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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 8jd8:

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

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase, PDB code: 8jd8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8jd8

Go back to Zinc Binding Sites List in 8jd8
Zinc binding site 1 out of 5 in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase


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 Citrus Limon Cu-Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:20.1
occ:1.00
 ND1 A:HIS75 1.9 19.9 1.0
ND1 A:HIS92 2.0 20.7 1.0
OD1 A:ASP95 2.1 19.1 1.0
ND1 A:HIS83 2.1 23.9 1.0
CG A:ASP95 2.8 19.7 1.0
CE1 A:HIS75 2.8 19.5 1.0
CE1 A:HIS92 2.9 21.4 1.0
OD2 A:ASP95 2.9 21.4 1.0
CG A:HIS75 2.9 19.6 1.0
CG A:HIS92 3.1 18.7 1.0
CE1 A:HIS83 3.1 19.9 1.0
CG A:HIS83 3.1 20.5 1.0
CB A:HIS75 3.3 19.9 1.0
CB A:HIS83 3.4 20.3 1.0
CB A:HIS92 3.5 19.9 1.0
O A:THR148 3.7 27.4 1.0
CA A:HIS83 3.7 24.2 1.0
NE2 A:HIS75 4.0 20.5 1.0
CD2 A:HIS75 4.0 18.9 1.0
NE2 A:HIS92 4.0 17.9 1.0
CD2 A:HIS92 4.1 19.7 1.0
NE2 A:HIS83 4.2 18.1 1.0
CD2 A:HIS83 4.2 18.6 1.0
CB A:ASP95 4.3 19.4 1.0
C A:THR148 4.7 24.8 1.0
N A:HIS92 4.7 20.2 1.0
N A:HIS83 4.7 23.0 1.0
CA A:HIS92 4.7 20.0 1.0
CA A:ASP95 4.8 17.7 1.0
C A:HIS83 4.8 22.4 1.0
N A:GLY84 4.8 22.3 1.0
CA A:HIS75 4.9 22.4 1.0
O A:HOH346 4.9 23.9 1.0

Zinc binding site 2 out of 5 in 8jd8

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Zinc binding site 2 out of 5 in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase


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 Citrus Limon Cu-Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:33.9
occ:1.00
 O A:MET14 2.2 20.5 1.0
O C:GLY165 2.3 23.3 1.0
OXT A:GLY165 2.3 20.1 1.0
O C:MET14 2.3 20.9 1.0
O C:HOH313 2.5 18.8 1.0
O C:HOH317 2.5 18.1 1.0
C A:MET14 3.4 21.4 1.0
C C:GLY165 3.5 20.5 1.0
C A:GLY165 3.5 19.9 1.0
C C:MET14 3.6 20.7 1.0
OXT C:GLY165 4.1 21.5 1.0
O A:GLY165 4.1 25.1 1.0
O C:HOH312 4.1 28.2 1.0
O A:HOH309 4.2 23.6 1.0
CG C:MET14 4.3 38.0 1.0
NE2 C:GLN13 4.3 56.7 1.0
CA A:MET14 4.3 23.7 1.0
N C:MET14 4.3 23.6 1.0
N A:VAL15 4.4 21.3 1.0
CA C:MET14 4.4 23.9 1.0
N A:MET14 4.4 27.2 1.0
OE1 C:GLN13 4.5 52.6 1.0
CA A:VAL15 4.5 23.2 1.0
CA A:GLY165 4.5 18.4 1.0
N C:VAL15 4.5 23.8 1.0
CA C:GLY165 4.5 20.1 1.0
CB A:MET14 4.5 27.8 1.0
CA C:VAL15 4.6 20.2 1.0
CB C:MET14 4.6 26.5 1.0
CD C:GLN13 4.7 66.8 1.0

Zinc binding site 3 out of 5 in 8jd8

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Zinc binding site 3 out of 5 in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase


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 Citrus Limon Cu-Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:22.3
occ:1.00
 ND1 B:HIS75 1.9 18.2 1.0
OD1 B:ASP95 1.9 20.8 1.0
ND1 B:HIS83 2.0 20.8 1.0
ND1 B:HIS92 2.0 18.8 1.0
CG B:ASP95 2.7 21.2 1.0
CE1 B:HIS75 2.9 20.8 1.0
OD2 B:ASP95 2.9 23.4 1.0
CE1 B:HIS83 2.9 20.7 1.0
CE1 B:HIS92 2.9 22.7 1.0
CG B:HIS75 3.0 21.5 1.0
CG B:HIS92 3.1 18.3 1.0
CG B:HIS83 3.2 24.8 1.0
CB B:HIS75 3.4 18.8 1.0
CB B:HIS92 3.5 22.2 1.0
CB B:HIS83 3.6 25.3 1.0
CA B:HIS83 3.8 23.3 1.0
NE2 B:HIS75 4.0 22.4 1.0
O B:THR148 4.1 29.6 1.0
CD2 B:HIS75 4.1 20.2 1.0
NE2 B:HIS83 4.1 23.4 1.0
NE2 B:HIS92 4.1 18.9 1.0
CB B:ASP95 4.1 21.5 1.0
CD2 B:HIS92 4.2 20.7 1.0
CD2 B:HIS83 4.2 25.9 1.0
CA B:ASP95 4.6 19.9 1.0
N B:HIS92 4.7 21.2 1.0
CA B:HIS92 4.7 20.8 1.0
N B:GLY84 4.8 20.6 1.0
N B:HIS83 4.8 21.1 1.0
C B:HIS83 4.8 23.1 1.0
N B:ASP95 4.9 18.5 1.0
CA B:HIS75 4.9 17.3 1.0
O B:HOH330 4.9 24.4 1.0

