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Calcium in PDB 7any: Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate

Protein crystallography data

The structure of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate, PDB code: 7any was solved by M.R.Zeronian, N.M.Pearce, M.Lutz, T.M.Wood, N.I.Martin, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.76 / 1.14
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.132, 68.321, 40.132, 90, 120, 90
R / Rfree (%) 16 / 19.2

Other elements in 7any:

The structure of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate also contains other interesting chemical elements:

Chlorine (Cl) 14 atoms
Cadmium (Cd) 3 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Calcium atom in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate (pdb code 7any). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 42 binding sites of Calcium where determined in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate, PDB code: 7any:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 42 in 7any

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Calcium binding site 1 out of 42 in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca101

b:5.6
occ:1.00
 O3 A:RDZ103 2.3 7.5 1.0
OD1 A:ASP5 2.3 9.1 1.0
O A:GLY8 2.3 5.9 1.0
O A:VAL10 2.3 7.3 1.0
O A:DNP2 2.4 7.1 1.0
O A:GLY6 2.4 8.7 1.0
CG A:ASP5 3.5 8.1 1.0
C A:VAL10 3.5 7.6 1.0
C A:GLY8 3.5 6.5 1.0
C A:DNP2 3.5 8.5 1.0
C A:GLY6 3.6 7.9 1.0
P1 A:RDZ103 3.7 8.1 1.0
N A:DNP2 3.9 8.5 1.0
N A:GLY8 4.0 6.5 1.0
OD2 A:ASP5 4.0 7.1 1.0
N A:VAL10 4.0 8.1 1.0
N A:GLY6 4.2 7.9 1.0
C A:ASP7 4.2 7.5 1.0
C A:2RA9 4.3 7.3 1.0
C A:ASP5 4.3 8.8 1.0
CA A:VAL10 4.3 8.1 1.0
CA A:GLY8 4.3 6.3 1.0
O2 A:RDZ103 4.3 7.3 1.0
CA A:DNP2 4.3 8.3 1.0
NG A:DNP2 4.3 8.6 1.0
N A:PRO11 4.4 8.5 1.0
C A:PRO11 4.4 9.1 1.0
CA A:PRO11 4.4 9.4 1.0
CA A:CPI3 4.4 9.3 1.0
O4 A:RDZ103 4.4 8.2 1.0
CA A:GLY6 4.5 9.4 1.0
N A:2RA9 4.5 6.2 1.0
N A:CPI3 4.5 9.0 1.0
O A:HOH203 4.5 19.6 1.0
O A:ASP7 4.5 8.7 1.0
N A:ASP7 4.5 8.3 1.0
CA A:ASP7 4.6 7.8 1.0
N A:ASP5 4.6 8.5 1.0
CA A:2RA9 4.6 6.9 1.0
O1 A:RDZ103 4.7 8.4 1.0
CB A:ASP5 4.7 8.6 1.0
O A:ASP5 4.7 11.6 1.0
CA A:ASP5 4.7 9.0 1.0
O A:2RA9 4.8 8.0 1.0
O A:PRO11 4.9 8.3 1.0
CB A:DNP2 4.9 8.0 1.0
CB A:VAL10 4.9 7.7 1.0
C A:ASN1 5.0 10.3 1.0
CB A:ASN1 5.0 11.6 1.0

Calcium binding site 2 out of 42 in 7any

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Calcium binding site 2 out of 42 in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:6.0
occ:1.00
 O4 A:RDZ103 2.2 8.2 1.0
OD1 A:ASP7 2.2 7.9 1.0
O B:HOH204 2.3 7.8 1.0
OD1 A:ASN1 2.3 13.1 1.0
O A:9GE0 2.3 11.0 1.0
C A:9GE0 3.3 12.9 1.0
CG A:ASP7 3.4 9.0 1.0
CG A:ASN1 3.5 12.5 1.0
P1 A:RDZ103 3.6 8.1 1.0
CA A:ASN1 3.8 11.0 1.0
N A:ASN1 3.9 10.6 1.0
O B:2RA9 3.9 7.9 1.0
CA A:ASP7 4.0 7.8 1.0
CB A:ASP7 4.1 8.3 1.0
O1 A:RDZ103 4.2 8.4 1.0
CB A:ASN1 4.2 11.6 1.0
C8 A:RDZ103 4.3 11.1 1.0
NG B:2RA9 4.4 8.0 1.0
N A:GLY8 4.4 6.5 1.0
CA A:9GE0 4.4 14.7 1.0
O4 B:RDZ103 4.4 7.4 1.0
OD2 A:ASP7 4.4 11.6 1.0
O2 A:RDZ103 4.5 7.3 1.0
ND2 A:ASN1 4.5 13.4 1.0
O3 A:RDZ103 4.6 7.5 1.0
C04 A:9GE0 4.6 15.8 1.0
CA B:GLY8 4.7 7.6 1.0
C A:ASP7 4.7 7.5 1.0
N B:2RA9 4.8 7.4 1.0
CG B:PRO11 4.9 9.8 1.0
C B:GLY8 5.0 8.2 1.0

