Calcium in PDB 7pjd: The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.

The structure of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori., PDB code: 7pjd was solved by J.Guo, J.Cooper, R.M.Keegan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.50 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.64, 79.43, 100.93, 90, 91.6, 90
R / Rfree (%)	19 / 24.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. (pdb code 7pjd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori., PDB code: 7pjd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:33.4 occ:1.00 OD1 A:ASP19 2.2 30.6 1.0 O A:VAL25 2.3 33.8 1.0 O A:HOH332 2.4 33.8 1.0 OD1 A:ASP21 2.4 38.7 1.0 OG A:SER23 2.4 34.6 1.0 OD2 A:ASP30 2.5 32.6 1.0 OD1 A:ASP30 2.5 33.8 1.0 CG A:ASP30 2.8 33.2 1.0 CG A:ASP21 3.3 37.9 1.0 CG A:ASP19 3.4 31.2 1.0 CB A:SER23 3.5 36.1 1.0 C A:VAL25 3.5 35.4 1.0 OD2 A:ASP21 3.7 38.5 1.0 N A:SER23 3.9 36.3 1.0 CA A:ASP19 4.2 31.4 1.0 CA A:SER23 4.2 35.9 1.0 OD2 A:ASP19 4.2 31.4 1.0 N A:VAL25 4.3 36.5 1.0 CA A:VAL26 4.3 32.6 1.0 N A:VAL26 4.3 33.0 1.0 CB A:ASP30 4.3 32.1 1.0 CB A:ASP19 4.3 31.1 1.0 N A:ASP21 4.5 34.0 1.0 CB A:ASP21 4.5 36.8 1.0 N A:LYS22 4.5 37.7 1.0 CA A:VAL25 4.5 36.5 1.0 C A:ASP19 4.5 32.4 1.0 OE2 A:GLU27 4.6 45.3 1.0 N A:GLU27 4.6 34.4 1.0 N A:GLY24 4.7 34.1 1.0 C A:ASP21 4.8 37.6 1.0 CA A:ASP21 4.8 37.0 1.0 C A:SER23 4.8 35.6 1.0 O A:ASP19 4.9 34.0 1.0 C A:VAL26 4.9 33.7 1.0 N A:SER20 5.0 31.9 1.0 C A:LYS22 5.0 36.8 1.0

Calcium binding site 2 out of 18 in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:34.3 occ:1.00 O A:LYS76 2.2 32.7 1.0 OD1 A:ASP70 2.2 36.5 1.0 O A:HOH363 2.2 44.7 1.0 OD1 A:ASP72 2.3 39.1 1.0 OD1 A:ASP74 2.4 36.6 1.0 OE1 A:GLU81 2.5 34.1 1.0 OE2 A:GLU81 2.6 38.5 1.0 CD A:GLU81 2.9 35.9 1.0 CG A:ASP70 3.3 35.6 1.0 CG A:ASP74 3.3 38.2 1.0 C A:LYS76 3.3 33.5 1.0 CG A:ASP72 3.5 40.0 1.0 OD2 A:ASP74 3.7 40.0 1.0 OD2 A:ASP72 4.0 44.7 1.0 CB A:ASP70 4.0 34.8 1.0 CA A:ASP70 4.0 35.3 1.0 N A:LYS76 4.1 34.7 1.0 OD2 A:ASP70 4.1 37.4 1.0 CA A:LYS76 4.2 34.2 1.0 N A:VAL77 4.3 32.1 1.0 CG A:GLU81 4.4 36.1 1.0 N A:ASP74 4.4 38.4 1.0 N A:ASP72 4.4 38.5 1.0 C A:ASP70 4.4 36.4 1.0 CB A:LYS76 4.5 35.8 1.0 N A:ALA71 4.5 37.2 1.0 CB A:ASP74 4.5 39.0 1.0 CA A:VAL77 4.5 31.8 1.0 O A:HOH312 4.6 42.8 1.0 CB A:ASP72 4.7 40.5 1.0 N A:GLY73 4.7 38.9 1.0 N A:THR78 4.8 32.7 1.0 CA A:ASP72 4.9 39.9 1.0 CA A:ASP74 4.9 39.1 1.0 N A:GLY75 4.9 36.2 1.0

