Copper in PDB 8jd8: Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase

All present enzymatic activity of Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase:
1.15.1.1;

The structure of Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase, PDB code: 8jd8 was solved by R.A.Utami, H.Yoshida, D.S.Retnoningrum, W.T.Ismaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.36 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.111, 74.554, 61.686, 90, 106.86, 90
R / Rfree (%)	17.3 / 26.6

The structure of Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

The binding sites of Copper atom in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase (pdb code 8jd8). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase, PDB code: 8jd8:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:40.6 occ:0.25 NE2 A:HIS132 1.9 21.8 1.0 NE2 A:HIS60 2.4 21.7 1.0 NE2 A:HIS75 2.4 20.5 1.0 ND1 A:HIS58 2.5 24.4 1.0 O A:HOH319 2.7 31.2 1.0 CD2 A:HIS132 2.9 20.5 1.0 CE1 A:HIS132 2.9 21.9 1.0 CE1 A:HIS60 3.0 20.7 1.0 CD2 A:HIS75 3.1 18.9 1.0 CG A:HIS58 3.2 23.1 1.0 CB A:HIS58 3.3 20.9 1.0 O A:HOH356 3.4 28.7 1.0 CD2 A:HIS60 3.5 20.7 1.0 CE1 A:HIS75 3.5 19.5 1.0 CE1 A:HIS58 3.5 27.9 1.0 ND1 A:HIS132 3.9 18.6 1.0 CG A:HIS132 3.9 17.9 1.0 ND1 A:HIS60 4.1 19.7 1.0 CG A:HIS75 4.2 19.6 1.0 CD2 A:HIS58 4.4 26.6 1.0 CG A:HIS60 4.4 19.1 1.0 ND1 A:HIS75 4.4 19.9 1.0 NE2 A:HIS58 4.5 27.1 1.0 CA A:HIS58 4.7 19.8 1.0 O A:HOH358 4.8 28.5 1.0 CB A:VAL130 4.8 18.2 1.0 CG1 A:VAL130 4.9 19.9 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu202 b:37.9 occ:0.50 NE2 B:HIS132 1.8 21.3 1.0 NE2 B:HIS60 2.1 18.2 1.0 ND1 B:HIS58 2.3 27.3 1.0 CE1 B:HIS132 2.7 24.1 1.0 CD2 B:HIS132 2.8 28.8 1.0 CE1 B:HIS60 2.8 18.2 1.0 NE2 B:HIS75 2.9 22.4 1.0 CG B:HIS58 3.2 21.6 1.0 CE1 B:HIS58 3.3 30.6 1.0 CD2 B:HIS60 3.3 21.0 1.0 CB B:HIS58 3.4 21.4 1.0 CD2 B:HIS75 3.4 20.2 1.0 ND1 B:HIS132 3.7 29.2 1.0 CG B:HIS132 3.8 24.3 1.0 CE1 B:HIS75 4.0 20.8 1.0 ND1 B:HIS60 4.0 21.9 1.0 CG B:HIS60 4.3 20.9 1.0 CD2 B:HIS58 4.3 28.3 1.0 NE2 B:HIS58 4.3 26.7 1.0 CG B:HIS75 4.6 21.5 1.0 CG1 B:VAL130 4.7 20.7 1.0 CB B:VAL130 4.7 20.1 1.0 CA B:HIS58 4.7 19.7 1.0 ND1 B:HIS75 4.8 18.2 1.0 N B:HIS58 5.0 18.4 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu202 b:23.0 occ:0.20 NE2 C:HIS132 1.9 19.9 1.0 ND1 C:HIS58 2.3 23.1 1.0 NE2 C:HIS75 2.3 24.8 1.0 NE2 C:HIS60 2.6 24.6 1.0 CD2 C:HIS132 2.7 20.6 1.0 O C:HOH323 2.8 28.3 1.0 CE1 C:HIS132 2.9 21.7 1.0 CD2 C:HIS75 2.9 25.6 1.0 CG C:HIS58 3.0 24.0 1.0 CE1 C:HIS58 3.1 25.9 1.0 CE1 C:HIS60 3.3 21.9 1.0 CB C:HIS58 3.3 20.4 1.0 CE1 C:HIS75 3.5 20.5 1.0 O C:HOH332 3.5 26.1 1.0 CD2 C:HIS60 3.6 22.8 1.0 CG C:HIS132 3.8 21.6 1.0 ND1 C:HIS132 3.8 24.0 1.0 CD2 C:HIS58 4.0 26.7 1.0 NE2 C:HIS58 4.1 21.8 1.0 CG C:HIS75 4.2 24.2 1.0 ND1 C:HIS75 4.4 20.5 1.0 ND1 C:HIS60 4.5 23.7 1.0 CA C:HIS58 4.6 17.7 1.0 CG C:HIS60 4.6 23.6 1.0 N C:HIS58 4.8 18.1 1.0 CB C:VAL130 5.0 21.4 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu202 b:34.7 occ:1.00 NE2 D:HIS132 1.9 25.3 1.0 NE2 D:HIS60 2.1 24.1 1.0 ND1 D:HIS58 2.4 22.2 1.0 CD2 D:HIS132 2.8 25.9 1.0 CE1 D:HIS60 2.8 21.5 1.0 CE1 D:HIS132 2.9 26.1 1.0 NE2 D:HIS75 3.2 24.4 1.0 CD2 D:HIS60 3.3 21.7 1.0 CE1 D:HIS58 3.3 20.4 1.0 CG D:HIS58 3.3 20.5 1.0 CB D:HIS58 3.6 21.4 1.0 CD2 D:HIS75 3.7 19.9 1.0 CG D:HIS132 4.0 23.8 1.0 ND1 D:HIS132 4.0 26.2 1.0 ND1 D:HIS60 4.0 22.5 1.0 CE1 D:HIS75 4.3 20.3 1.0 CG D:HIS60 4.3 20.8 1.0 CG1 D:VAL130 4.4 20.3 1.0 CB D:VAL130 4.5 20.3 1.0 NE2 D:HIS58 4.5 19.9 1.0 CD2 D:HIS58 4.5 21.6 1.0 NE D:ARG155 4.9 23.8 1.0 CG D:HIS75 4.9 20.7 1.0 CA D:HIS58 4.9 19.8 1.0

R.A.Utami, H.Yoshida, L.H.Kartadinata, V.A.Abdillah, C.R.Faratilla, D.S.Retnoningrum, W.T.Ismaya. Direct Relationship Between Dimeric Form and Activity in the Acidic Copper-Zinc Superoxide Dismutase From Lemon. Acta Crystallogr.,Sect.F V. 79 301 2023.
ISSN: ESSN 2053-230X
PubMed: 38108885
DOI: 10.1107/S2053230X23010646