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Calcium in PDB 1m63: Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes

Enzymatic activity of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes

All present enzymatic activity of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes:
3.1.3.16; 5.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes, PDB code: 1m63 was solved by Q.Huai, H.-Y.Kim, Y.Liu, Y.Zhao, A.Mondragon, J.O.Liu, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.657, 108.657, 316.590, 90.00, 90.00, 90.00
R / Rfree (%) 26 / 32.2

Other elements in 1m63:

The structure of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes (pdb code 1m63). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes, PDB code: 1m63:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1m63

Go back to Calcium Binding Sites List in 1m63
Calcium binding site 1 out of 8 in the Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca500

b:0.0
occ:1.00
 OD1 B:ASP32 2.4 97.8 1.0
OD1 B:ASP30 2.4 0.0 1.0
OE1 B:GLU41 2.4 0.0 1.0
O B:SER36 2.4 0.0 1.0
OG B:SER34 2.5 0.0 1.0
OE2 B:GLU41 3.1 0.0 1.0
CD B:GLU41 3.2 0.0 1.0
C B:SER36 3.3 0.0 1.0
CG B:ASP32 3.4 97.5 1.0
CG B:ASP30 3.6 0.0 1.0
N B:GLY35 3.7 0.0 1.0
N B:SER34 3.8 0.0 1.0
CB B:SER34 3.8 99.0 1.0
N B:SER36 3.8 0.0 1.0
OD2 B:ASP32 3.9 95.4 1.0
N B:LEU37 4.1 0.0 1.0
CA B:SER36 4.2 0.0 1.0
CA B:SER34 4.2 0.0 1.0
C B:GLY35 4.2 0.0 1.0
CA B:LEU37 4.3 99.1 1.0
N B:ASP32 4.3 0.0 1.0
N B:ASN33 4.4 0.0 1.0
CA B:ASP30 4.4 98.8 1.0
C B:SER34 4.5 0.0 1.0
CB B:ASP30 4.5 0.0 1.0
OD2 B:ASP30 4.5 0.0 1.0
N B:LEU31 4.5 97.3 1.0
CA B:GLY35 4.6 0.0 1.0
OG B:SER36 4.6 0.0 1.0
CG B:GLU41 4.6 0.0 1.0
CB B:ASP32 4.6 99.0 1.0
C B:ASP32 4.7 99.9 1.0
C B:ASN33 4.7 0.0 1.0
C B:ASP30 4.7 97.0 1.0
O B:GLY35 4.8 0.0 1.0
CA B:ASP32 4.8 99.6 1.0
CA B:ASN33 4.9 0.0 1.0

Calcium binding site 2 out of 8 in 1m63

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Calcium binding site 2 out of 8 in the Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:94.6
occ:1.00
 OE1 B:GLU73 2.3 88.4 1.0
OD1 B:ASN66 2.4 92.0 1.0
OD1 B:ASP62 2.4 98.8 1.0
O B:GLU68 2.4 90.0 1.0
OD1 B:ASP64 2.4 0.0 1.0
OD2 B:ASP70 2.5 0.0 1.0
OE2 B:GLU73 2.7 88.0 1.0
CD B:GLU73 2.8 91.0 1.0
CG B:ASN66 3.3 95.3 1.0
CG B:ASP64 3.3 0.0 1.0
OD2 B:ASP64 3.5 0.0 1.0
ND2 B:ASN66 3.6 96.7 1.0
C B:GLU68 3.6 91.4 1.0
CG B:ASP62 3.6 95.7 1.0
CG B:ASP70 3.7 0.0 1.0
CA B:VAL69 3.9 96.3 1.0
N B:ASP70 4.0 97.3 1.0
N B:VAL69 4.2 93.0 1.0
CG B:GLU73 4.2 93.5 1.0
C B:VAL69 4.3 97.6 1.0
OD2 B:ASP62 4.4 97.5 1.0
OD1 B:ASP70 4.5 0.0 1.0
CA B:ASP62 4.6 92.6 1.0
CB B:ASP62 4.6 93.1 1.0
CB B:ASN66 4.6 96.4 1.0
CB B:ASP64 4.6 0.0 1.0
CB B:ASP70 4.7 98.1 1.0
CA B:GLU68 4.8 93.2 1.0
N B:GLU68 4.9 94.6 1.0
CB B:GLU73 4.9 96.7 1.0
N B:ASP64 4.9 0.0 1.0
CA B:ASP70 5.0 96.7 1.0

