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Zinc in PDB 7zd3: Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions

Enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions

All present enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions, PDB code: 7zd3 was solved by P.H.Malecki, M.Gawel, K.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.53 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.19, 134.05, 108.46, 90, 105.71, 90
R / Rfree (%) 18 / 22.2

Other elements in 7zd3:

The structure of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Potassium (K) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions (pdb code 7zd3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions, PDB code: 7zd3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 7zd3

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Zinc binding site 1 out of 16 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:30.8
occ:1.00
 OD1 A:ASP139 2.0 26.1 1.0
O A:ASP139 2.1 26.7 1.0
NE2 A:HIS323 2.3 30.6 1.0
SG A:CYS85 2.3 24.6 1.0
CG A:ASP139 2.9 28.8 1.0
C A:ASP139 2.9 24.2 1.0
CD2 A:HIS323 3.1 28.5 1.0
CB A:CYS85 3.2 22.0 1.0
CB A:ASP139 3.2 26.1 1.0
CE1 A:HIS323 3.4 34.1 1.0
O5' A:ADN502 3.6 39.8 1.0
CA A:ASP139 3.6 24.4 1.0
NE2 A:HIS61 3.8 26.7 1.0
N A:GLY140 3.8 20.8 1.0
CE1 A:HIS61 3.9 22.5 1.0
OD2 A:ASP139 4.0 23.2 1.0
CA A:GLY140 4.1 23.6 1.0
O A:HOH888 4.2 29.8 1.0
CG A:HIS323 4.3 34.2 1.0
O A:CYS85 4.3 28.5 1.0
ND1 A:HIS323 4.4 32.0 1.0
CA A:CYS85 4.5 26.1 1.0
O A:HOH663 4.6 28.1 1.0
CD2 A:HIS61 4.6 23.7 1.0
C A:CYS85 4.6 26.7 1.0
N A:ASP139 4.6 24.6 1.0
O A:HOH756 4.7 33.7 1.0
ND1 A:HIS61 4.7 20.7 1.0
C5' A:ADN502 4.9 29.4 1.0

Zinc binding site 2 out of 16 in 7zd3

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Zinc binding site 2 out of 16 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:57.6
occ:1.00
 O A:HOH637 1.9 47.5 1.0
OE2 A:GLU421 2.2 43.5 1.0
O A:HOH771 2.3 43.0 0.5
NE2 A:HIS400 2.3 47.4 1.0
O A:HOH927 2.6 44.0 1.0
O A:HOH771 2.7 32.2 0.5
CD2 A:HIS400 3.1 36.8 1.0
CD A:GLU421 3.3 49.1 1.0
CE1 A:HIS400 3.4 54.5 1.0
OE1 A:GLU421 3.6 54.3 1.0
O A:HOH849 3.7 40.7 1.0
CG A:HIS400 4.4 41.2 1.0
O A:HOH904 4.4 37.8 1.0
OE1 A:GLN404 4.4 41.9 1.0
ND1 A:HIS400 4.4 47.8 1.0
CG A:GLU421 4.6 41.3 1.0

Zinc binding site 3 out of 16 in 7zd3

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Zinc binding site 3 out of 16 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:47.6
occ:0.93
 O A:HOH632 2.0 45.5 1.0
OD2 A:ASP174 2.1 41.0 1.0
NE2 A:HIS170 2.3 40.0 1.0
O A:HOH1004 2.5 53.0 1.0
O A:HOH973 2.7 51.4 1.0
CG A:ASP174 3.0 39.5 1.0
CD2 A:HIS170 3.2 41.9 1.0
OD1 A:ASP174 3.2 39.1 1.0
CE1 A:HIS170 3.3 47.2 1.0
O D:TYR453 3.6 35.1 1.0
O A:HOH878 4.0 38.2 1.0
O A:HOH988 4.3 59.2 1.0
CG A:HIS170 4.3 40.0 1.0
ND1 A:HIS170 4.4 43.2 1.0
CB A:ASP174 4.4 37.1 1.0
O D:GLU452 4.6 32.3 1.0
C D:TYR453 4.6 26.9 1.0
N D:GLY455 4.8 27.2 1.0
C5 A:PG4505 4.9 72.0 1.0
C D:ILE454 4.9 32.6 1.0

