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Zinc in PDB 5g1a: Bordetella Alcaligenes Hdah Bound to Pfsaha

Enzymatic activity of Bordetella Alcaligenes Hdah Bound to Pfsaha

All present enzymatic activity of Bordetella Alcaligenes Hdah Bound to Pfsaha:
3.5.1.4;

Protein crystallography data

The structure of Bordetella Alcaligenes Hdah Bound to Pfsaha, PDB code: 5g1a 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) 87.96 / 1.42
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.440, 101.440, 175.930, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17

Other elements in 5g1a:

The structure of Bordetella Alcaligenes Hdah Bound to Pfsaha also contains other interesting chemical elements:

Fluorine (F) 24 atoms
Potassium (K) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Bordetella Alcaligenes Hdah Bound to Pfsaha (pdb code 5g1a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Bordetella Alcaligenes Hdah Bound to Pfsaha, PDB code: 5g1a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5g1a

Go back to Zinc Binding Sites List in 5g1a
Zinc binding site 1 out of 2 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn370

b:10.9
occ:0.50
OD2 A:ASP268 1.9 9.7 1.0
OD1 A:ASP180 2.0 8.9 1.0
O A:7H1373 2.1 13.5 0.7
ND1 A:HIS182 2.2 9.8 1.0
O1 A:7H1373 2.2 15.0 0.7
OD2 A:ASP180 2.5 11.0 1.0
CG A:ASP180 2.6 9.4 1.0
N A:7H1373 2.7 14.3 0.7
C A:7H1373 2.8 17.0 0.7
CG A:ASP268 3.0 9.1 1.0
CE1 A:HIS182 3.0 10.2 1.0
CG A:HIS182 3.2 8.8 1.0
OD1 A:ASP268 3.5 9.0 1.0
CB A:HIS182 3.6 8.1 1.0
N A:HIS182 4.0 7.6 1.0
NE2 A:HIS142 4.0 13.2 1.0
CB A:ASP180 4.1 8.9 1.0
NE2 A:HIS182 4.2 10.2 1.0
CA A:GLY310 4.2 9.7 1.0
CB A:ASP268 4.2 8.3 1.0
CE2 A:TYR312 4.3 11.6 1.0
CD2 A:HIS182 4.3 9.6 1.0
C1 A:7H1373 4.3 18.8 0.7
OH A:TYR312 4.4 15.6 1.0
CE1 A:HIS142 4.4 11.4 1.0
CG1 A:VAL181 4.4 7.6 1.0
N A:VAL181 4.4 7.9 1.0
CA A:HIS182 4.4 8.2 1.0
N A:GLY310 4.5 9.7 1.0
F2 A:7H1373 4.6 22.1 0.7
F3 A:7H1373 4.7 23.2 0.7
CZ A:TYR312 4.8 12.1 1.0
CA A:ASP180 4.8 8.6 1.0
C A:ASP180 4.8 8.8 1.0
C2 A:7H1373 4.9 20.9 0.7
NE2 A:HIS143 4.9 17.1 1.0
C A:GLY310 4.9 9.4 1.0
O A:HOH2276 4.9 36.3 1.0
N A:GLY311 4.9 9.6 1.0
C A:VAL181 5.0 7.9 1.0
F1 A:7H1373 5.0 23.6 0.7

Zinc binding site 2 out of 2 in 5g1a

Go back to Zinc Binding Sites List in 5g1a
Zinc binding site 2 out of 2 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn370

b:12.5
occ:0.50
OD2 B:ASP268 2.0 10.2 1.0
OD1 B:ASP180 2.0 9.7 1.0
O B:7H1373 2.0 14.5 0.7
ND1 B:HIS182 2.1 11.2 1.0
O1 B:7H1373 2.2 16.3 0.7
OD2 B:ASP180 2.5 11.7 1.0
CG B:ASP180 2.6 9.6 1.0
N B:7H1373 2.7 16.9 0.7
C B:7H1373 2.8 19.0 0.7
CG B:ASP268 3.0 10.4 1.0
CE1 B:HIS182 3.0 12.1 1.0
CG B:HIS182 3.2 10.4 1.0
OD1 B:ASP268 3.5 10.5 1.0
CB B:HIS182 3.6 8.5 1.0
N B:HIS182 4.0 8.6 1.0
NE2 B:HIS142 4.0 15.0 1.0
CB B:ASP180 4.1 9.6 1.0
NE2 B:HIS182 4.2 11.6 1.0
CA B:GLY310 4.2 9.3 1.0
CB B:ASP268 4.2 9.7 1.0
CE2 B:TYR312 4.3 12.0 1.0
C1 B:7H1373 4.3 21.8 0.7
CD2 B:HIS182 4.3 11.1 1.0
CE1 B:HIS142 4.3 13.9 1.0
OH B:TYR312 4.4 15.8 1.0
CG1 B:VAL181 4.4 8.8 1.0
CA B:HIS182 4.4 8.6 1.0
N B:VAL181 4.4 9.1 1.0
N B:GLY310 4.5 9.5 1.0
O B:HOH2255 4.6 45.3 1.0
F2 B:7H1373 4.7 25.1 0.7
CZ B:TYR312 4.8 12.4 1.0
NE2 B:HIS143 4.8 17.8 1.0
F3 B:7H1373 4.8 28.5 0.7
CA B:ASP180 4.9 9.2 1.0
C B:ASP180 4.9 9.2 1.0
F1 B:7H1373 4.9 24.9 0.7
C2 B:7H1373 4.9 23.8 0.7
C B:GLY310 4.9 9.5 1.0
N B:GLY311 5.0 9.8 1.0
C B:VAL181 5.0 8.7 1.0

Reference:

C.Meyners, A.Kramer, O.Yildiz, F.J.Meyer-Almes. The Thermodynamic Signature of Ligand Binding to Histone Deacetylase-Like Amidohydrolases Is Most Sensitive to the Flexibility in the L2-Loop Lining the Active Site Pocket. Biochim. Biophys. Acta V.1861 1855 2017.
ISSN: ISSN 0006-3002
PubMed: 28389333
DOI: 10.1016/J.BBAGEN.2017.04.001
Page generated: Wed Dec 16 06:18:23 2020

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