Calcium binding site 3 out of 8 in 1m63

Go back to Calcium Binding Sites List in 1m63
Calcium binding site 3 out of 8 in the Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:58.8
occ:1.00
 OD1 B:ASP99 2.3 59.2 1.0
OE2 B:GLU110 2.4 58.6 1.0
OE1 B:GLU110 2.4 58.5 1.0
OD1 B:ASP101 2.4 62.2 1.0
O B:TYR105 2.4 54.5 1.0
OD1 B:ASP103 2.4 66.5 1.0
CD B:GLU110 2.7 54.5 1.0
CG B:ASP101 3.3 63.1 1.0
CG B:ASP99 3.4 61.0 1.0
C B:TYR105 3.6 52.9 1.0
CG B:ASP103 3.6 64.5 1.0
N B:ASP101 3.7 62.5 1.0
CA B:ASP99 3.7 58.5 1.0
OD2 B:ASP101 3.8 65.1 1.0
N B:MET100 3.8 57.1 1.0
C B:ASP99 3.9 58.2 1.0
CB B:ASP99 4.1 61.0 1.0
N B:LYS102 4.1 63.8 1.0
CG B:GLU110 4.2 47.8 1.0
N B:ASP103 4.2 61.7 1.0
OD2 B:ASP103 4.2 66.3 1.0
CA B:ASP101 4.3 62.9 1.0
OD2 B:ASP99 4.3 58.6 1.0
C B:ASP101 4.3 64.3 1.0
CA B:ILE106 4.3 40.7 1.0
CB B:ASP101 4.4 61.5 1.0
N B:ILE106 4.4 46.2 1.0
N B:TYR105 4.5 51.8 1.0
C B:MET100 4.6 58.3 1.0
CA B:TYR105 4.6 53.5 1.0
CA B:MET100 4.7 57.3 1.0
O B:ASP99 4.7 62.7 1.0
CB B:ASP103 4.8 61.5 1.0
CA B:LYS102 4.9 63.1 1.0
N B:SER107 4.9 36.4 1.0
CB B:GLU110 4.9 42.7 1.0
CA B:ASP103 4.9 59.4 1.0

Calcium binding site 4 out of 8 in 1m63

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Calcium binding site 4 out of 8 in the Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:46.6
occ:1.00
 OE2 B:GLU151 2.0 73.4 1.0
OD1 B:ASP142 2.3 54.0 1.0
OD1 B:ASP140 2.3 36.5 1.0
OD1 B:ASP144 2.4 48.0 1.0
O B:ARG146 2.5 49.5 1.0
OE1 B:GLU151 2.5 62.7 1.0
CD B:GLU151 2.6 69.9 1.0
OD2 B:ASP142 2.9 47.5 1.0
CG B:ASP142 3.0 52.1 1.0
CG B:ASP144 3.3 45.8 1.0
OD2 B:ASP144 3.4 44.4 1.0
CG B:ASP140 3.5 42.3 1.0
C B:ARG146 3.6 47.4 1.0
CA B:ILE147 4.0 41.5 1.0
CG B:GLU151 4.1 67.1 1.0
N B:SER148 4.1 43.9 1.0
OD2 B:ASP140 4.2 40.1 1.0
N B:ILE147 4.2 43.1 1.0
CB B:ASP142 4.4 51.7 1.0
C B:ILE147 4.5 43.1 1.0
CB B:ASP140 4.5 47.4 1.0
CA B:ASP140 4.6 52.6 1.0
N B:ASP142 4.7 54.4 1.0
CB B:ASP144 4.7 47.2 1.0
CA B:ARG146 4.7 49.9 1.0
CG B:ARG146 4.7 64.3 1.0
N B:ARG146 4.7 49.6 1.0
N B:ASP144 4.8 44.6 1.0
CB B:GLU151 4.9 65.6 1.0
CB B:SER148 4.9 47.3 1.0
CE1 B:TYR105 4.9 64.3 1.0
OG B:SER148 4.9 44.0 1.0
N B:LYS141 5.0 53.6 1.0