Zinc binding site 4 out of 16 in 7zd3

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Zinc binding site 4 out of 16 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn511

b:63.3
occ:0.50
 O A:HOH974 2.3 52.2 1.0
ND1 A:HIS170 2.3 43.2 1.0
O A:HOH1056 2.5 51.5 1.0
O1 A:PG4505 2.7 76.7 1.0
CE1 A:HIS170 3.0 47.2 1.0
O A:HOH959 3.3 48.8 1.0
CG A:HIS170 3.4 40.0 1.0
O D:HOH681 3.5 38.8 1.0
C1 A:PG4505 3.6 75.0 1.0
CB A:HIS170 3.9 38.1 1.0
NE2 A:HIS170 4.2 40.0 1.0
CA A:HIS170 4.2 32.7 1.0
O D:ILE454 4.3 32.6 1.0
CD2 A:HIS170 4.4 41.9 1.0
O D:HOH1055 4.5 48.1 1.0
C2 A:PG4505 4.6 74.0 1.0
CD1 A:LEU173 4.8 31.4 1.0
O A:HOH1011 4.8 54.4 1.0
O A:HIS170 4.9 28.6 1.0

Zinc binding site 5 out of 16 in 7zd3

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Zinc binding site 5 out of 16 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn506

b:37.1
occ:1.00
 OD1 B:ASP139 2.0 37.2 1.0
O B:ASP139 2.0 36.8 1.0
NE2 B:HIS323 2.3 33.9 1.0
SG B:CYS85 2.3 31.3 1.0
CG B:ASP139 2.8 32.3 1.0
C B:ASP139 2.8 29.9 1.0
CD2 B:HIS323 3.1 32.1 1.0
CB B:ASP139 3.1 33.4 1.0
CB B:CYS85 3.2 28.4 1.0
CE1 B:HIS323 3.3 38.6 1.0
CA B:ASP139 3.6 31.4 1.0
O5' B:ADN502 3.7 44.4 1.0
N B:GLY140 3.8 32.8 1.0
NE2 B:HIS61 3.8 29.6 1.0
OD2 B:ASP139 3.9 34.7 1.0
CE1 B:HIS61 3.9 28.0 1.0
CA B:GLY140 4.1 32.2 1.0
O B:HOH822 4.3 34.1 1.0
CG B:HIS323 4.3 36.0 1.0
O B:CYS85 4.3 33.2 1.0
ND1 B:HIS323 4.4 36.4 1.0
CA B:CYS85 4.5 30.6 1.0
O B:HOH743 4.5 38.5 1.0
O B:HOH694 4.5 44.8 1.0
N B:ASP139 4.6 30.9 1.0
CD2 B:HIS61 4.6 30.2 1.0
C B:CYS85 4.6 33.6 1.0
ND1 B:HIS61 4.8 29.8 1.0
C5' B:ADN502 4.9 34.0 1.0

Zinc binding site 6 out of 16 in 7zd3

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Zinc binding site 6 out of 16 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn507

b:62.9
occ:0.80
 O B:HOH605 2.0 59.2 1.0
OE2 B:GLU421 2.2 57.9 1.0
NE2 B:HIS400 2.3 59.6 1.0
O B:HOH928 2.4 49.2 0.5
O B:HOH928 2.4 45.7 0.5
O B:HOH929 2.4 56.1 1.0
CD2 B:HIS400 3.1 53.1 1.0
CD B:GLU421 3.2 56.2 1.0
CE1 B:HIS400 3.4 60.1 1.0
OE1 B:GLU421 3.7 50.2 1.0
O B:HOH741 3.8 45.4 1.0
OE1 B:GLN404 4.3 56.9 1.0
CG B:HIS400 4.4 52.2 1.0
ND1 B:HIS400 4.4 60.4 1.0
O B:HOH791 4.5 50.6 1.0
CG B:GLU421 4.5 44.5 1.0

Zinc binding site 7 out of 16 in 7zd3

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Zinc binding site 7 out of 16 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn508

b:62.4
occ:1.00
 OD2 B:ASP174 2.0 44.7 1.0
NE2 B:HIS170 2.3 47.2 1.0
O B:HOH603 2.7 64.7 1.0
O C:HOH1008 2.8 57.8 1.0
CG B:ASP174 2.9 46.4 1.0
O B:HOH933 3.0 58.4 1.0
CD2 B:HIS170 3.2 50.6 1.0
OD1 B:ASP174 3.2 50.3 1.0
CE1 B:HIS170 3.3 50.6 1.0
O C:TYR453 3.8 36.9 1.0
O B:HOH892 4.2 47.9 1.0
CB B:ASP174 4.3 44.3 1.0
O4 B:BCN510 4.3 70.6 1.0
CG B:HIS170 4.3 46.4 1.0
ND1 B:HIS170 4.4 49.6 1.0
O B:HOH922 4.4 58.1 1.0
O B:HOH970 4.7 60.2 1.0
O C:GLU452 4.8 40.5 1.0
C C:TYR453 4.8 34.6 1.0

Zinc binding site 8 out of 16 in 7zd3

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Zinc binding site 8 out of 16 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn509

b:69.3
occ:1.00
 NE2 B:HIS360 2.3 40.0 1.0
O B:HOH1011 2.7 45.6 1.0
O B:HOH974 2.8 42.5 1.0
O A:HOH1018 2.8 56.7 1.0
O B:HOH1001 3.0 29.8 0.5
CD2 B:HIS360 3.2 37.8 1.0
CE1 B:HIS360 3.4 40.2 1.0
O B:HOH1001 3.7 33.1 0.5
CG B:HIS360 4.4 36.4 1.0
ND1 B:HIS360 4.4 37.7 1.0
CD1 A:ILE29 4.7 26.0 1.0
O A:HOH905 4.8 39.4 1.0
CD A:ARG25 4.9 30.8 1.0
CB B:ALA359 5.0 26.7 1.0

Zinc binding site 9 out of 16 in 7zd3

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Zinc binding site 9 out of 16 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn509

b:31.9
occ:1.00
 OD1 C:ASP139 1.9 32.9 1.0
O C:ASP139 2.1 28.5 1.0
SG C:CYS85 2.3 27.9 1.0
NE2 C:HIS323 2.3 34.2 1.0
CG C:ASP139 2.9 29.3 1.0
C C:ASP139 2.9 27.3 1.0
CD2 C:HIS323 3.1 27.6 1.0
CB C:CYS85 3.1 23.9 1.0
CB C:ASP139 3.2 27.6 1.0
CE1 C:HIS323 3.4 40.1 1.0
O5' C:ADN503 3.6 40.6 1.0
CA C:ASP139 3.6 25.7 1.0
NE2 C:HIS61 3.8 31.1 1.0
N C:GLY140 3.8 25.1 1.0
CE1 C:HIS61 4.0 29.1 1.0
OD2 C:ASP139 4.0 32.1 1.0
CA C:GLY140 4.1 27.2 1.0
CG C:HIS323 4.3 34.6 1.0
O C:CYS85 4.4 30.7 1.0
ND1 C:HIS323 4.4 33.4 1.0
O C:HOH820 4.4 31.8 1.0
CA C:CYS85 4.4 29.9 1.0
O C:HOH665 4.5 34.7 1.0
O C:HOH812 4.5 35.4 1.0
CD2 C:HIS61 4.6 25.7 1.0
C C:CYS85 4.6 30.1 1.0
N C:ASP139 4.6 24.7 1.0
ND1 C:HIS61 4.8 21.6 1.0
C5' C:ADN503 4.9 31.9 1.0

Zinc binding site 10 out of 16 in 7zd3

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Zinc binding site 10 out of 16 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn510

b:60.9
occ:1.00
 NE2 C:HIS400 2.3 47.6 1.0
OE2 C:GLU421 2.3 46.6 1.0
O C:HOH634 2.4 52.9 1.0
O C:HOH944 2.5 43.8 1.0
O C:HOH1053 2.9 26.7 0.2
CD2 C:HIS400 3.1 40.4 1.0
CD C:GLU421 3.3 51.5 1.0
O C:HOH1053 3.4 35.5 0.5
CE1 C:HIS400 3.4 46.9 1.0
O C:HOH821 3.7 43.0 1.0
OE1 C:GLU421 3.7 47.8 1.0
CG C:HIS400 4.3 41.8 1.0
ND1 C:HIS400 4.4 45.6 1.0
NE2 C:GLN404 4.5 37.5 1.0
O C:HOH786 4.6 35.5 1.0
CG C:GLU421 4.6 38.8 1.0

Reference:

P.H.Malecki, M.Gawel, K.Brzezinski. Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By ZN2+ Ions To Be Published.
Page generated: Wed Oct 30 16:22:10 2024

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