Zinc in PDB 6ksy: Crystal Structure of Arginase From Zymomonas Mobilis ZM4

The structure of Crystal Structure of Arginase From Zymomonas Mobilis ZM4, PDB code: 6ksy was solved by S.Y.Park, S.A.Hwangbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.107, 100.324, 79.600, 90.00, 113.31, 90.00
R / Rfree (%)	16.5 / 18.8

The binding sites of Zinc atom in the Crystal Structure of Arginase From Zymomonas Mobilis ZM4 (pdb code 6ksy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Arginase From Zymomonas Mobilis ZM4, PDB code: 6ksy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Arginase From Zymomonas Mobilis ZM4


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 Arginase From Zymomonas Mobilis ZM4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.9 occ:1.00 OD2 A:ASP116 2.0 17.6 1.0 OD2 A:ASP120 2.1 17.5 1.0 O A:HOH420 2.1 21.8 1.0 SG A:CYS92 2.3 24.4 1.0 OD2 A:ASP212 2.3 17.6 1.0 CG A:ASP120 3.0 20.8 1.0 CG A:ASP116 3.1 17.5 1.0 OD1 A:ASP120 3.3 21.3 1.0 CG A:ASP212 3.3 18.2 1.0 OD1 A:ASP116 3.4 18.5 1.0 CB A:CYS92 3.4 12.7 1.0 ZN A:ZN302 3.4 29.4 1.0 CB A:ASP212 3.6 15.7 1.0 NE1 A:TRP114 4.1 19.6 1.0 NE2 A:HIS210 4.2 18.2 1.0 O A:HOH547 4.3 29.5 1.0 CB A:ASP116 4.4 15.5 1.0 CB A:ASP120 4.4 17.6 1.0 OD1 A:ASP212 4.5 19.4 1.0 CZ2 A:TRP114 4.5 17.0 1.0 O A:HIS131 4.6 18.6 1.0 CE2 A:TRP114 4.7 14.7 1.0 O A:HIS118 4.7 20.7 1.0 CA A:CYS92 4.8 10.9 1.0 CG A:GLU269 4.8 15.8 1.0 CD2 A:HIS210 4.8 15.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Arginase From Zymomonas Mobilis ZM4


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 Arginase From Zymomonas Mobilis ZM4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:29.4 occ:1.00 OD2 A:ASP214 2.2 20.4 1.0 OD2 A:ASP212 2.4 17.6 1.0 OD1 A:ASP116 2.4 18.5 1.0 O A:HOH420 2.4 21.8 1.0 OD1 A:ASP214 2.4 21.6 1.0 ND1 A:HIS118 2.5 20.4 1.0 CG A:ASP214 2.7 20.4 1.0 O A:HOH547 2.8 29.5 1.0 CG A:ASP212 3.2 18.2 1.0 CE1 A:HIS118 3.3 21.3 1.0 CG A:ASP116 3.3 17.5 1.0 ZN A:ZN301 3.4 21.9 1.0 CG A:HIS118 3.6 19.8 1.0 OD1 A:ASP212 3.6 19.4 1.0 OD2 A:ASP116 3.6 17.6 1.0 CB A:HIS118 3.9 19.0 1.0 CB A:ASP214 4.2 20.1 1.0 N A:HIS118 4.2 17.6 1.0 CB A:ASP212 4.2 15.7 1.0 N A:SER117 4.5 19.9 1.0 NE2 A:HIS118 4.5 21.8 1.0 O A:HOH559 4.5 38.1 1.0 O A:HOH473 4.6 24.2 1.0 CD2 A:HIS118 4.6 21.8 1.0 CA A:HIS118 4.7 19.7 1.0 OD1 A:ASP120 4.7 21.3 1.0 CB A:ASP116 4.7 15.5 1.0 CB A:SER117 4.8 21.1 1.0 SG A:CYS92 5.0 24.4 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Arginase From Zymomonas Mobilis ZM4


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 Arginase From Zymomonas Mobilis ZM4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:32.0 occ:1.00 OD2 B:ASP212 2.2 17.4 1.0 OD2 B:ASP214 2.3 23.6 1.0 O B:HOH419 2.4 24.9 1.0 OD1 B:ASP116 2.4 21.1 1.0 ND1 B:HIS118 2.5 22.0 1.0 OD1 B:ASP214 2.5 22.7 1.0 CG B:ASP214 2.8 23.3 1.0 O B:HOH567 2.9 36.9 1.0 CG B:ASP212 3.1 20.8 1.0 CE1 B:HIS118 3.3 24.4 1.0 CG B:ASP116 3.4 21.9 1.0 ZN B:ZN302 3.4 25.7 1.0 CG B:HIS118 3.6 23.1 1.0 OD2 B:ASP116 3.6 19.3 1.0 OD1 B:ASP212 3.7 21.5 1.0 CB B:HIS118 3.9 22.5 1.0 CB B:ASP212 4.2 17.6 1.0 CB B:ASP214 4.3 20.4 1.0 N B:HIS118 4.3 17.8 1.0 O B:HOH428 4.5 26.1 1.0 NE2 B:HIS118 4.5 22.7 1.0 N B:SER117 4.5 18.9 1.0 O B:HOH570 4.6 37.6 1.0 OD1 B:ASP120 4.6 23.3 1.0 CD2 B:HIS118 4.7 22.7 1.0 CA B:HIS118 4.7 21.7 1.0 CB B:ASP116 4.8 18.3 1.0 SG B:CYS92 4.9 20.6 1.0 CB B:SER117 4.9 20.0 1.0 OD2 B:ASP120 5.0 21.6 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Arginase From Zymomonas Mobilis ZM4


