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Zinc in PDB 4onx: 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens.

Protein crystallography data

The structure of 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens., PDB code: 4onx was solved by G.Minasov, A.Halavaty, L.Shuvalova, I.Dubrovska, J.Winsor, K.Kwon, S.Shatsman, W.F.Anderson, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.51 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.903, 82.739, 73.954, 90.00, 105.92, 90.00
R / Rfree (%) 19.7 / 25

Other elements in 4onx:

The structure of 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens. also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens. (pdb code 4onx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens., PDB code: 4onx:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4onx

Go back to Zinc Binding Sites List in 4onx
Zinc binding site 1 out of 3 in the 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:52.8
occ:1.00
OE1 A:GLU72 1.9 62.6 1.0
OE1 C:GLU72 1.9 58.5 1.0
NE2 A:HIS76 2.1 51.7 1.0
NE2 C:HIS76 2.1 47.5 1.0
CD A:GLU72 2.6 58.9 1.0
CD C:GLU72 2.6 55.2 1.0
OE2 A:GLU72 2.7 60.9 1.0
OE2 C:GLU72 2.7 58.9 1.0
CE1 C:HIS76 3.0 45.5 1.0
CE1 A:HIS76 3.0 50.1 1.0
CD2 A:HIS76 3.1 48.7 1.0
CD2 C:HIS76 3.2 45.2 1.0
NH1 C:ARG69 3.7 68.6 1.0
CG A:GLU72 4.0 58.7 1.0
CG C:GLU72 4.1 51.4 1.0
ND1 A:HIS76 4.1 51.0 1.0
ND1 C:HIS76 4.1 47.7 1.0
O A:GLU72 4.2 50.7 1.0
O C:GLU72 4.2 49.0 1.0
CG A:HIS76 4.2 49.5 1.0
CG C:HIS76 4.2 46.2 1.0
NH1 A:ARG69 4.3 55.6 1.0
C A:GLU72 4.3 50.5 1.0
CA A:TYR73 4.4 52.7 1.0
C C:GLU72 4.4 50.8 1.0
CA C:TYR73 4.4 44.6 1.0
N A:TYR73 4.4 53.0 1.0
N C:TYR73 4.5 43.9 1.0
CB A:GLU72 4.6 54.8 1.0
CB C:GLU72 4.7 48.5 1.0
NH2 A:ARG69 4.7 58.3 1.0
CZ C:ARG69 4.7 58.3 1.0
NH2 C:ARG69 4.8 55.3 1.0
CZ A:ARG69 5.0 54.8 1.0

Zinc binding site 2 out of 3 in 4onx

Go back to Zinc Binding Sites List in 4onx
Zinc binding site 2 out of 3 in the 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:81.1
occ:1.00
OE1 F:GLU72 2.1 0.8 1.0
OE1 B:GLU72 2.1 0.4 1.0
NE2 F:HIS76 2.1 84.9 1.0
NE2 B:HIS76 2.1 77.1 1.0
CD F:GLU72 2.7 89.8 1.0
OE2 F:GLU72 2.8 91.2 1.0
CD B:GLU72 2.8 91.5 1.0
OE2 B:GLU72 2.9 95.2 1.0
CE1 F:HIS76 2.9 81.6 1.0
CE1 B:HIS76 3.0 82.7 1.0
CD2 F:HIS76 3.2 81.6 1.0
CD2 B:HIS76 3.2 75.2 1.0
ND1 F:HIS76 4.1 77.5 1.0
CG F:GLU72 4.1 92.7 1.0
NH1 B:ARG69 4.2 82.1 1.0
ND1 B:HIS76 4.2 80.9 1.0
CG B:GLU72 4.2 89.5 1.0
NH1 F:ARG69 4.2 90.3 1.0
CG F:HIS76 4.3 76.0 1.0
CG B:HIS76 4.3 73.2 1.0
O F:GLU72 4.4 85.3 1.0
O B:GLU72 4.4 78.2 1.0
NH2 B:ARG69 4.5 81.8 1.0
CA B:TYR73 4.5 78.2 1.0
CA F:TYR73 4.5 84.6 1.0
NH2 F:ARG69 4.6 85.3 1.0
C F:GLU72 4.6 86.2 1.0
C B:GLU72 4.6 86.1 1.0
N B:TYR73 4.6 78.3 1.0
N F:TYR73 4.6 81.6 1.0
CB F:GLU72 4.8 90.4 1.0
CZ B:ARG69 4.8 82.9 1.0
CB B:GLU72 4.8 85.6 1.0
CZ F:ARG69 4.9 90.6 1.0

Zinc binding site 3 out of 3 in 4onx

Go back to Zinc Binding Sites List in 4onx
Zinc binding site 3 out of 3 in the 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:84.2
occ:1.00
OE1 E:GLU72 2.0 97.6 1.0
OE1 D:GLU72 2.1 0.4 1.0
NE2 E:HIS76 2.1 87.7 1.0
NE2 D:HIS76 2.1 78.0 1.0
CD E:GLU72 2.7 91.3 1.0
OE2 E:GLU72 2.7 92.8 1.0
CD D:GLU72 2.8 0.2 1.0
OE2 D:GLU72 2.8 0.8 1.0
CE1 E:HIS76 2.9 85.2 1.0
CE1 D:HIS76 3.0 80.6 1.0
CD2 E:HIS76 3.2 79.8 1.0
CD2 D:HIS76 3.2 71.8 1.0
ND1 E:HIS76 4.1 79.9 1.0
CG E:GLU72 4.1 93.0 1.0
ND1 D:HIS76 4.1 81.9 1.0
NH1 D:ARG69 4.2 95.5 1.0
CG D:GLU72 4.2 0.6 1.0
NH1 E:ARG69 4.2 88.0 1.0
CG E:HIS76 4.3 77.3 1.0
CG D:HIS76 4.3 72.6 1.0
O E:GLU72 4.4 96.9 1.0
O D:GLU72 4.4 0.0 1.0
NH2 D:ARG69 4.5 95.2 1.0
CA D:TYR73 4.5 0.6 1.0
NH2 E:ARG69 4.6 84.2 1.0
CA E:TYR73 4.6 82.6 1.0
C D:GLU72 4.6 0.2 1.0
C E:GLU72 4.6 87.9 1.0
N D:TYR73 4.6 0.2 1.0
N E:TYR73 4.7 83.8 1.0
CB E:GLU72 4.8 87.8 1.0
CB D:GLU72 4.8 0.2 1.0
CZ D:ARG69 4.8 95.8 1.0
CZ E:ARG69 4.9 90.3 1.0

Reference:

G.Minasov, A.Halavaty, L.Shuvalova, I.Dubrovska, J.Winsor, K.Kwon, S.Shatsman, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase From Clostridium Perfringens. To Be Published.
Page generated: Wed Dec 16 05:39:21 2020

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