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Zinc in PDB 6f3n: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of 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 Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations, PDB code: 6f3n 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) 24.82 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.585, 99.275, 111.721, 90.00, 101.90, 90.00
R / Rfree (%) 15.1 / 17.6

Other elements in 6f3n:

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of 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 Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations (pdb code 6f3n). 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 Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations, PDB code: 6f3n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6f3n

Go back to Zinc Binding Sites List in 6f3n
Zinc binding site 1 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of 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 Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:33.6
occ:0.35
 O A:ASP139 2.1 19.1 1.0
CE1 A:HIS323 2.2 25.2 0.7
OD1 A:ASP139 2.2 25.4 1.0
SG A:CYS85 2.3 18.7 1.0
NE2 A:HIS323 2.4 25.9 0.3
CG A:ASP139 2.7 21.0 1.0
C A:ASP139 2.9 19.1 1.0
CB A:ASP139 3.1 19.9 1.0
NE2 A:HIS323 3.1 25.9 0.7
CB A:CYS85 3.1 18.4 1.0
CD2 A:HIS323 3.2 24.7 0.3
ND1 A:HIS323 3.2 23.8 0.7
O5' A:ADN505 3.3 27.0 0.7
CE1 A:HIS323 3.4 26.2 0.3
CA A:ASP139 3.5 18.7 1.0
OD2 A:ASP139 3.6 23.2 1.0
NE2 A:HIS61 3.7 18.7 1.0
N A:GLY140 3.8 18.5 1.0
CE1 A:HIS61 4.0 18.6 1.0
CA A:GLY140 4.2 18.4 1.0
CD2 A:HIS323 4.3 25.5 0.7
CG A:HIS323 4.3 24.7 0.3
O A:CYS85 4.3 17.7 1.0
CG A:HIS323 4.3 24.4 0.7
O A:HOH635 4.4 23.8 1.0
ND1 A:HIS323 4.4 25.7 0.3
CD2 A:HIS61 4.5 17.6 1.0
CA A:CYS85 4.5 18.0 1.0
O A:HOH692 4.5 32.1 1.0
O A:HOH860 4.5 33.0 1.0
N A:ASP139 4.5 18.0 1.0
C A:CYS85 4.6 17.8 1.0
C5' A:ADN505 4.7 26.6 0.7
ND1 A:HIS61 4.8 18.2 1.0
C5' A:ADN505 4.8 20.3 0.3
CG2 A:THR165 4.9 21.0 1.0
O5' A:ADN505 5.0 19.9 0.3
C4' A:ADN505 5.0 20.4 0.3

Zinc binding site 2 out of 4 in 6f3n

Go back to Zinc Binding Sites List in 6f3n
Zinc binding site 2 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of 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 Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:29.5
occ:0.35
 O B:ASP139 2.1 16.1 1.0
CE1 B:HIS323 2.2 21.7 0.7
OD1 B:ASP139 2.2 23.1 1.0
NE2 B:HIS323 2.3 23.5 0.3
SG B:CYS85 2.3 16.0 1.0
CG B:ASP139 2.7 19.8 1.0
C B:ASP139 2.9 16.3 1.0
CE1 B:HIS323 2.9 24.1 0.3
CB B:ASP139 3.1 17.8 1.0
NE2 B:HIS323 3.1 22.2 0.7
ND1 B:HIS323 3.2 20.6 0.7
CB B:CYS85 3.2 15.5 1.0
O5' B:ADN505 3.3 25.6 0.7
CD2 B:HIS323 3.3 22.5 0.3
CA B:ASP139 3.5 16.9 1.0
OD2 B:ASP139 3.6 21.9 1.0
NE2 B:HIS61 3.6 17.1 1.0
N B:GLY140 3.8 16.5 1.0
CE1 B:HIS61 3.9 16.6 1.0
ND1 B:HIS323 4.0 23.6 0.3
CA B:GLY140 4.2 16.6 1.0
CG B:HIS323 4.3 22.4 0.3
CD2 B:HIS323 4.3 21.4 0.7
O B:HOH618 4.3 19.2 1.0
O B:CYS85 4.3 15.6 1.0
CG B:HIS323 4.3 20.9 0.7
CD2 B:HIS61 4.4 16.0 1.0
CA B:CYS85 4.5 15.8 1.0
O B:HOH824 4.5 26.7 1.0
N B:ASP139 4.6 16.1 1.0
C5' B:ADN505 4.6 25.3 0.7
C B:CYS85 4.6 16.0 1.0
O B:HOH649 4.6 27.1 1.0
C5' B:ADN505 4.8 19.6 0.3
ND1 B:HIS61 4.8 16.2 1.0
CG2 B:THR165 4.9 16.3 1.0
O5' B:ADN505 4.9 19.3 0.3
C4' B:ADN505 4.9 19.6 0.3
C4' B:ADN505 5.0 24.4 0.7