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 Arginase From Zymomonas Mobilis ZM4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:25.7 occ:1.00 OD2 B:ASP116 2.1 19.3 1.0 OD2 B:ASP120 2.1 21.6 1.0 SG B:CYS92 2.3 20.6 1.0 O B:HOH419 2.4 24.9 1.0 OD2 B:ASP212 2.4 17.4 1.0 CG B:ASP120 3.1 22.1 1.0 CG B:ASP116 3.1 21.9 1.0 OD1 B:ASP120 3.3 23.3 1.0 CG B:ASP212 3.3 20.8 1.0 CB B:CYS92 3.4 20.1 1.0 ZN B:ZN301 3.4 32.0 1.0 OD1 B:ASP116 3.5 21.1 1.0 CB B:ASP212 3.6 17.6 1.0 NE1 B:TRP114 4.1 18.0 1.0 O B:HOH567 4.2 36.9 1.0 NE2 B:HIS210 4.2 17.7 1.0 CB B:ASP116 4.4 18.3 1.0 CB B:ASP120 4.4 22.5 1.0 OD1 B:ASP212 4.5 21.5 1.0 CZ2 B:TRP114 4.5 17.0 1.0 O B:HIS131 4.6 21.1 1.0 CE2 B:TRP114 4.7 18.0 1.0 CA B:CYS92 4.8 15.3 1.0 O B:HIS118 4.8 22.1 1.0 CG B:GLU269 4.9 18.2 1.0 CD2 B:HIS210 4.9 16.4 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Arginase From Zymomonas Mobilis ZM4


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 Arginase From Zymomonas Mobilis ZM4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:21.8 occ:1.00 OD2 C:ASP116 2.0 18.0 1.0 OD2 C:ASP120 2.1 18.2 1.0 O C:HOH408 2.2 20.8 1.0 SG C:CYS92 2.3 18.4 1.0 OD2 C:ASP212 2.4 16.8 1.0 CG C:ASP120 3.0 23.2 1.0 CG C:ASP116 3.0 18.5 1.0 OD1 C:ASP120 3.2 20.1 1.0 CB C:CYS92 3.3 15.9 1.0 CG C:ASP212 3.3 19.8 1.0 OD1 C:ASP116 3.4 17.7 1.0 ZN C:ZN302 3.4 27.6 1.0 CB C:ASP212 3.6 15.0 1.0 NE1 C:TRP114 4.2 16.0 1.0 NE2 C:HIS210 4.2 15.0 1.0 O C:HOH533 4.2 27.8 1.0 CB C:ASP116 4.4 16.6 1.0 CB C:ASP120 4.4 20.2 1.0 CZ2 C:TRP114 4.5 16.0 1.0 OD1 C:ASP212 4.5 19.7 1.0 O C:HIS131 4.5 20.2 1.0 CE2 C:TRP114 4.7 15.8 1.0 CA C:CYS92 4.7 16.0 1.0 O C:HIS118 4.7 15.6 1.0 CD2 C:HIS210 4.8 14.9 1.0 CG C:GLU269 4.9 15.6 1.0 O C:HOH572 5.0 46.8 1.0 CA C:ASP212 5.0 17.2 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Arginase From Zymomonas Mobilis ZM4