Calcium binding site 3 out of 18 in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:34.9 occ:1.00 O A:HOH339 2.2 36.5 1.0 OD1 A:ASP112 2.3 34.5 1.0 OE1 A:GLU123 2.4 34.9 1.0 OD1 A:ASP116 2.4 40.5 1.0 O A:SER118 2.4 32.0 1.0 OE2 A:GLU123 2.5 35.4 1.0 OG A:SER114 2.6 37.8 1.0 CD A:GLU123 2.7 36.7 1.0 CG A:ASP112 3.4 33.0 1.0 CG A:ASP116 3.5 42.5 1.0 C A:SER118 3.6 34.8 1.0 CB A:SER114 3.8 39.3 1.0 N A:SER114 4.1 37.4 1.0 OD2 A:ASP112 4.2 33.0 1.0 CA A:ASP112 4.2 32.3 1.0 OD2 A:ASP116 4.2 45.4 1.0 CG A:GLU123 4.3 34.5 1.0 CB A:ASP112 4.3 31.8 1.0 N A:SER118 4.4 37.0 1.0 N A:ASP116 4.4 42.1 1.0 CA A:SER114 4.4 39.8 1.0 OD2 A:ASP120 4.4 36.0 1.0 CA A:VAL119 4.4 32.5 1.0 O A:HOH340 4.5 45.1 1.0 N A:VAL119 4.5 33.6 1.0 C A:ASP112 4.5 32.5 1.0 CB A:ASP116 4.5 43.0 1.0 CA A:SER118 4.6 36.5 1.0 N A:ASP120 4.6 31.6 1.0 N A:ASN115 4.7 43.0 1.0 C A:SER114 4.7 41.5 1.0 N A:SER113 4.7 33.6 1.0 N A:GLY117 4.8 38.1 1.0 CA A:ASP116 4.9 42.2 1.0 O A:ASP112 5.0 33.4 1.0

Calcium binding site 4 out of 18 in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:36.0 occ:1.00 OD1 B:ASP19 2.2 34.4 1.0 O B:VAL25 2.3 36.4 1.0 OD2 B:ASP30 2.4 34.5 1.0 OD1 B:ASP21 2.4 41.1 1.0 O B:HOH332 2.5 40.3 1.0 OG B:SER23 2.5 36.1 1.0 OD1 B:ASP30 2.7 35.6 1.0 CG B:ASP30 2.9 33.9 1.0 CG B:ASP21 3.3 40.4 1.0 CG B:ASP19 3.4 34.9 1.0 CB B:SER23 3.5 38.5 1.0 C B:VAL25 3.5 36.1 1.0 OD2 B:ASP21 3.7 40.2 1.0 N B:SER23 3.8 36.9 1.0 O B:HOH312 4.1 44.6 1.0 CA B:SER23 4.2 38.1 1.0 OD2 B:ASP19 4.2 35.9 1.0 CA B:VAL26 4.2 34.7 1.0 CA B:ASP19 4.2 32.7 1.0 N B:VAL26 4.3 35.9 1.0 N B:VAL25 4.3 37.6 1.0 CB B:ASP19 4.3 33.1 1.0 CB B:ASP30 4.4 33.9 1.0 N B:GLU27 4.5 36.4 1.0 CB B:ASP21 4.5 41.0 1.0 N B:LYS22 4.5 38.7 1.0 N B:ASP21 4.5 37.9 1.0 CA B:VAL25 4.5 37.2 1.0 N B:GLY24 4.5 37.0 1.0 C B:ASP19 4.6 33.1 1.0 C B:ASP21 4.7 41.8 1.0 CA B:ASP21 4.7 40.2 1.0 C B:SER23 4.7 38.8 1.0 C B:VAL26 4.8 35.4 1.0 OE2 B:GLU27 4.8 43.0 1.0 C B:LYS22 4.9 37.5 1.0

