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Zinc in PDB 6f3o: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations, PDB code: 6f3o was solved by J.Czyrko, K.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.839, 99.614, 111.825, 90.00, 101.97, 90.00
R / Rfree (%) 14 / 16.7

Other elements in 6f3o:

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations also contains other interesting chemical elements:

Potassium (K) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations (pdb code 6f3o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations, PDB code: 6f3o:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6f3o

Go back to Zinc Binding Sites List in 6f3o
Zinc binding site 1 out of 2 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:21.0
occ:0.11
O A:ASP139 2.1 23.6 1.0
CE1 A:HIS323 2.1 24.8 0.9
NE2 A:HIS323 2.2 25.2 0.1
SG A:CYS85 2.3 23.3 1.0
OD1 A:ASP139 2.5 26.2 1.0
C A:ASP139 2.8 22.8 1.0
CG A:ASP139 2.9 25.9 1.0
NE2 A:HIS323 3.0 26.1 0.9
CE1 A:HIS323 3.0 25.4 0.1
ND1 A:HIS323 3.1 24.4 0.9
CB A:ASP139 3.2 23.4 1.0
CB A:CYS85 3.2 24.2 1.0
CD2 A:HIS323 3.3 25.0 0.1
CA A:ASP139 3.6 22.1 1.0
O A:HOH650 3.6 24.9 0.5
N A:GLY140 3.7 21.9 1.0
OD2 A:ASP139 3.7 27.9 1.0
NE2 A:HIS61 3.8 22.0 1.0
CA A:GLY140 4.0 21.9 1.0
ND1 A:HIS323 4.0 25.3 0.1
CE1 A:HIS61 4.1 21.4 1.0
O A:HOH676 4.2 34.7 1.0
CD2 A:HIS323 4.2 25.8 0.9
CG A:HIS323 4.2 25.0 0.1
O A:HOH651 4.2 30.8 1.0
CG A:HIS323 4.3 24.7 0.9
O A:CYS85 4.3 24.7 1.0
CA A:CYS85 4.5 24.0 1.0
N A:ASP139 4.6 21.8 1.0
CD2 A:HIS61 4.6 20.7 1.0
C A:CYS85 4.6 24.5 1.0
O A:HOH795 4.7 28.5 1.0
CG2 A:THR165 4.8 23.3 1.0
ND1 A:HIS61 4.9 22.1 1.0

Zinc binding site 2 out of 2 in 6f3o

Go back to Zinc Binding Sites List in 6f3o
Zinc binding site 2 out of 2 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenine, K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn507

b:30.9
occ:0.19
O D:ASP139 2.0 24.1 1.0
CE1 D:HIS323 2.2 25.6 0.8
NE2 D:HIS323 2.2 24.2 0.2
SG D:CYS85 2.3 21.8 1.0
OD1 D:ASP139 2.5 26.7 1.0
C D:ASP139 2.8 22.7 1.0
CG D:ASP139 2.8 25.1 1.0
NE2 D:HIS323 3.0 25.7 0.8
CB D:CYS85 3.1 20.9 1.0
CB D:ASP139 3.1 22.5 1.0
CE1 D:HIS323 3.1 24.4 0.2
CD2 D:HIS323 3.2 23.8 0.2
ND1 D:HIS323 3.3 24.7 0.8
CA D:ASP139 3.5 21.7 1.0
OD2 D:ASP139 3.7 25.8 1.0
N D:GLY140 3.7 20.9 1.0
O D:HOH842 3.8 33.0 0.7
NE2 D:HIS61 3.9 20.8 1.0
CA D:GLY140 4.0 21.0 1.0
O D:HOH646 4.1 27.7 1.0
CE1 D:HIS61 4.1 19.6 1.0
O D:HOH732 4.2 18.1 0.5
CD2 D:HIS323 4.3 25.7 0.8
O D:CYS85 4.3 21.8 1.0
ND1 D:HIS323 4.3 24.0 0.2
CG D:HIS323 4.4 23.5 0.2
CG D:HIS323 4.4 24.1 0.8
CA D:CYS85 4.4 20.9 1.0
N D:ASP139 4.5 22.5 1.0
C D:CYS85 4.6 20.8 1.0
CD2 D:HIS61 4.6 20.4 1.0
O D:HOH790 4.6 30.3 1.0
CG2 D:THR165 4.9 23.4 1.0
ND1 D:HIS61 4.9 20.2 1.0

Reference:

J.Czyrko, J.Sliwiak, B.Imiolczyk, Z.Gdaniec, M.Jaskolski, K.Brzezinski. Metal-Cation Regulation of Enzyme Dynamics Is A Key Factor Influencing the Activity of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa. Sci Rep V. 8 11334 2018.
ISSN: ESSN 2045-2322
PubMed: 30054521
DOI: 10.1038/S41598-018-29535-Y
Page generated: Mon Oct 28 20:39:10 2024

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