Calcium in PDB 5ed4: Structure of A Phop-Dna Complex

Enzymatic activity of Structure of A Phop-Dna Complex

All present enzymatic activity of Structure of A Phop-Dna Complex:
3.1.3.1;

Protein crystallography data

The structure of Structure of A Phop-Dna Complex, PDB code: 5ed4 was solved by S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.60 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.240, 98.176, 167.888, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.7

Other elements in 5ed4:

The structure of Structure of A Phop-Dna Complex also contains other interesting chemical elements:

Arsenic (As) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A Phop-Dna Complex (pdb code 5ed4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of A Phop-Dna Complex, PDB code: 5ed4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5ed4

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Calcium binding site 1 out of 6 in the Structure of A Phop-Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Phop-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:77.5
occ:1.00
 O A:HOH422 2.1 75.9 1.0
OD1 A:ASP28 2.3 76.3 1.0
OD2 A:ASP71 2.3 72.6 1.0
O A:HOH447 2.3 78.4 1.0
O A:MET73 2.4 74.3 1.0
O A:HOH438 3.0 93.2 1.0
CG A:ASP28 3.2 78.6 1.0
CG A:ASP71 3.3 67.4 1.0
OD2 A:ASP28 3.4 81.4 1.0
C A:MET73 3.6 73.1 1.0
OD1 A:ASP71 3.7 70.6 1.0
NZ A:LYS121 3.9 81.4 1.0
OD1 A:ASP27 4.2 90.9 1.0
CG A:MET74 4.3 68.7 1.0
N A:MET74 4.4 66.8 1.0
CA A:MET74 4.5 66.3 1.0
CA A:MET73 4.6 73.7 1.0
CB A:ASP28 4.6 74.9 1.0
CB A:ASP71 4.6 58.7 1.0
CB A:MET73 4.7 79.4 1.0
OE1 A:GLU29 4.7 0.5 1.0
CG A:ASP27 4.7 89.0 1.0
CD A:GLU29 4.7 0.2 1.0
OD2 A:ASP27 4.8 99.7 1.0
N A:ASP28 4.8 72.1 1.0
O A:HOH409 4.9 72.9 1.0
OE2 A:GLU29 4.9 0.7 1.0
CB A:MET74 5.0 66.4 1.0

Calcium binding site 2 out of 6 in 5ed4

Go back to Calcium Binding Sites List in 5ed4
Calcium binding site 2 out of 6 in the Structure of A Phop-Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Phop-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:0.2
occ:1.00
 O B:MET73 2.1 0.0 1.0
OD2 B:ASP71 2.1 0.4 1.0
OD1 B:ASP28 2.2 0.6 1.0
O B:HOH406 2.3 80.9 1.0
O B:HOH424 2.6 93.4 1.0
CG B:ASP28 3.1 0.5 1.0
O B:HOH425 3.2 0.7 1.0
CG B:ASP71 3.2 0.1 1.0
OD2 B:ASP28 3.3 0.8 1.0
C B:MET73 3.3 0.4 1.0
OD1 B:ASP71 3.7 0.3 1.0
CB B:MET73 4.2 0.5 1.0
CA B:MET73 4.2 0.1 1.0
OD1 B:ASP27 4.3 99.2 1.0
N B:MET74 4.3 0.2 1.0
CA B:MET74 4.4 0.4 1.0
CB B:ASP28 4.4 0.5 1.0
CG B:MET74 4.5 0.8 1.0
CB B:ASP71 4.5 96.7 1.0
NZ B:LYS121 4.6 0.7 1.0
N B:MET73 4.7 0.8 1.0
N B:ASP28 4.8 90.6 1.0
OE1 B:GLU29 4.9 0.9 1.0

Calcium binding site 3 out of 6 in 5ed4

Go back to Calcium Binding Sites List in 5ed4
Calcium binding site 3 out of 6 in the Structure of A Phop-Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A Phop-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:79.5
occ:1.00
 OD1 B:ASP200 2.2 71.5 1.0
O B:HOH416 2.6 74.0 1.0
O B:HOH419 3.1 67.8 1.0
O B:HOH415 3.3 67.6 1.0
CG B:ASP200 3.4 74.6 1.0
OD2 B:ASP200 4.2 82.9 1.0
CB B:ASP200 4.3 65.5 1.0
CA B:ASP200 4.3 61.6 1.0
N B:ASP200 4.8 60.5 1.0