Calcium binding site 5 out of 18 in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:39.3 occ:1.00 O B:LYS76 2.2 41.4 1.0 OD1 B:ASP72 2.3 37.2 1.0 O B:HOH316 2.3 41.7 1.0 OD1 B:ASP70 2.3 37.7 1.0 OD1 B:ASP74 2.4 36.9 1.0 OE2 B:GLU81 2.5 37.4 1.0 OE1 B:GLU81 2.5 33.4 1.0 CD B:GLU81 2.8 35.9 1.0 CG B:ASP72 3.3 37.8 1.0 CG B:ASP74 3.3 39.9 1.0 CG B:ASP70 3.4 37.1 1.0 C B:LYS76 3.5 38.9 1.0 OD2 B:ASP72 3.7 38.0 1.0 OD2 B:ASP74 3.8 38.8 1.0 CA B:ASP70 4.2 35.5 1.0 N B:LYS76 4.2 40.5 1.0 CB B:ASP70 4.2 36.4 1.0 OD2 B:ASP70 4.2 38.0 1.0 CA B:LYS76 4.3 39.9 1.0 N B:ASP74 4.3 41.4 1.0 CG B:GLU81 4.3 35.5 1.0 N B:VAL77 4.4 35.4 1.0 CB B:ASP74 4.4 42.2 1.0 N B:ASP72 4.4 38.6 1.0 C B:ASP70 4.5 36.8 1.0 O B:HOH305 4.5 36.6 1.0 CA B:VAL77 4.5 33.7 1.0 CB B:ASP72 4.6 39.9 1.0 CB B:LYS76 4.6 41.9 1.0 N B:ALA71 4.6 36.1 1.0 N B:GLY73 4.7 39.8 1.0 CA B:ASP74 4.8 42.1 1.0 N B:GLY75 4.9 42.5 1.0 CA B:ASP72 4.9 40.2 1.0 N B:THR78 4.9 34.1 1.0

Calcium binding site 6 out of 18 in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:31.2 occ:1.00 OD1 B:ASP116 2.2 35.5 1.0 O B:HOH325 2.2 34.8 1.0 OD1 B:ASP112 2.3 30.9 1.0 O B:SER118 2.3 29.8 1.0 OE1 B:GLU123 2.4 29.4 1.0 OG B:SER114 2.4 35.9 1.0 OE2 B:GLU123 2.5 29.9 1.0 CD B:GLU123 2.8 30.8 1.0 CG B:ASP116 3.2 40.8 1.0 CG B:ASP112 3.4 32.2 1.0 C B:SER118 3.6 31.6 1.0 CB B:SER114 3.7 38.0 1.0 OD2 B:ASP116 3.8 45.6 1.0 O B:HOH315 4.2 43.8 1.0 CA B:ASP112 4.2 31.5 1.0 N B:SER114 4.2 37.1 1.0 OD2 B:ASP112 4.3 31.7 1.0 CB B:ASP112 4.3 31.5 1.0 CG B:GLU123 4.3 30.9 1.0 CA B:SER114 4.3 37.7 1.0 CB B:ASP116 4.4 41.8 1.0 N B:ASP116 4.4 39.4 1.0 N B:SER118 4.4 33.8 1.0 CA B:VAL119 4.4 28.7 1.0 N B:VAL119 4.5 30.0 1.0 OD2 B:ASP120 4.5 37.8 1.0 CA B:SER118 4.5 33.8 1.0 OG B:SER118 4.5 39.9 1.0 C B:ASP112 4.5 32.3 1.0 N B:ASP120 4.6 28.8 1.0 C B:SER114 4.7 39.0 1.0 N B:ASN115 4.8 38.5 1.0 CA B:ASP116 4.8 40.9 1.0 N B:SER113 4.9 33.1 1.0 O B:ASP112 4.9 31.8 1.0 C B:VAL119 5.0 29.1 1.0 CG B:ASP120 5.0 35.0 1.0

