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Calcium in PDB 3u17: Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid

Protein crystallography data

The structure of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid, PDB code: 3u17 was solved by A.M.Gulick, E.J.Drake, C.C.Aldrich, J.Neres, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.368, 144.232, 148.735, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid (pdb code 3u17). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid, PDB code: 3u17:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3u17

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Calcium binding site 1 out of 7 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca544

b:42.1
occ:1.00
 OD1 A:ASN330 2.5 34.7 1.0
O A:GLU327 2.5 30.9 1.0
O A:HOH696 2.6 40.2 1.0
O A:HOH711 2.7 40.0 1.0
O A:HOH698 3.1 51.4 1.0
CG A:ASN330 3.4 37.6 1.0
C A:GLU327 3.5 35.2 1.0
ND2 A:ASN330 3.9 34.3 1.0
O A:PRO326 4.1 35.4 1.0
CA A:GLU327 4.3 38.3 1.0
N A:VAL328 4.5 33.0 1.0
CB A:ASN330 4.6 32.7 1.0
CA A:VAL328 4.7 31.4 1.0
OE2 A:GLU327 4.7 66.5 1.0
CA A:ASN330 4.8 35.1 1.0
O A:VAL328 4.9 35.2 1.0
C A:VAL328 4.9 34.4 1.0
N A:ASN330 5.0 31.4 1.0

Calcium binding site 2 out of 7 in 3u17

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Calcium binding site 2 out of 7 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca545

b:40.5
occ:1.00
 O A:GLN53 2.4 41.2 1.0
O A:HOH707 2.5 45.7 1.0
OE1 A:GLU58 2.6 39.4 1.0
O A:HOH708 2.7 42.5 1.0
O A:HOH723 2.7 48.8 1.0
OE2 A:GLU58 2.7 48.7 1.0
CD A:GLU58 3.0 45.6 1.0
C A:GLN53 3.7 40.2 1.0
O A:HOH564 3.9 39.9 1.0
CA A:LEU54 4.4 37.8 1.0
N A:LEU54 4.5 39.0 1.0
CG A:GLU58 4.5 36.1 1.0
CA A:GLN53 4.6 38.4 1.0
N A:SER55 4.6 33.5 1.0
CB A:GLN53 4.7 34.8 1.0
N A:GLN53 4.8 38.3 1.0

Calcium binding site 3 out of 7 in 3u17

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Calcium binding site 3 out of 7 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca546

b:35.1
occ:1.00
 O A:LEU307 2.4 31.5 1.0
O A:ASN330 2.5 33.6 1.0
O A:HOH700 2.5 32.8 1.0
O A:HOH699 2.5 33.7 1.0
O A:GLN305 2.5 35.0 0.5
O A:GLN305 2.5 35.0 0.5
C A:GLN305 3.6 36.4 0.5
C A:LEU307 3.6 33.8 1.0
C A:GLN305 3.6 36.4 0.5
C A:ASN330 3.6 36.2 1.0
N A:LEU307 4.0 31.9 1.0
CB A:ASN330 4.2 32.7 1.0
CA A:GLN305 4.2 36.3 0.5
C A:SER306 4.3 35.4 1.0
CA A:LEU307 4.3 30.6 1.0
CA A:GLN305 4.4 36.4 0.5
O A:ILE304 4.4 33.0 1.0
CA A:CYS331 4.4 35.3 1.0
CB A:CYS331 4.4 29.9 1.0
N A:CYS331 4.5 35.6 1.0
N A:SER306 4.5 36.1 1.0
CA A:ASN330 4.5 35.1 1.0
N A:LYS308 4.6 32.1 1.0
CB A:LEU307 4.6 34.3 1.0
O A:LEU329 4.6 38.4 1.0
O A:SER306 4.7 33.8 1.0
CA A:SER306 4.7 36.4 1.0
CA A:LYS308 4.7 30.8 1.0

Calcium binding site 4 out of 7 in 3u17

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Calcium binding site 4 out of 7 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca547

b:73.6
occ:1.00
 O A:HOH718 2.5 43.2 1.0
O A:HOH611 2.8 39.2 1.0
O A:HOH717 3.0 36.1 1.0
O A:SER418 3.1 36.9 1.0
O A:HOH719 3.2 46.6 1.0
C A:SER418 4.2 39.2 1.0
O A:GLY198 4.3 45.8 1.0
OH A:TYR416 4.4 38.1 1.0
NE A:ARG435 4.5 64.4 1.0
O A:HOH632 4.6 30.6 1.0
OD1 A:ASP420 4.6 40.6 1.0
O A:HOH716 4.7 36.7 1.0
CZ A:ARG435 4.7 61.7 1.0
CB A:SER418 4.7 33.7 1.0
CA A:SER418 4.7 34.5 1.0
NH2 A:ARG435 4.8 54.4 1.0
OD2 A:ASP420 4.8 36.5 1.0
CD A:ARG435 5.0 53.2 1.0