Calcium binding site 3 out of 42 in 7any

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Calcium binding site 3 out of 42 in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca104

b:32.5
occ:1.00
 O A:HOH207 1.8 14.3 1.0
CL A:CL105 2.8 27.8 1.0
O A:HOH211 2.9 14.8 1.0
O A:HOH209 2.9 19.1 1.0
O A:HOH204 3.8 18.9 1.0
OD1 A:ASP4 4.3 10.5 1.0
CA A:ASP4 4.3 8.0 1.0
CB A:ASN1 4.5 11.6 1.0
N A:GLY6 4.6 7.9 1.0
CA A:GLY6 4.7 9.4 1.0
N A:ASP4 4.8 7.5 1.0
ND2 A:ASN1 4.9 13.4 1.0
C A:ASP4 4.9 9.6 1.0

Calcium binding site 4 out of 42 in 7any

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Calcium binding site 4 out of 42 in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca101

b:5.5
occ:1.00
 O3 B:RDZ103 2.1 9.1 1.0
O B:VAL10 2.3 6.4 1.0
O B:DNP2 2.3 7.9 1.0
O B:GLY8 2.3 9.0 1.0
O B:GLY6 2.4 7.1 1.0
OD1 B:ASP5 2.4 7.9 1.0
C B:VAL10 3.5 8.7 1.0
C B:DNP2 3.5 8.7 1.0
C B:GLY8 3.5 8.2 1.0
CG B:ASP5 3.6 7.9 1.0
C B:GLY6 3.6 7.3 1.0
P1 B:RDZ103 3.6 8.0 1.0
N B:DNP2 3.8 9.1 1.0
OD2 B:ASP5 4.1 8.6 1.0
N B:VAL10 4.1 7.6 1.0
N B:GLY8 4.1 7.6 1.0
C B:ASP7 4.2 8.7 1.0
NG B:DNP2 4.2 8.0 1.0
N B:GLY6 4.3 8.0 1.0
O4 B:RDZ103 4.3 7.4 1.0
CA B:DNP2 4.3 8.3 1.0
C B:2RA9 4.3 7.2 1.0
C B:ASP5 4.3 9.0 1.0
CA B:VAL10 4.3 8.6 1.0
CA B:GLY8 4.3 7.6 1.0
CA B:PRO11 4.3 8.8 1.0
C B:PRO11 4.4 8.4 1.0
N B:PRO11 4.4 9.2 1.0
CA B:CPI3 4.4 9.4 1.0
O2 B:RDZ103 4.4 8.1 1.0
O B:HOH202 4.4 18.9 1.0
N B:CPI3 4.5 8.8 1.0
O B:ASP7 4.5 9.9 1.0
O1 B:RDZ103 4.5 7.4 1.0
N B:ASP7 4.5 7.4 1.0
CA B:GLY6 4.5 7.3 1.0
CA B:ASP7 4.6 7.8 1.0
O B:ASP5 4.6 11.7 1.0
N B:2RA9 4.6 7.4 1.0
N B:ASP5 4.6 9.2 1.0
CA B:2RA9 4.8 8.0 1.0
CB B:ASP5 4.8 8.3 1.0
O B:2RA9 4.8 7.9 1.0
CA B:ASP5 4.8 8.7 1.0
C B:ASN1 4.9 11.0 1.0
CB B:ASN1 4.9 11.4 1.0
O B:PRO11 4.9 8.2 1.0
CB B:DNP2 4.9 8.4 1.0
CB B:VAL10 5.0 9.4 1.0

Calcium binding site 5 out of 42 in 7any

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Calcium binding site 5 out of 42 in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:5.3
occ:1.00
 O2 B:RDZ103 2.1 8.1 1.0
OD1 B:ASP7 2.2 7.6 1.0
O B:9GE0 2.3 11.8 1.0
OD1 B:ASN1 2.3 11.4 1.0
OD2 D:ASP4 2.3 10.0 1.0
O A:HOH205 2.3 6.6 1.0
C B:9GE0 3.2 12.1 1.0
CG D:ASP4 3.4 9.5 1.0
CG B:ASP7 3.5 8.2 1.0
CG B:ASN1 3.5 13.8 1.0
P1 B:RDZ103 3.6 8.0 1.0
CA B:ASN1 3.8 12.7 1.0
N B:ASN1 3.9 11.8 1.0
O A:2RA9 3.9 8.0 1.0
C8 B:RDZ103 4.0 10.6 1.0
CA B:ASP7 4.1 7.8 1.0
CB B:ASP7 4.2 7.5 1.0
OD1 D:ASP4 4.2 12.2 1.0
CB B:ASN1 4.2 11.4 1.0
O1 B:RDZ103 4.2 7.4 1.0
CA B:9GE0 4.4 13.1 1.0
NG A:2RA9 4.4 9.6 1.0
N B:GLY8 4.4 7.6 1.0
OD2 B:ASP7 4.4 10.3 1.0
CB D:ASP4 4.4 9.6 1.0
O2 A:RDZ103 4.5 7.3 1.0
O4 B:RDZ103 4.5 7.4 1.0
ND2 B:ASN1 4.5 12.9 1.0
O3 B:RDZ103 4.6 9.1 1.0
C04 B:9GE0 4.6 13.5 1.0
N A:2RA9 4.7 6.2 1.0
CA A:GLY8 4.7 6.3 1.0
C B:ASP7 4.8 8.7 1.0
C A:GLY8 4.9 6.5 1.0
CG A:PRO11 5.0 10.7 1.0

