0 HD1 C:HIS77 4.8 42.2 1.0 HB3 C:LEU76 4.9 29.6 1.0 ND2 C:ASN80 4.9 50.7 1.0 O C:HIS73 4.9 22.7 0.5 CB C:HIS77 5.0 26.0 1.0

A.Kakkis, E.Golub. Crystal Structure of A Zn-Bound RIDC1 Variant To Be Published.