Zinc binding site 3 out of 4 in 6f3n

Go back to Zinc Binding Sites List in 6f3n
Zinc binding site 3 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of 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 Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:27.2
occ:0.30
 O C:ASP139 2.1 23.8 1.0
OD1 C:ASP139 2.1 25.1 1.0
SG C:CYS85 2.2 20.9 1.0
CE1 C:HIS323 2.3 27.3 0.7
NE2 C:HIS323 2.3 27.5 0.3
CG C:ASP139 2.6 22.5 1.0
C C:ASP139 2.9 22.8 1.0
CE1 C:HIS323 2.9 28.4 0.3
CB C:ASP139 3.0 22.1 1.0
CB C:CYS85 3.1 21.4 1.0
NE2 C:HIS323 3.2 28.0 0.7
ND1 C:HIS323 3.2 25.9 0.7
O5' C:ADN505 3.4 30.4 0.7
CD2 C:HIS323 3.4 26.5 0.3
CA C:ASP139 3.5 22.0 1.0
OD2 C:ASP139 3.5 24.2 1.0
NE2 C:HIS61 3.6 20.2 1.0
N C:GLY140 3.8 23.1 1.0
CE1 C:HIS61 3.9 20.4 1.0
ND1 C:HIS323 4.1 27.8 0.3
CA C:GLY140 4.2 22.9 1.0
CG C:HIS323 4.3 26.7 0.3
CD2 C:HIS61 4.3 19.4 1.0
O C:CYS85 4.4 22.6 1.0
CD2 C:HIS323 4.4 27.1 0.7
CG C:HIS323 4.4 26.4 0.7
CA C:CYS85 4.5 21.6 1.0
N C:ASP139 4.5 21.5 1.0
O C:HOH640 4.5 28.4 1.0
O C:HOH653 4.5 35.3 1.0
O C:HOH753 4.6 35.9 1.0
C C:CYS85 4.6 21.6 1.0
C5' C:ADN505 4.7 30.0 0.7
C5' C:ADN505 4.8 20.2 0.3
ND1 C:HIS61 4.8 19.9 1.0
C4' C:ADN505 4.9 19.9 0.3
CG2 C:THR165 4.9 23.8 1.0
O5' C:ADN505 4.9 19.8 0.3
C4' C:ADN505 5.0 27.9 0.7

Zinc binding site 4 out of 4 in 6f3n

Go back to Zinc Binding Sites List in 6f3n
Zinc binding site 4 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of 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 Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:27.7
occ:0.35
 O D:ASP139 2.1 18.3 1.0
SG D:CYS85 2.2 16.6 1.0
CE1 D:HIS323 2.2 26.4 0.7
NE2 D:HIS323 2.3 26.3 0.3
OD1 D:ASP139 2.3 22.7 1.0
CG D:ASP139 2.8 20.6 1.0
C D:ASP139 2.9 18.2 1.0
CB D:CYS85 3.0 16.3 1.0
CB D:ASP139 3.1 18.9 1.0
NE2 D:HIS323 3.1 26.7 0.7
CD2 D:HIS323 3.2 24.8 0.3
CE1 D:HIS323 3.3 26.5 0.3
ND1 D:HIS323 3.3 24.5 0.7
O5' D:ADN506 3.4 25.8 0.7
CA D:ASP139 3.5 18.1 1.0
OD2 D:ASP139 3.6 23.6 1.0
NE2 D:HIS61 3.7 16.4 1.0
N D:GLY140 3.8 17.2 1.0
CE1 D:HIS61 4.0 16.1 1.0
CA D:GLY140 4.2 16.7 1.0
O D:CYS85 4.2 16.8 1.0
CD2 D:HIS323 4.3 25.9 0.7
O D:HOH669 4.3 26.3 1.0
CA D:CYS85 4.3 16.2 1.0
ND1 D:HIS323 4.4 25.8 0.3
CG D:HIS323 4.4 24.6 0.3
O D:HOH810 4.4 12.3 0.5
CG D:HIS323 4.4 24.7 0.7
CD2 D:HIS61 4.4 15.5 1.0
C D:CYS85 4.5 16.0 1.0
N D:ASP139 4.5 17.6 1.0
C5' D:ADN506 4.7 25.9 0.7
ND1 D:HIS61 4.8 15.2 1.0
C5' D:ADN506 4.8 21.5 0.3
C4' D:ADN506 5.0 21.3 0.3

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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