Calcium binding site 6 out of 42 in 7any

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Calcium binding site 6 out of 42 in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca104

b:30.5
occ:1.00
 O B:HOH210 1.9 13.8 1.0
O B:HOH203 2.2 19.0 1.0
O B:HOH212 2.7 24.6 1.0
O B:HOH216 2.7 25.1 1.0
O B:HOH209 2.9 29.5 1.0
CL B:CL105 3.1 26.5 1.0
O B:HOH206 4.1 26.9 1.0
OD1 B:ASP4 4.2 9.5 1.0
CA B:ASP4 4.5 8.0 1.0
CB B:ASN1 4.5 11.4 1.0
N B:GLY6 4.6 8.0 1.0
CA B:GLY6 4.8 7.3 1.0
N B:ASP4 4.8 8.4 1.0
ND2 B:ASN1 4.8 12.9 1.0
O B:HOH201 4.9 28.5 1.0
C B:ASP4 4.9 9.4 1.0

Calcium binding site 7 out of 42 in 7any

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Calcium binding site 7 out of 42 in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:5.0
occ:1.00
 O3 C:RDZ103 2.2 8.3 1.0
O C:VAL10 2.3 7.1 1.0
O C:GLY8 2.3 6.0 1.0
OD1 C:ASP5 2.4 8.0 1.0
O C:DNP2 2.4 8.0 1.0
O C:GLY6 2.5 7.3 1.0
C C:VAL10 3.4 8.0 1.0
C C:GLY8 3.5 6.8 1.0
CG C:ASP5 3.5 9.2 1.0
C C:DNP2 3.6 8.2 1.0
P1 C:RDZ103 3.6 7.0 1.0
C C:GLY6 3.7 7.2 1.0
N C:DNP2 4.0 6.8 1.0
N C:VAL10 4.0 7.4 1.0
OD2 C:ASP5 4.0 10.9 1.0
N C:GLY8 4.1 8.0 1.0
N C:GLY6 4.1 8.1 1.0
C C:ASP7 4.2 7.8 1.0
C C:2RA9 4.2 8.1 1.0
NG C:DNP2 4.2 8.2 1.0
CA C:VAL10 4.3 7.4 1.0
CA C:GLY8 4.3 7.0 1.0
C C:ASP5 4.3 8.8 1.0
CA C:DNP2 4.3 7.9 1.0
C C:PRO11 4.3 8.3 1.0
O2 C:RDZ103 4.4 7.2 1.0
O4 C:RDZ103 4.4 7.9 1.0
N C:PRO11 4.4 8.4 1.0
CA C:PRO11 4.4 8.6 1.0
N C:2RA9 4.5 7.2 1.0
CA C:GLY6 4.5 7.9 1.0
N C:CPI3 4.6 8.3 1.0
O C:ASP5 4.6 8.8 1.0
O C:ASP7 4.6 8.9 1.0
N C:ASP5 4.6 9.4 1.0
O1 C:RDZ103 4.6 7.9 1.0
N C:ASP7 4.6 7.1 1.0
CA C:CPI3 4.6 8.2 1.0
CA C:ASP7 4.6 7.9 1.0
CA C:2RA9 4.7 7.4 1.0
O C:2RA9 4.7 6.6 1.0
CB C:ASP5 4.7 9.4 1.0
CA C:ASP5 4.7 9.0 1.0
CB C:VAL10 4.8 7.9 1.0
CB C:ASN1 4.9 10.1 1.0
CB C:DNP2 4.9 7.7 1.0
O C:PRO11 4.9 9.3 1.0

