Zinc in PDB 2yww: Crystal Structure of Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii

The structure of Crystal Structure of Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii, PDB code: 2yww was solved by M.Kanagawa, S.Baba, S.Kuramitsu, S.Yokoyama, G.Kawai, G.Sampei, 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)	30.96 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.003, 71.398, 92.975, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 22.6

The binding sites of Zinc atom in the Crystal Structure of Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii (pdb code 2yww). 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 Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii, PDB code: 2yww:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii


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 Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:28.6 occ:1.00 O3G A:ATP402 1.9 25.6 1.0 O1G A:ATP403 2.1 30.9 1.0 O1B A:ATP403 2.2 26.1 1.0 O A:HOH546 2.3 31.7 1.0 O A:HOH572 2.3 33.8 1.0 O2B A:ATP402 2.4 26.8 1.0 PB A:ATP402 3.0 26.6 1.0 PB A:ATP403 3.1 30.2 1.0 PG A:ATP403 3.3 29.5 1.0 O3B A:ATP402 3.4 24.2 1.0 PG A:ATP402 3.4 24.3 1.0 NZ A:LYS51 3.5 31.4 1.0 O3B A:ATP403 3.5 29.8 1.0 O3G A:ATP403 3.7 37.0 1.0 O A:HOH517 3.7 31.6 1.0 O3A A:ATP403 3.9 27.7 1.0 CE1 A:HIS20 4.1 15.4 1.0 O1G A:ATP402 4.1 28.8 1.0 O3A A:ATP402 4.2 27.4 1.0 PA A:ATP402 4.2 30.9 1.0 O1B A:ATP402 4.4 29.0 1.0 OD2 A:ASP19 4.4 20.0 1.0 O2G A:ATP402 4.4 24.6 1.0 NE2 A:HIS20 4.5 19.4 1.0 O1A A:ATP402 4.5 28.3 1.0 O2B A:ATP403 4.6 31.1 1.0 O2G A:ATP403 4.7 29.6 1.0 CE A:LYS51 4.7 30.7 1.0 NZ A:LYS55 4.8 19.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii


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 Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:27.5 occ:1.00 SG A:CYS136 2.3 25.3 1.0 SG A:CYS139 2.4 24.2 1.0 SG A:CYS108 2.4 32.4 1.0 SG A:CYS113 2.5 27.3 1.0 CB A:CYS136 3.1 23.3 1.0 CB A:CYS113 3.1 28.3 1.0 CB A:CYS108 3.4 38.1 1.0 CB A:CYS139 3.4 25.8 1.0 N A:CYS139 3.7 26.0 1.0 CA A:CYS139 4.1 26.6 1.0 OG1 A:THR115 4.3 29.6 1.0 CA A:CYS113 4.4 29.9 1.0 O A:HOH510 4.5 29.1 1.0 O A:HOH515 4.5 31.6 1.0 CA A:CYS136 4.5 24.2 1.0 CB A:ASN110 4.6 37.1 1.0 CB A:TYR138 4.6 26.8 1.0 ND2 A:ASN110 4.7 35.5 1.0 CA A:CYS108 4.8 38.7 1.0 C A:TYR138 4.8 27.4 1.0 C A:CYS139 4.9 26.9 1.0 N A:TYR138 5.0 26.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii


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 Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:29.5 occ:1.00 O3G B:ATP401 2.0 25.2 1.0 O1G B:ATP400 2.0 30.5 1.0 O1B B:ATP400 2.1 27.4 1.0 O B:HOH565 2.2 31.3 1.0 O2B B:ATP401 2.5 29.6 1.0 PB B:ATP401 3.1 31.7 1.0 PB B:ATP400 3.1 30.4 1.0 PG B:ATP400 3.3 29.4 1.0 O3B B:ATP401 3.3 28.0 1.0 PG B:ATP401 3.5 28.2 1.0 O3B B:ATP400 3.5 29.5 1.0 O3G B:ATP400 3.7 33.1 1.0 O3A B:ATP400 3.7 27.1 1.0 CE1 B:HIS20 3.9 18.9 1.0 NZ B:LYS51 4.0 43.8 1.0 O1G B:ATP401 4.2 31.3 1.0 PA B:ATP401 4.3 34.9 1.0 NE2 B:HIS20 4.3 21.8 1.0 O3A B:ATP401 4.3 30.8 1.0 CE B:LYS51 4.3 41.4 1.0 OD2 B:ASP19 4.3 23.8 1.0 O2G B:ATP401 4.4 24.3 1.0 O1B B:ATP401 4.4 31.4 1.0 O1A B:ATP401 4.6 36.0 1.0 O2B B:ATP400 4.6 33.2 1.0 O2G B:ATP400 4.7 28.8 1.0 NZ B:LYS55 4.7 21.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii


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 Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:20.8 occ:1.00 SG B:CYS108 2.3 22.5 1.0 SG B:CYS139 2.4 19.4 1.0 SG B:CYS113 2.4 19.4 1.0 SG B:CYS136 2.4 21.6 1.0 CB B:CYS113 3.0 21.2 1.0 CB B:CYS136 3.1 22.4 1.0 CB B:CYS139 3.3 21.0 1.0 CB B:CYS108 3.4 24.5 1.0 N B:CYS139 3.8 21.0 1.0 CA B:CYS139 4.1 22.0 1.0 OG1 B:THR115 4.2 21.2 1.0 O B:HOH508 4.3 24.6 1.0 CA B:CYS113 4.4 21.3 1.0 CB B:ASN110 4.4 22.8 1.0 CA B:CYS136 4.5 21.5 1.0 O B:HOH507 4.6 18.9 1.0 CA B:CYS108 4.7 24.6 1.0 ND2 B:ASN110 4.8 20.6 1.0 C B:TYR138 4.9 22.8 1.0 CB B:TYR138 4.9 23.4 1.0 C B:CYS139 4.9 23.4 1.0 N B:GLU140 5.0 23.6 1.0

M.Kanagawa, S.Baba, S.Kuramitsu, S.Yokoyama, G.Kawai, G.Sampei. Crystal Structure of Aspartate Carbamoyltransferase Regulatory Chain From Methanocaldococcus Jannaschii To Be Published.