Calcium binding site 5 out of 7 in 3u17

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Calcium binding site 5 out of 7 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca544

b:48.4
occ:1.00
 O B:GLN305 2.5 38.2 1.0
O B:LEU307 2.5 34.2 1.0
O B:ASN330 2.5 42.8 1.0
O B:HOH713 2.6 47.0 1.0
O B:HOH720 2.6 49.2 1.0
O B:HOH719 2.6 40.4 1.0
O B:HOH712 2.7 48.3 1.0
C B:GLN305 3.5 37.2 1.0
C B:LEU307 3.7 42.7 1.0
C B:ASN330 3.8 44.4 1.0
N B:LEU307 4.1 39.0 1.0
CA B:GLN305 4.1 44.1 1.0
CB B:ASN330 4.2 41.0 1.0
C B:SER306 4.4 40.1 1.0
CA B:LEU307 4.4 38.9 1.0
O B:ILE304 4.4 39.0 1.0
N B:SER306 4.5 35.6 1.0
CA B:ASN330 4.6 40.2 1.0
CA B:CYS331 4.6 40.3 1.0
N B:CYS331 4.6 40.5 1.0
N B:LYS308 4.7 40.3 1.0
CB B:CYS331 4.7 36.6 1.0
CA B:SER306 4.7 38.8 1.0
CB B:LEU307 4.8 39.3 1.0
O B:SER306 4.8 41.9 1.0
O B:LEU329 4.8 43.1 1.0
CA B:LYS308 4.8 38.6 1.0
CD B:LYS308 4.8 50.1 1.0
CB B:GLN305 4.9 40.0 1.0

Calcium binding site 6 out of 7 in 3u17

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Calcium binding site 6 out of 7 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca545

b:77.6
occ:1.00
 O B:GLN53 2.7 58.3 1.0
O B:HOH717 2.7 56.9 1.0
O B:HOH715 2.8 58.2 1.0
OE1 B:GLU58 3.0 51.5 1.0
OE2 B:GLU58 3.0 61.2 1.0
CD B:GLU58 3.4 57.0 1.0
O B:HOH716 3.8 59.2 1.0
C B:GLN53 3.9 57.2 1.0
CB B:GLN53 4.8 56.8 1.0
CA B:GLN53 4.8 52.9 1.0
CA B:LEU54 4.8 46.7 1.0
N B:LEU54 4.8 51.9 1.0
CG B:GLU58 4.8 48.8 1.0
N B:GLN53 4.9 52.1 1.0

Calcium binding site 7 out of 7 in 3u17

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Calcium binding site 7 out of 7 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 6-(P-Benzoyl)Phenyl-1-(Pyridin-4-Ylmethyl)-1H-Pyrazolo[3,4- B]Pyridine-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca546

b:69.5
occ:1.00
 O B:HOH694 2.6 40.5 1.0
O B:HOH723 2.7 46.2 1.0
O B:HOH696 2.7 48.3 1.0
O B:HOH641 2.8 36.0 1.0
O B:HOH722 2.8 36.0 1.0
O B:SER418 2.8 38.5 1.0
O B:HOH634 3.7 43.6 1.0
C B:SER418 4.0 38.2 1.0
OD1 B:ASP420 4.4 36.3 1.0
CB B:SER418 4.5 32.6 1.0
OH B:TYR416 4.5 32.3 1.0
CA B:SER418 4.5 34.9 1.0
OD2 B:ASP420 4.6 39.6 1.0
O B:GLY198 4.6 44.6 1.0
O B:HOH672 4.7 40.2 1.0
O B:HOH743 4.7 48.2 1.0
CG B:ASP420 4.8 40.7 1.0
O B:HOH628 4.8 26.9 1.0

Reference:

J.Neres, E.Drake, A.M.Gulick, C.C.Aldrich. Structure-Activity Relationship of Base To Be Published.
Page generated: Sat Jul 13 19:58:07 2024

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