Calcium binding site 8 out of 42 in 7any

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Calcium binding site 8 out of 42 in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca102

b:5.5
occ:1.00
 OD1 C:ASP7 2.3 7.9 1.0
O4 C:RDZ103 2.3 7.9 1.0
OD1 C:ASN1 2.3 10.0 1.0
OD2 F:ASP4 2.3 9.8 1.0
O D:HOH202 2.3 6.5 1.0
O C:9GE0 2.4 10.6 1.0
C C:9GE0 3.3 9.7 1.0
CG F:ASP4 3.5 11.3 1.0
CG C:ASN1 3.5 11.3 1.0
CG C:ASP7 3.5 9.6 1.0
P1 C:RDZ103 3.7 7.0 1.0
CA C:ASN1 3.8 9.7 1.0
O D:2RA9 3.9 5.9 1.0
N C:ASN1 3.9 9.9 1.0
O F:HOH206 3.9 27.9 1.0
CA C:ASP7 4.0 7.9 1.0
OD1 F:ASP4 4.1 10.6 1.0
CB C:ASN1 4.2 10.1 1.0
C8 C:RDZ103 4.2 9.3 1.0
CB C:ASP7 4.2 8.2 1.0
O1 C:RDZ103 4.2 7.9 1.0
NG D:2RA9 4.3 10.1 1.0
N C:GLY8 4.3 8.0 1.0
OD2 C:ASP7 4.4 11.9 1.0
O2 C:RDZ103 4.4 7.2 1.0
CB F:ASP4 4.5 10.2 1.0
CA C:9GE0 4.5 10.9 1.0
O3 D:RDZ104 4.5 6.3 1.0
ND2 C:ASN1 4.5 11.9 1.0
CA D:GLY8 4.6 7.5 1.0
O3 C:RDZ103 4.7 8.3 1.0
C C:ASP7 4.7 7.8 1.0
C04 C:9GE0 4.7 11.6 1.0
N D:2RA9 4.8 8.3 1.0
C D:GLY8 4.8 7.5 1.0
CG D:PRO11 4.8 9.7 1.0
C D:2RA9 5.0 7.5 1.0

Calcium binding site 9 out of 42 in 7any

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Calcium binding site 9 out of 42 in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca104

b:4.8
occ:0.55
 CD C:CD105 0.1 20.7 0.5
O K:HOH204 2.3 19.8 1.0
OD2 C:ASP7 2.4 11.9 1.0
O K:HOH216 2.5 8.5 1.0
O D:HOH201 2.5 14.3 1.0
CL C:CL108 3.0 13.3 1.0
CG C:ASP7 3.4 9.6 1.0
CB C:ASP7 3.7 8.2 1.0
NG D:2RA9 3.8 10.1 1.0
O C:HOH214 4.0 18.3 1.0
O K:ASP5 4.0 10.3 1.0
O F:HOH206 4.2 27.9 1.0
CB D:2RA9 4.3 8.5 1.0
OD1 C:ASP7 4.4 7.9 1.0
O D:HOH210 4.4 25.4 1.0
OD2 K:ASP5 4.4 10.6 1.0
CA K:2RA9 4.5 7.6 1.0
O K:ASP7 4.7 8.8 1.0
N K:2RA9 4.7 7.1 1.0
O K:HOH214 4.7 19.3 1.0
N D:2RA9 4.8 8.3 1.0
CG K:ASP5 4.8 9.9 1.0
CB K:2RA9 4.9 7.4 1.0
O K:HOH206 4.9 17.5 1.0
O C:HOH206 5.0 26.8 1.0

Calcium binding site 10 out of 42 in 7any

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Calcium binding site 10 out of 42 in the Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of the Laspartomycin C Friulimicin-Like Mutant in Complex with Geranyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca106

b:36.8
occ:1.00
 O C:HOH205 2.0 12.1 1.0
O C:HOH212 2.7 23.4 1.0
CL C:CL107 2.8 25.7 1.0
O C:HOH211 3.2 31.5 1.0
O C:HOH210 3.5 26.3 1.0
OD1 C:ASP4 4.2 12.1 1.0
CA C:ASP4 4.4 9.1 1.0
CB C:ASN1 4.7 10.1 1.0
N C:ASP4 4.8 7.9 1.0
N C:GLY6 4.8 8.1 1.0
C C:ASP4 4.9 9.3 1.0
CA C:GLY6 4.9 7.9 1.0
ND2 C:ASN1 5.0 11.9 1.0

Reference:

T.M.Wood, M.R.Zeronian, N.Buijs, K.Bertheussen, H.K.Abedian, A.V.Johnson, N.M.Pearce, M.Lutz, J.Kemmink, T.Seirsma, L.W.Hamoen, B.J.C.Janssen, N.I.Martin. Mechanistic Insights Into the C55-P Targeting Lipopeptide Antibiotics Revealed By Structure-Activity Studies and High-Resolution Crystal Structures Chem Sci V. 13 2985 2022.
ISSN: ESSN 2041-6539
DOI: 10.1039/D1SC07190D
Page generated: Thu Jul 18 22:55:11 2024

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