Calcium binding site 7 out of 18 in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:32.7 occ:1.00 O C:VAL25 2.3 31.5 1.0 OD1 C:ASP21 2.3 34.5 1.0 OD1 C:ASP19 2.4 30.8 1.0 O C:HOH308 2.4 32.0 1.0 OD2 C:ASP30 2.5 30.6 1.0 OG C:SER23 2.5 31.1 1.0 OD1 C:ASP30 2.6 29.1 1.0 CG C:ASP30 2.8 30.7 1.0 CG C:ASP21 3.2 36.5 1.0 OD2 C:ASP21 3.4 36.1 1.0 CB C:SER23 3.5 32.0 1.0 C C:VAL25 3.5 30.1 1.0 CG C:ASP19 3.6 31.0 1.0 N C:SER23 3.9 34.5 1.0 CA C:SER23 4.2 33.7 1.0 CA C:VAL26 4.3 30.4 1.0 N C:VAL25 4.3 30.6 1.0 N C:VAL26 4.3 30.5 1.0 CB C:ASP30 4.4 30.8 1.0 OD2 C:ASP19 4.4 30.5 1.0 CA C:ASP19 4.4 31.0 1.0 CB C:ASP21 4.5 36.1 1.0 CA C:VAL25 4.5 30.6 1.0 CB C:ASP19 4.5 30.5 1.0 N C:ASP21 4.5 35.3 1.0 N C:LYS22 4.5 38.2 1.0 N C:GLU27 4.6 31.2 1.0 N C:GLY24 4.6 32.3 1.0 C C:ASP19 4.7 31.1 1.0 C C:SER23 4.7 33.1 1.0 C C:ASP21 4.8 38.1 1.0 CA C:ASP21 4.8 36.3 1.0 C C:VAL26 4.9 31.2 1.0 C C:LYS22 5.0 37.3 1.0

Calcium binding site 8 out of 18 in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:38.5 occ:1.00 OD1 C:ASP70 2.2 40.1 1.0 OD1 C:ASP72 2.2 36.5 1.0 O C:LYS76 2.3 37.8 1.0 O C:HOH304 2.5 35.4 1.0 OD1 C:ASP74 2.5 39.6 1.0 OE2 C:GLU81 2.6 37.1 1.0 OE1 C:GLU81 2.6 33.0 1.0 CD C:GLU81 2.9 35.9 1.0 CG C:ASP72 3.3 38.0 1.0 CG C:ASP70 3.3 39.7 1.0 CG C:ASP74 3.4 40.3 1.0 C C:LYS76 3.6 37.4 1.0 OD2 C:ASP72 3.7 36.9 1.0 OD2 C:ASP74 3.9 40.3 1.0 CA C:ASP70 4.0 38.6 1.0 CB C:ASP70 4.1 38.6 1.0 N C:ASP74 4.2 41.3 1.0 OD2 C:ASP70 4.2 40.7 1.0 CG C:LYS76 4.2 47.3 1.0 N C:LYS76 4.3 39.4 1.0 N C:ASP72 4.3 40.6 1.0 C C:ASP70 4.4 39.9 1.0 CG C:GLU81 4.5 37.0 1.0 CA C:LYS76 4.5 38.6 1.0 N C:VAL77 4.5 34.8 1.0 CB C:ASP74 4.5 42.1 1.0 CB C:ASP72 4.5 40.8 1.0 N C:GLY73 4.5 41.5 1.0 O C:HOH309 4.5 38.5 1.0 N C:ALA71 4.6 40.0 1.0 CA C:VAL77 4.6 34.6 1.0 CA C:ASP74 4.8 41.5 1.0 CA C:ASP72 4.8 42.3 1.0 N C:GLY75 4.8 40.0 1.0 C C:ASP72 4.8 43.0 1.0 CE C:LYS76 4.9 53.4 1.0 CB C:LYS76 5.0 41.7 1.0 N C:THR78 5.0 34.2 1.0 O C:ASP70 5.0 40.9 1.0