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 Arginase From Zymomonas Mobilis ZM4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:27.6 occ:1.00 OD2 C:ASP214 2.2 19.9 1.0 OD2 C:ASP212 2.3 16.8 1.0 OD1 C:ASP116 2.4 17.7 1.0 O C:HOH408 2.4 20.8 1.0 OD1 C:ASP214 2.5 21.1 1.0 ND1 C:HIS118 2.5 22.8 1.0 O C:HOH533 2.6 27.8 1.0 CG C:ASP214 2.7 19.6 1.0 CG C:ASP212 3.2 19.8 1.0 CE1 C:HIS118 3.3 21.8 1.0 CG C:ASP116 3.4 18.5 1.0 ZN C:ZN301 3.4 21.8 1.0 CG C:HIS118 3.6 22.2 1.0 OD1 C:ASP212 3.7 19.7 1.0 OD2 C:ASP116 3.7 18.0 1.0 CB C:HIS118 4.0 19.7 1.0 CB C:ASP214 4.2 16.7 1.0 N C:HIS118 4.2 16.2 1.0 CB C:ASP212 4.2 15.0 1.0 O C:HOH572 4.3 46.8 1.0 O C:HOH573 4.4 33.2 1.0 N C:SER117 4.5 17.1 1.0 O C:HOH446 4.5 20.6 1.0 NE2 C:HIS118 4.5 19.3 1.0 OD1 C:ASP120 4.6 20.1 1.0 CA C:HIS118 4.7 17.4 1.0 CD2 C:HIS118 4.7 21.8 1.0 CB C:ASP116 4.8 16.6 1.0 CB C:SER117 4.8 16.2 1.0 SG C:CYS92 4.9 18.4 1.0 O C:HIS118 5.0 15.6 1.0 OD2 C:ASP120 5.0 18.2 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Arginase From Zymomonas Mobilis ZM4


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 Arginase From Zymomonas Mobilis ZM4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:23.8 occ:1.00 O D:HOH410 2.1 22.4 1.0 OD2 D:ASP116 2.1 18.5 1.0 OD2 D:ASP120 2.1 17.6 1.0 SG D:CYS92 2.3 19.9 1.0 OD2 D:ASP212 2.3 20.8 1.0 CG D:ASP120 3.0 20.9 1.0 CG D:ASP116 3.1 18.0 1.0 OD1 D:ASP120 3.2 20.9 1.0 CG D:ASP212 3.3 20.5 1.0 CB D:CYS92 3.4 18.7 1.0 ZN D:ZN302 3.4 29.9 1.0 OD1 D:ASP116 3.5 19.0 1.0 CB D:ASP212 3.6 15.8 1.0 NE1 D:TRP114 4.2 15.5 1.0 O D:HOH544 4.2 28.4 1.0 NE2 D:HIS210 4.3 17.3 1.0 OD1 D:ASP212 4.4 19.4 1.0 CB D:ASP116 4.4 18.6 1.0 CB D:ASP120 4.4 21.0 1.0 CZ2 D:TRP114 4.5 16.4 1.0 O D:HIS131 4.5 19.0 1.0 CE2 D:TRP114 4.7 18.9 1.0 CA D:CYS92 4.8 16.8 1.0 O D:HIS118 4.8 19.8 1.0 CG D:GLU269 4.9 17.6 1.0 CD2 D:HIS210 4.9 16.7 1.0 CA D:ASP212 5.0 19.4 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Arginase From Zymomonas Mobilis ZM4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Arginase From Zymomonas Mobilis ZM4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:29.9 occ:1.00 OD2 D:ASP212 2.3 20.8 1.0 OD2 D:ASP214 2.3 21.4 1.0 O D:HOH410 2.3 22.4 1.0 OD1 D:ASP116 2.4 19.0 1.0 OD1 D:ASP214 2.5 21.0 1.0 ND1 D:HIS118 2.6 20.5 1.0 O D:HOH544 2.7 28.4 1.0 CG D:ASP214 2.7 21.6 1.0 CG D:ASP212 3.1 20.5 1.0 CG D:ASP116 3.3 18.0 1.0 CE1 D:HIS118 3.4 22.6 1.0 ZN D:ZN301 3.4 23.8 1.0 OD2 D:ASP116 3.6 18.5 1.0 OD1 D:ASP212 3.6 19.4 1.0 CG D:HIS118 3.7 21.6 1.0 CB D:HIS118 4.0 21.3 1.0 CB D:ASP212 4.2 15.8 1.0 CB D:ASP214 4.3 19.2 1.0 N D:HIS118 4.3 18.7 1.0 O D:HOH568 4.3 42.9 1.0 O D:HOH449 4.5 23.8 1.0 N D:SER117 4.6 18.4 1.0 NE2 D:HIS118 4.6 21.6 1.0 OD1 D:ASP120 4.6 20.9 1.0 CD2 D:HIS118 4.7 21.3 1.0 CA D:HIS118 4.7 21.8 1.0 CB D:ASP116 4.8 18.6 1.0 SG D:CYS92 4.9 19.9 1.0 CB D:SER117 4.9 19.4 1.0

S.A.Hwangbo, J.W.Kim, S.J.Jung, K.S.Jin, J.O.Lee, J.S.Kim, S.Y.Park. Characterization of A Dimeric Arginase Fromzymomonas MOBILISZM4. Front Microbiol V. 10 2755 2019.
ISSN: ESSN 1664-302X
PubMed: 32038508
DOI: 10.3389/FMICB.2019.02755