Zinc in PDB 3vpb: Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate

All present enzymatic activity of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate:
3.5.1.16;

The structure of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate, PDB code: 3vpb was solved by T.Tomita, T.Ouchi, T.Kuzuyama, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.91 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.546, 113.988, 78.582, 90.00, 102.43, 90.00
R / Rfree (%)	18.7 / 23.5

The structure of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate (pdb code 3vpb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate, PDB code: 3vpb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:23.8 occ:1.00 O1B A:ADP500 1.9 18.7 1.0 O2 A:SO4504 2.0 20.7 1.0 O A:HOH696 2.1 19.1 1.0 OE2 A:GLU250 2.2 17.3 1.0 OE1 A:GLU250 2.3 16.6 1.0 OD1 A:ASN252 2.3 24.5 1.0 CD A:GLU250 2.5 17.8 1.0 PB A:ADP500 3.1 15.9 1.0 S A:SO4504 3.2 20.0 1.0 O2B A:ADP500 3.3 16.6 1.0 CG A:ASN252 3.3 23.3 1.0 O4 A:SO4504 3.5 19.7 1.0 MG A:MG502 3.6 16.8 1.0 ND2 A:ASN252 3.7 24.1 1.0 O A:HOH618 3.7 28.2 1.0 O3 A:SO4504 3.9 19.5 1.0 NZ A:LYS87 4.0 19.0 1.0 O A:GLY131 4.0 20.6 1.0 OG A:SER132 4.0 22.6 1.0 CG A:GLU250 4.0 17.3 1.0 O3A A:ADP500 4.1 17.6 1.0 CA A:SER132 4.1 19.5 1.0 O1 A:SO4504 4.2 20.6 1.0 O3B A:ADP500 4.2 14.3 1.0 CB A:SER132 4.4 20.3 1.0 O2A A:ADP500 4.5 16.0 1.0 O A:HOH611 4.6 19.9 1.0 CE A:LYS87 4.6 19.4 1.0 CB A:ASN252 4.7 20.6 1.0 OXT E:GLU56 4.7 33.7 1.0 C A:GLY131 4.9 20.5 1.0 CB A:GLU250 4.9 16.3 1.0 OD1 A:ASP237 4.9 22.3 1.0 N A:TRP133 5.0 18.9 1.0 CB E:GLU56 5.0 31.4 1.0

Zinc binding site 2 out of 4 in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:23.4 occ:1.00 O1B B:ADP500 2.0 17.8 1.0 O1 B:SO4504 2.1 21.0 1.0 O B:HOH651 2.1 15.6 1.0 OE1 B:GLU250 2.1 18.6 1.0 OD1 B:ASN252 2.4 20.2 1.0 OE2 B:GLU250 2.4 17.0 1.0 CD B:GLU250 2.6 18.8 1.0 PB B:ADP500 3.1 15.6 1.0 S B:SO4504 3.3 19.7 1.0 CG B:ASN252 3.4 20.6 1.0 O2B B:ADP500 3.4 18.0 1.0 MG B:MG502 3.5 17.9 1.0 O3 B:SO4504 3.6 18.1 1.0 ND2 B:ASN252 3.8 19.2 1.0 O B:HOH632 3.8 25.3 1.0 O4 B:SO4504 3.9 17.7 1.0 OG B:SER132 4.0 22.7 1.0 O B:GLY131 4.0 19.1 1.0 CG B:GLU250 4.1 15.9 1.0 NZ B:LYS87 4.1 18.5 1.0 CA B:SER132 4.1 18.4 1.0 O3A B:ADP500 4.1 18.4 1.0 O3B B:ADP500 4.3 15.2 1.0 CB B:SER132 4.3 18.9 1.0 O2 B:SO4504 4.4 19.8 1.0 CE B:LYS87 4.5 19.6 1.0 O2A B:ADP500 4.6 16.1 1.0 OXT F:GLU56 4.6 32.1 1.0 O B:HOH605 4.7 18.7 1.0 CB B:ASN252 4.7 18.5 1.0 C B:GLY131 4.9 18.9 1.0 CB B:GLU250 4.9 17.1 1.0 CB F:GLU56 5.0 30.7 1.0 OD2 B:ASP237 5.0 19.6 1.0 PA B:ADP500 5.0 17.7 1.0 N B:SER132 5.0 17.8 1.0

Zinc binding site 3 out of 4 in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn100 b:28.5 occ:1.00 ND1 E:HIS27 2.1 33.5 1.0 SG E:CYS6 2.2 29.0 1.0 SG E:CYS9 2.3 33.2 1.0 SG E:CYS29 2.3 28.7 1.0 CE1 E:HIS27 3.0 33.2 1.0 CB E:CYS6 3.1 32.1 1.0 CG E:HIS27 3.2 33.0 1.0 CB E:CYS29 3.2 29.2 1.0 CB E:CYS9 3.3 36.0 1.0 CB E:HIS27 3.6 31.9 1.0 N E:CYS9 3.8 35.6 1.0 CA E:CYS9 4.1 35.9 1.0 NE2 E:HIS27 4.2 33.9 1.0 N E:CYS29 4.3 30.2 1.0 CD2 E:HIS27 4.3 34.1 1.0 CA E:CYS29 4.4 29.4 1.0 CB E:VAL8 4.5 35.0 1.0 CA E:CYS6 4.6 31.8 1.0 C E:VAL8 4.8 35.4 1.0 C E:CYS9 4.8 37.4 1.0 CB E:ALA31 4.9 28.6 1.0 CA E:HIS27 4.9 32.4 1.0 N E:ASN10 4.9 38.2 1.0 CG1 E:VAL8 5.0 35.7 1.0 N E:GLY11 5.0 40.2 1.0 C E:HIS27 5.0 32.1 1.0

Zinc binding site 4 out of 4 in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn100 b:27.8 occ:1.00 ND1 F:HIS27 2.1 32.4 1.0 SG F:CYS9 2.3 32.1 1.0 SG F:CYS6 2.3 29.1 1.0 SG F:CYS29 2.3 26.5 1.0 CE1 F:HIS27 3.1 32.2 1.0 CB F:CYS6 3.1 32.9 1.0 CG F:HIS27 3.2 30.7 1.0 CB F:CYS29 3.2 28.1 1.0 CB F:CYS9 3.4 36.0 1.0 CB F:HIS27 3.5 30.5 1.0 N F:CYS9 3.8 36.0 1.0 CA F:CYS9 4.2 36.2 1.0 NE2 F:HIS27 4.2 31.9 1.0 N F:CYS29 4.2 29.8 1.0 CD2 F:HIS27 4.3 31.8 1.0 CA F:CYS29 4.3 28.1 1.0 CB F:VAL8 4.5 35.1 1.0 CA F:CYS6 4.6 33.1 1.0 CA F:HIS27 4.9 30.5 1.0 C F:VAL8 4.9 35.6 1.0 CB F:ALA31 4.9 26.7 1.0 C F:CYS9 4.9 37.8 1.0 CG1 F:VAL8 5.0 34.6 1.0

T.Ouchi, T.Tomita, A.Horie, A.Yoshida, K.Takahashi, H.Nishida, K.Lassak, H.Taka, R.Mineki, T.Fujimura, S.Kosono, C.Nishiyama, R.Masui, S.Kuramitsu, S.V.Albers, T.Kuzuyama, M.Nishiyama. Lysine and Arginine Biosyntheses Mediated By A Common Carrier Protein in Sulfolobus Nat.Chem.Biol. V. 9 277 2013.
ISSN: ISSN 1552-4450
PubMed: 23434852
DOI: 10.1038/NCHEMBIO.1200