Calcium binding site 9 out of 18 in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:39.4 occ:1.00 OD1 C:ASP112 2.2 36.3 1.0 OD1 C:ASP116 2.2 47.2 1.0 O C:HOH315 2.3 46.4 1.0 OE1 C:GLU123 2.4 35.0 1.0 O C:SER118 2.4 37.1 1.0 OG C:SER114 2.5 38.3 1.0 OE2 C:GLU123 2.5 34.6 1.0 CD C:GLU123 2.7 34.8 1.0 CG C:ASP112 3.3 36.0 1.0 CG C:ASP116 3.4 47.5 1.0 C C:SER118 3.6 38.7 1.0 CB C:SER114 3.7 41.7 1.0 OD2 C:ASP116 4.1 51.2 1.0 OD2 C:ASP112 4.1 36.0 1.0 N C:SER114 4.2 42.4 1.0 CG C:GLU123 4.2 33.9 1.0 OD2 C:ASP120 4.3 42.1 1.0 CB C:ASP112 4.3 34.8 1.0 CA C:ASP112 4.3 34.5 1.0 N C:ASP116 4.3 46.2 1.0 N C:SER118 4.4 40.1 1.0 CA C:VAL119 4.4 34.2 1.0 CA C:SER114 4.4 40.7 1.0 N C:VAL119 4.4 35.8 1.0 CB C:ASP116 4.4 47.9 1.0 N C:ASP120 4.5 34.9 1.0 CA C:SER118 4.6 40.6 1.0 OG C:SER118 4.6 46.8 1.0 N C:ASN115 4.6 43.8 1.0 C C:SER114 4.7 42.2 1.0 C C:ASP112 4.7 35.1 1.0 CA C:ASP116 4.9 46.1 1.0 N C:SER113 4.9 35.5 1.0 CG C:ASP120 4.9 39.6 1.0 C C:VAL119 4.9 35.1 1.0

Calcium binding site 10 out of 18 in the The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silk Worm Bombyx Mori. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:35.0 occ:1.00 OD1 D:ASP19 2.3 33.6 1.0 OD1 D:ASP21 2.3 31.7 1.0 OD2 D:ASP30 2.3 31.3 1.0 O D:VAL25 2.4 35.8 1.0 OG D:SER23 2.5 34.8 1.0 O D:HOH313 2.5 34.3 1.0 OD1 D:ASP30 2.6 34.2 1.0 CG D:ASP30 2.8 34.2 1.0 CG D:ASP21 3.2 34.1 1.0 C D:VAL25 3.5 37.1 1.0 CG D:ASP19 3.6 34.3 1.0 CB D:SER23 3.6 36.9 1.0 OD2 D:ASP21 3.7 32.6 1.0 N D:SER23 4.0 36.0 1.0 CA D:VAL26 4.2 35.9 1.0 N D:VAL26 4.3 37.0 1.0 N D:VAL25 4.3 37.8 1.0 CB D:ASP30 4.3 32.4 1.0 OD2 D:ASP19 4.3 36.0 1.0 CA D:SER23 4.4 36.7 1.0 N D:ASP21 4.4 35.4 1.0 CA D:ASP19 4.4 34.0 1.0 CB D:ASP21 4.5 34.4 1.0 N D:GLU27 4.5 34.3 1.0 CA D:VAL25 4.6 38.1 1.0 CB D:ASP19 4.6 33.6 1.0 N D:LYS22 4.6 36.4 1.0 OE1 D:GLU27 4.6 41.8 1.0 N D:GLY24 4.7 36.4 1.0 C D:ASP19 4.7 34.0 1.0 CA D:ASP21 4.7 35.2 1.0 C D:ASP21 4.7 36.1 1.0 CG D:GLU27 4.8 42.7 1.0 C D:VAL26 4.8 36.3 1.0 C D:SER23 4.8 37.6 1.0 N D:SER20 5.0 33.6 1.0

J.Guo, R.M.Keegan, D.J.Rigden, P.T.Erskine, S.P.Wood, S.Li, J.B.Cooper. The X-Ray Structure of Juvenile Hormone Diol Kinase From the Silkworm Bombyx Mori. Acta Crystallogr.,Sect.F V. 77 465 2021.
ISSN: ESSN 2053-230X
PubMed: 34866602
DOI: 10.1107/S2053230X21012012