Zinc in PDB 5g12: Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.

Protein crystallography data

The structure of Pseudomonas Aeruginosa Hdah (Y313F) Unliganded., PDB code: 5g12 was solved by A.Kraemer, F.J.Meyer-Almes, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.79 / 2.02
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.560, 81.560, 205.150, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.4

Other elements in 5g12:

The structure of Pseudomonas Aeruginosa Hdah (Y313F) Unliganded. also contains other interesting chemical elements:

Potassium (K) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded. (pdb code 5g12). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded., PDB code: 5g12:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5g12

Go back to Zinc Binding Sites List in 5g12
Zinc binding site 1 out of 2 in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pseudomonas Aeruginosa Hdah (Y313F) Unliganded. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1372

b:16.7
occ:0.70
OD2 A:ASP269 2.0 16.5 1.0
OD1 A:ASP181 2.0 14.0 1.0
ND1 A:HIS183 2.1 14.9 1.0
O A:HOH2077 2.3 24.8 1.0
O A:HOH2094 2.4 37.7 1.0
OD2 A:ASP181 2.7 14.2 1.0
CG A:ASP181 2.7 14.0 1.0
CE1 A:HIS183 2.9 15.2 1.0
CG A:ASP269 3.0 15.9 1.0
CG A:HIS183 3.2 14.2 1.0
OD1 A:ASP269 3.3 17.1 1.0
CB A:HIS183 3.7 14.1 1.0
N A:HIS183 4.1 13.6 1.0
NE2 A:HIS183 4.1 14.7 1.0
CA A:GLY311 4.2 20.5 1.0
CB A:ASP181 4.2 13.8 1.0
NE2 A:HIS143 4.2 21.8 1.0
O A:HOH2076 4.2 43.3 1.0
CE2 A:PHE313 4.3 22.4 0.5
CD2 A:HIS183 4.3 14.6 1.0
CB A:ASP269 4.3 14.8 1.0
N A:VAL182 4.3 12.8 1.0
CG1 A:VAL182 4.3 13.4 1.0
CA A:HIS183 4.5 13.5 1.0
N A:GLY311 4.6 19.6 1.0
NE2 A:HIS144 4.6 18.3 1.0
CE1 A:HIS143 4.6 21.5 1.0
CZ A:PHE313 4.7 22.5 0.5
C A:ASP181 4.8 12.9 1.0
CA A:ASP181 4.8 13.1 1.0
C A:GLY311 4.9 20.2 1.0
C A:VAL182 5.0 13.0 1.0

Zinc binding site 2 out of 2 in 5g12

Go back to Zinc Binding Sites List in 5g12
Zinc binding site 2 out of 2 in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pseudomonas Aeruginosa Hdah (Y313F) Unliganded. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1377

b:18.6
occ:0.70
OD2 B:ASP269 2.0 17.5 1.0
OD1 B:ASP181 2.0 15.8 1.0
ND1 B:HIS183 2.1 16.1 1.0
O B:HOH2063 2.2 28.0 1.0
O B:HOH2081 2.5 42.5 1.0
OD2 B:ASP181 2.7 16.1 1.0
CG B:ASP181 2.7 15.1 1.0
CE1 B:HIS183 2.9 16.4 1.0
CG B:ASP269 3.0 15.7 1.0
CG B:HIS183 3.2 15.2 1.0
OD1 B:ASP269 3.4 16.1 1.0
CB B:HIS183 3.7 14.3 1.0
O B:HOH2064 3.8 56.2 1.0
N B:HIS183 4.0 14.2 1.0
NE2 B:HIS183 4.1 16.1 1.0
CA B:GLY311 4.1 21.8 1.0
NE2 B:HIS143 4.2 21.4 1.0
CB B:ASP181 4.2 14.6 1.0
CD2 B:HIS183 4.3 15.7 1.0
CE2 B:PHE313 4.3 25.5 0.5
CG1 B:VAL182 4.3 13.6 1.0
CB B:ASP269 4.3 14.3 1.0
N B:VAL182 4.3 14.2 1.0
CA B:HIS183 4.5 14.1 1.0
N B:GLY311 4.6 22.2 1.0
NE2 B:HIS144 4.6 21.1 1.0
CE1 B:HIS143 4.6 20.7 1.0
CZ B:PHE313 4.7 26.4 0.5
C B:ASP181 4.8 14.2 1.0
CA B:ASP181 4.9 14.2 1.0
C B:VAL182 5.0 13.7 1.0
C B:GLY311 5.0 22.4 1.0

Reference:

A.Kramer, T.Wagner, O.Yildiz, F.J.Meyer-Almes. Crystal Structure of A Histone Deacetylase Homologue From Pseudomonas Aeruginosa. Biochemistry V. 55 6858 2016.
ISSN: ISSN 1520-4995
PubMed: 27951649
DOI: 10.1021/ACS.BIOCHEM.6B00613
Page generated: Wed Dec 16 06:18:20 2020

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