Zinc binding site 4 out of 5 in 8jd8

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Zinc binding site 4 out of 5 in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase


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 Citrus Limon Cu-Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:22.5
occ:1.00
 ND1 C:HIS75 2.0 20.5 1.0
ND1 C:HIS92 2.0 20.9 1.0
OD1 C:ASP95 2.0 22.0 1.0
ND1 C:HIS83 2.1 22.5 1.0
CG C:ASP95 2.8 22.2 1.0
CE1 C:HIS92 2.8 26.1 1.0
CE1 C:HIS75 2.9 20.5 1.0
OD2 C:ASP95 2.9 24.8 1.0
CG C:HIS75 3.0 24.2 1.0
CE1 C:HIS83 3.0 20.8 1.0
CG C:HIS92 3.1 19.7 1.0
CG C:HIS83 3.2 22.1 1.0
CB C:HIS75 3.4 22.2 1.0
CB C:HIS83 3.5 26.4 1.0
CB C:HIS92 3.5 24.6 1.0
O C:THR148 3.7 28.9 1.0
CA C:HIS83 3.8 23.0 1.0
NE2 C:HIS92 4.0 17.8 1.0
NE2 C:HIS75 4.0 24.8 1.0
CD2 C:HIS75 4.1 25.6 1.0
CD2 C:HIS92 4.1 22.9 1.0
NE2 C:HIS83 4.2 22.3 1.0
CB C:ASP95 4.2 21.6 1.0
CD2 C:HIS83 4.3 22.8 1.0
N C:HIS92 4.7 19.5 1.0
C C:THR148 4.7 25.3 1.0
CA C:ASP95 4.7 21.5 1.0
CA C:HIS92 4.7 20.1 1.0
N C:HIS83 4.8 21.1 1.0
N C:GLY84 4.8 23.1 1.0
C C:HIS83 4.8 25.7 1.0
CA C:HIS75 4.9 26.3 1.0
CD2 C:HIS58 5.0 26.7 1.0
N C:ASP95 5.0 21.5 1.0

Zinc binding site 5 out of 5 in 8jd8

Go back to Zinc Binding Sites List in 8jd8
Zinc binding site 5 out of 5 in the Crystal Structure of Citrus Limon Cu-Zn Superoxide Dismutase


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 Citrus Limon Cu-Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:22.2
occ:1.00
 OD1 D:ASP95 1.9 21.6 1.0
ND1 D:HIS92 2.0 17.9 1.0
ND1 D:HIS75 2.0 18.9 1.0
ND1 D:HIS83 2.1 29.6 1.0
CG D:ASP95 2.7 19.4 1.0
CE1 D:HIS92 2.8 20.1 1.0
CE1 D:HIS83 2.9 25.2 1.0
OD2 D:ASP95 2.9 23.4 1.0
CE1 D:HIS75 3.0 20.3 1.0
CG D:HIS75 3.0 20.7 1.0
CG D:HIS92 3.1 17.0 1.0
CG D:HIS83 3.2 26.3 1.0
CB D:HIS75 3.4 20.6 1.0
CB D:HIS92 3.5 18.9 1.0
CB D:HIS83 3.7 22.6 1.0
CA D:HIS83 3.9 21.6 1.0
O D:THR148 4.0 25.8 1.0
NE2 D:HIS92 4.0 18.1 1.0
NE2 D:HIS83 4.1 24.0 1.0
CD2 D:HIS92 4.1 19.9 1.0
NE2 D:HIS75 4.1 24.4 1.0
CB D:ASP95 4.1 19.2 1.0
CD2 D:HIS75 4.2 19.9 1.0
CD2 D:HIS83 4.3 25.1 1.0
CA D:ASP95 4.7 18.2 1.0
CA D:HIS92 4.8 18.9 1.0
N D:HIS92 4.8 18.8 1.0
N D:HIS83 4.8 24.3 1.0
N D:GLY84 4.8 21.7 1.0
N D:ASP95 4.9 18.5 1.0
C D:HIS83 4.9 24.4 1.0
O D:HOH341 4.9 31.1 1.0
CA D:HIS75 4.9 19.9 1.0
C D:THR148 4.9 25.9 1.0

Reference:

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
Page generated: Thu Oct 31 08:15:35 2024

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