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Zinc in PDB 6f3m: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations

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

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, 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 Adenosine, K+ and ZN2+ Cations, PDB code: 6f3m 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) 48.70 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.976, 104.145, 107.634, 90.00, 100.71, 90.00
R / Rfree (%) 15.1 / 17.4

Other elements in 6f3m:

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, 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 Adenosine, K+ and ZN2+ Cations (pdb code 6f3m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations, PDB code: 6f3m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6f3m

Go back to Zinc Binding Sites List in 6f3m
Zinc binding site 1 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, 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 Adenosine, K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:31.6
occ:0.50
 OD2 A:ASP139 1.8 26.3 0.5
CE1 A:HIS323 2.0 33.9 0.5
OD1 A:ASP139 2.1 26.3 0.5
NE2 A:HIS323 2.1 35.6 0.5
O A:ASP139 2.3 26.8 1.0
SG A:CYS85 2.3 31.7 1.0
CG A:ASP139 2.6 26.3 0.5
CG A:ASP139 2.7 26.2 0.5
NE2 A:HIS323 2.9 34.1 0.5
C A:ASP139 3.0 25.9 1.0
CD2 A:HIS323 3.0 34.2 0.5
ND1 A:HIS323 3.1 32.8 0.5
CB A:ASP139 3.1 25.9 0.5
CB A:CYS85 3.1 29.2 1.0
CB A:ASP139 3.1 26.0 0.5
CE1 A:HIS323 3.2 35.7 0.5
O5' A:ADN502 3.4 34.3 0.5
OD1 A:ASP139 3.6 27.1 0.5
OD2 A:ASP139 3.6 26.7 0.5
NE2 A:HIS61 3.6 24.9 1.0
CA A:ASP139 3.6 25.8 0.5
CA A:ASP139 3.6 25.8 0.5
CE1 A:HIS61 3.9 25.2 1.0
N A:GLY140 3.9 25.6 1.0
CD2 A:HIS323 4.1 34.1 0.5
O A:CYS85 4.2 28.3 1.0
CG A:HIS323 4.2 33.8 0.5
CG A:HIS323 4.2 32.8 0.5
CA A:GLY140 4.2 25.2 1.0
ND1 A:HIS323 4.2 35.2 0.5
O A:HOH611 4.3 31.1 1.0
O A:HOH848 4.3 32.2 1.0
CA A:CYS85 4.4 27.6 1.0
C A:CYS85 4.5 27.8 1.0
CD2 A:HIS61 4.5 24.4 1.0
O A:HOH769 4.6 37.3 1.0
C5' A:ADN502 4.7 33.5 1.0
N A:ASP139 4.7 26.1 1.0
ND1 A:HIS61 4.7 23.8 1.0

Zinc binding site 2 out of 4 in 6f3m

Go back to Zinc Binding Sites List in 6f3m
Zinc binding site 2 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, 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 Adenosine, K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:33.6
occ:0.50
 OD2 B:ASP139 1.8 27.0 0.5
CE1 B:HIS323 2.0 34.2 0.5
OD1 B:ASP139 2.0 27.1 0.5
NE2 B:HIS323 2.1 34.7 0.5
O B:ASP139 2.3 30.1 1.0
SG B:CYS85 2.4 33.3 1.0
CG B:ASP139 2.6 28.2 0.5
CG B:ASP139 2.6 28.1 0.5
NE2 B:HIS323 2.9 34.8 0.5
CD2 B:HIS323 2.9 33.5 0.5
C B:ASP139 3.0 27.9 1.0
ND1 B:HIS323 3.0 33.3 0.5
CB B:ASP139 3.1 27.7 0.5
CB B:ASP139 3.1 27.8 0.5
CE1 B:HIS323 3.2 34.7 0.5
CB B:CYS85 3.2 30.9 1.0
O5' B:ADN502 3.2 32.7 0.5
OD1 B:ASP139 3.5 28.3 0.5
OD2 B:ASP139 3.6 27.6 0.5
NE2 B:HIS61 3.6 26.1 1.0
CA B:ASP139 3.6 27.5 0.5
CA B:ASP139 3.6 27.6 0.5
CE1 B:HIS61 3.9 26.0 1.0
N B:GLY140 3.9 28.5 1.0
CD2 B:HIS323 4.1 33.8 0.5
CG B:HIS323 4.2 33.4 0.5
CG B:HIS323 4.2 33.3 0.5
CA B:GLY140 4.2 27.8 1.0
O B:CYS85 4.2 32.2 1.0
ND1 B:HIS323 4.2 33.8 0.5
O B:HOH846 4.3 33.2 1.0
O B:HOH624 4.4 30.4 1.0
CA B:CYS85 4.5 30.2 1.0
CD2 B:HIS61 4.5 24.6 1.0
C5' B:ADN502 4.6 32.8 1.0
C B:CYS85 4.6 30.0 1.0
O B:HOH668 4.6 41.2 1.0
N B:ASP139 4.7 27.7 1.0
ND1 B:HIS61 4.8 25.5 1.0
CG2 B:THR165 5.0 26.0 1.0
C4' B:ADN502 5.0 32.0 1.0

Zinc binding site 3 out of 4 in 6f3m

Go back to Zinc Binding Sites List in 6f3m
Zinc binding site 3 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations


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

b:28.0
occ:0.50
 OD2 C:ASP139 1.9 25.0 0.5
CE1 C:HIS323 2.0 29.1 0.5
NE2 C:HIS323 2.1 30.9 0.5
OD1 C:ASP139 2.2 21.3 0.5
O C:ASP139 2.2 22.4 1.0
SG C:CYS85 2.4 28.9 1.0
CG C:ASP139 2.7 24.3 0.5
CG C:ASP139 2.7 23.0 0.5
NE2 C:HIS323 2.7 29.6 0.5
C C:ASP139 2.9 22.0 1.0
CD2 C:HIS323 3.0 29.2 0.5
ND1 C:HIS323 3.1 27.3 0.5
CB C:ASP139 3.1 22.5 0.5
CB C:ASP139 3.1 23.4 0.5
CB C:CYS85 3.2 26.6 1.0
CE1 C:HIS323 3.2 31.3 0.5
O5' C:ADN502 3.3 28.4 0.5
OD1 C:ASP139 3.6 24.0 0.5
CA C:ASP139 3.6 22.0 0.5
CA C:ASP139 3.6 22.4 0.5
OD2 C:ASP139 3.6 23.4 0.5
NE2 C:HIS61 3.7 20.6 1.0
N C:GLY140 3.8 20.6 1.0
CE1 C:HIS61 3.9 20.1 1.0
CD2 C:HIS323 4.0 29.1 0.5
CA C:GLY140 4.1 21.5 1.0
CG C:HIS323 4.2 27.5 0.5
O C:HOH809 4.2 30.1 1.0
CG C:HIS323 4.2 28.8 0.5
O C:CYS85 4.2 25.9 1.0
ND1 C:HIS323 4.2 30.8 0.5
O C:HOH629 4.3 28.6 1.0
CA C:CYS85 4.4 24.8 1.0
O C:HOH816 4.4 35.4 1.0
C C:CYS85 4.5 24.5 1.0
CD2 C:HIS61 4.5 19.5 1.0
N C:ASP139 4.6 22.1 1.0
C5' C:ADN502 4.7 28.6 1.0
ND1 C:HIS61 4.7 20.2 1.0

Zinc binding site 4 out of 4 in 6f3m

Go back to Zinc Binding Sites List in 6f3m
Zinc binding site 4 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations


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

b:26.1
occ:0.50
 OD2 D:ASP139 1.8 25.9 0.5
CE1 D:HIS323 2.1 29.0 0.5
NE2 D:HIS323 2.1 29.0 0.5
OD1 D:ASP139 2.2 21.1 0.5
O D:ASP139 2.2 21.0 1.0
SG D:CYS85 2.3 26.8 1.0
CG D:ASP139 2.6 23.1 0.5
CG D:ASP139 2.8 21.8 0.5
NE2 D:HIS323 2.8 30.1 0.5
C D:ASP139 3.0 20.8 1.0
CD2 D:HIS323 3.0 28.1 0.5
CB D:CYS85 3.1 25.3 1.0
CB D:ASP139 3.1 21.8 0.5
CE1 D:HIS323 3.2 29.3 0.5
CB D:ASP139 3.2 21.0 0.5
ND1 D:HIS323 3.2 28.5 0.5
O5' D:ADN502 3.4 28.8 0.5
OD1 D:ASP139 3.6 22.6 0.5
NE2 D:HIS61 3.6 21.1 1.0
CA D:ASP139 3.7 20.2 0.5
CA D:ASP139 3.7 20.5 0.5
OD2 D:ASP139 3.7 22.5 0.5
CE1 D:HIS61 3.9 21.8 1.0
N D:GLY140 3.9 20.0 1.0
CD2 D:HIS323 4.0 28.9 0.5
O D:CYS85 4.2 23.7 1.0
CA D:GLY140 4.2 19.9 1.0
CG D:HIS323 4.2 27.6 0.5
CG D:HIS323 4.2 28.0 0.5
ND1 D:HIS323 4.2 28.2 0.5
O D:HOH648 4.2 25.2 1.0
O D:HOH894 4.2 25.5 1.0
CA D:CYS85 4.3 22.9 1.0
C D:CYS85 4.5 23.6 1.0
CD2 D:HIS61 4.5 20.4 1.0
O D:HOH715 4.5 33.6 1.0
C5' D:ADN502 4.6 27.6 1.0
N D:ASP139 4.7 20.0 1.0
ND1 D:HIS61 4.7 21.6 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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