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: Wed Dec 16 11:45:57 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy