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Zinc in PDB 5g13: Pseudomonas Aeruginosa Hdah (H143A) Unliganded.

Protein crystallography data

The structure of Pseudomonas Aeruginosa Hdah (H143A) Unliganded., PDB code: 5g13 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) 75.74 / 1.99
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.495, 81.495, 205.265, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.7

Other elements in 5g13:

The structure of Pseudomonas Aeruginosa Hdah (H143A) 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 (H143A) Unliganded. (pdb code 5g13). 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 (H143A) Unliganded., PDB code: 5g13:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5g13

Go back to Zinc Binding Sites List in 5g13
Zinc binding site 1 out of 2 in the Pseudomonas Aeruginosa Hdah (H143A) 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 (H143A) Unliganded. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1372

b:14.3
occ:0.70
O A:HOH2131 2.0 22.9 1.0
OD2 A:ASP269 2.0 14.4 1.0
OD1 A:ASP181 2.0 13.1 1.0
ND1 A:HIS183 2.1 11.5 1.0
O A:HOH2113 2.2 25.2 1.0
OD2 A:ASP181 2.4 12.0 1.0
CG A:ASP181 2.5 12.3 1.0
CE1 A:HIS183 3.0 11.4 1.0
CG A:ASP269 3.0 12.8 1.0
CG A:HIS183 3.2 10.9 1.0
OD1 A:ASP269 3.4 12.9 1.0
CB A:HIS183 3.6 10.7 1.0
CB A:ASP181 4.0 11.9 1.0
N A:HIS183 4.1 10.1 1.0
CA A:GLY311 4.1 15.0 1.0
NE2 A:HIS183 4.2 10.9 1.0
CD2 A:HIS183 4.3 10.7 1.0
OH A:TYR313 4.3 19.3 1.0
NE2 A:HIS144 4.3 15.4 1.0
CE2 A:TYR313 4.3 18.3 1.0
CB A:ASP269 4.3 11.8 1.0
N A:VAL182 4.4 10.5 1.0
CG1 A:VAL182 4.4 9.9 1.0
CA A:HIS183 4.5 10.3 1.0
N A:GLY311 4.5 14.7 1.0
O A:HOH2116 4.5 39.5 1.0
O A:HOH2205 4.6 25.2 1.0
CA A:ASP181 4.8 11.4 1.0
C A:ASP181 4.8 11.2 1.0
CZ A:TYR313 4.8 18.3 1.0
O A:HOH2127 4.8 11.6 1.0

Zinc binding site 2 out of 2 in 5g13

Go back to Zinc Binding Sites List in 5g13
Zinc binding site 2 out of 2 in the Pseudomonas Aeruginosa Hdah (H143A) 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 (H143A) Unliganded. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1378

b:14.6
occ:0.70
OD2 B:ASP269 2.0 12.6 1.0
OD1 B:ASP181 2.0 12.9 1.0
O B:HOH2114 2.1 19.7 1.0
ND1 B:HIS183 2.1 11.7 1.0
O B:HOH2097 2.2 28.4 1.0
OD2 B:ASP181 2.5 12.6 1.0
CG B:ASP181 2.5 12.1 1.0
CE1 B:HIS183 3.0 11.7 1.0
CG B:ASP269 3.1 10.7 1.0
CG B:HIS183 3.2 11.0 1.0
OD1 B:ASP269 3.5 10.7 1.0
CB B:HIS183 3.7 10.7 1.0
CB B:ASP181 4.0 11.6 1.0
N B:HIS183 4.1 10.1 1.0
CA B:GLY311 4.1 15.3 1.0
OH B:TYR313 4.1 18.6 1.0
NE2 B:HIS183 4.2 11.3 1.0
CE2 B:TYR313 4.3 17.3 1.0
NE2 B:HIS144 4.3 15.3 1.0
CD2 B:HIS183 4.3 11.1 1.0
CB B:ASP269 4.4 10.3 1.0
N B:GLY311 4.5 15.6 1.0
O B:HOH2099 4.5 28.9 1.0
N B:VAL182 4.5 10.3 1.0
CG1 B:VAL182 4.5 9.7 1.0
CA B:HIS183 4.5 10.4 1.0
CZ B:TYR313 4.7 17.7 1.0
O B:HOH2110 4.8 17.6 1.0
CA B:ASP181 4.8 11.5 1.0
C B:ASP181 4.9 10.9 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 06:18:21 2020

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