Calcium binding site 4 out of 6 in 5ed4

Go back to Calcium Binding Sites List in 5ed4
Calcium binding site 4 out of 6 in the Structure of A Phop-Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A Phop-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:75.4
occ:1.00
 O E:MET73 2.3 77.7 1.0
OD2 E:ASP71 2.3 75.3 1.0
O E:HOH402 2.3 64.7 1.0
OD1 E:ASP28 2.4 70.1 1.0
O E:HOH462 2.4 75.6 1.0
O E:HOH410 2.5 82.2 1.0
CG E:ASP71 3.3 71.0 1.0
C E:MET73 3.4 76.7 1.0
CG E:ASP28 3.5 73.0 1.0
OD1 E:ASP71 3.6 75.7 1.0
OD2 E:ASP28 3.9 84.4 1.0
NZ E:LYS121 4.1 74.9 1.0
OD1 E:ASP27 4.2 74.1 1.0
N E:MET74 4.3 68.5 1.0
CA E:MET73 4.4 76.7 1.0
CB E:MET73 4.4 82.3 1.0
CA E:MET74 4.5 66.0 1.0
OE1 E:GLU29 4.5 88.0 1.0
CB E:ASP71 4.6 57.1 1.0
CB E:ASP28 4.8 64.2 1.0
N E:MET73 4.8 74.5 1.0
CG E:MET74 4.8 69.1 1.0
CG E:ASP27 4.8 72.9 1.0
N E:ASP28 4.9 60.7 1.0
OD2 E:ASP27 4.9 79.0 1.0
O E:HOH449 4.9 86.1 1.0

Calcium binding site 5 out of 6 in 5ed4

Go back to Calcium Binding Sites List in 5ed4
Calcium binding site 5 out of 6 in the Structure of A Phop-Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of A Phop-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:88.9
occ:1.00
 OE2 F:GLU62 2.3 0.8 1.0
CD F:GLU62 3.4 0.3 1.0
CG F:GLU62 3.9 0.3 1.0
OE1 F:GLU62 4.4 0.2 1.0

Calcium binding site 6 out of 6 in 5ed4

Go back to Calcium Binding Sites List in 5ed4
Calcium binding site 6 out of 6 in the Structure of A Phop-Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of A Phop-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca302

b:99.6
occ:1.00
 O F:HOH419 2.1 86.1 1.0
OD1 F:ASP28 2.2 90.4 1.0
OD2 F:ASP71 2.2 0.7 1.0
O F:MET73 2.4 0.8 1.0
O F:HOH403 2.5 97.4 1.0
CG F:ASP28 3.0 93.5 1.0
O F:HOH424 3.0 85.1 1.0
OD2 F:ASP28 3.2 0.7 1.0
CG F:ASP71 3.2 94.3 1.0
OD1 F:ASP71 3.7 95.3 1.0
C F:MET73 3.7 0.9 1.0
NZ F:LYS121 3.9 93.5 1.0
OD1 F:ASP27 4.2 88.7 1.0
CB F:ASP28 4.4 87.3 1.0
N F:MET74 4.5 0.8 1.0
CB F:ASP71 4.5 80.5 1.0
CA F:MET74 4.5 0.5 1.0
N F:ASP28 4.6 79.1 1.0
CG F:MET74 4.6 99.4 1.0
CG F:ASP27 4.6 86.0 1.0
CA F:MET73 4.6 0.8 1.0
OD2 F:ASP27 4.7 90.9 1.0
CB F:MET73 4.7 0.8 1.0
OE1 F:GLU29 4.8 0.1 1.0

Reference:

X.He, L.Wang, S.Wang. Structural Basis of Dna Sequence Recognition By the Response Regulator Phop in Mycobacterium Tuberculosis. Sci Rep V. 6 24442 2016.
ISSN: ESSN 2045-2322
PubMed: 27079268
DOI: 10.1038/SREP24442
Page generated: Sat Dec 12 05:23:17 2020

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