Calcium binding site 5 out of 8 in 1m63

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Calcium binding site 5 out of 8 in the Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca500

b:95.4
occ:1.00
 OD1 F:ASP30 2.4 98.6 1.0
O F:SER36 2.4 97.1 1.0
OD1 F:ASP32 2.4 0.0 1.0
OG F:SER34 2.4 94.7 1.0
OE1 F:GLU41 2.5 98.5 1.0
CD F:GLU41 3.2 100.0 1.0
OE2 F:GLU41 3.3 100.0 1.0
C F:SER36 3.4 97.8 1.0
CG F:ASP32 3.5 0.0 1.0
CG F:ASP30 3.6 0.0 1.0
CB F:SER34 3.8 96.8 1.0
OD2 F:ASP32 3.9 98.8 1.0
N F:SER36 4.0 99.3 1.0
N F:SER34 4.1 98.9 1.0
N F:LEU37 4.1 99.2 1.0
CA F:LEU37 4.3 99.2 1.0
CA F:SER36 4.3 97.6 1.0
OD2 F:ASP30 4.3 0.0 1.0
N F:GLY35 4.4 98.2 1.0
CA F:SER34 4.5 98.1 1.0
OE2 F:GLU68 4.5 99.8 1.0
CB F:ASP30 4.6 99.6 1.0
CA F:ASP30 4.6 99.9 1.0
OG F:SER36 4.7 99.1 1.0
N F:ASN33 4.7 99.2 1.0
CG F:GLU41 4.7 99.7 1.0
N F:SER38 4.7 98.5 1.0
N F:ASP32 4.8 0.0 1.0
CB F:ASP32 4.8 0.0 1.0
C F:SER34 4.9 98.0 1.0
CD1 F:LEU37 5.0 90.9 1.0

Calcium binding site 6 out of 8 in 1m63

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Calcium binding site 6 out of 8 in the Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca501

b:93.7
occ:1.00
 O F:GLU68 2.4 87.7 1.0
OD1 F:ASN66 2.4 89.2 1.0
OE1 F:GLU73 2.4 88.8 1.0
OD1 F:ASP62 2.4 0.0 1.0
OD1 F:ASP64 2.4 94.7 1.0
OD2 F:ASP70 2.5 98.5 1.0
OE2 F:GLU73 2.8 91.2 1.0
CD F:GLU73 2.9 90.4 1.0
CG F:ASP64 3.4 95.0 1.0
CG F:ASN66 3.5 88.7 1.0
OD2 F:ASP64 3.6 95.9 1.0
C F:GLU68 3.6 88.9 1.0
CG F:ASP62 3.7 0.0 1.0
CG F:ASP70 3.7 97.0 1.0
ND2 F:ASN66 3.9 88.1 1.0
N F:ASP70 4.1 91.8 1.0
CA F:VAL69 4.3 88.4 1.0
OD2 F:ASP62 4.3 0.0 1.0
N F:VAL69 4.4 89.2 1.0
CG F:GLU73 4.4 91.3 1.0
OD1 F:ASP70 4.4 99.0 1.0
CA F:GLU68 4.6 89.9 1.0
N F:GLU68 4.7 90.3 1.0
C F:VAL69 4.7 88.4 1.0
N F:ASN66 4.7 91.2 1.0
CB F:ASP70 4.8 95.2 1.0
CB F:ASP64 4.8 94.9 1.0
CB F:ASP62 4.8 0.0 1.0
CA F:ASP62 4.8 0.0 1.0
CB F:ASN66 4.8 89.5 1.0
N F:GLY65 4.8 93.1 1.0
N F:ASP64 5.0 97.3 1.0

Calcium binding site 7 out of 8 in 1m63

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Calcium binding site 7 out of 8 in the Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca502

b:97.2
occ:1.00
 OD1 F:ASP103 2.4 97.4 1.0
OD1 F:ASP101 2.4 98.8 1.0
O F:TYR105 2.4 99.0 1.0
OD1 F:ASP99 2.4 91.3 1.0
OE1 F:GLU110 2.4 99.0 1.0
OD2 F:ASP103 2.9 93.5 1.0
CG F:ASP103 2.9 96.9 1.0
CG F:ASP99 3.2 93.2 1.0
CG F:ASP101 3.3 0.0 1.0
OD2 F:ASP99 3.4 95.7 1.0
CD F:GLU110 3.4 0.0 1.0
OD2 F:ASP101 3.4 0.0 1.0
C F:TYR105 3.5 99.8 1.0
OE2 F:GLU110 4.0 100.0 1.0
N F:ASP103 4.3 99.1 1.0
CB F:ASP103 4.3 97.4 1.0
N F:SER107 4.3 99.9 1.0
N F:ILE106 4.3 0.0 1.0
CA F:ILE106 4.3 99.6 1.0
N F:TYR105 4.3 0.0 1.0
CG F:GLU110 4.4 0.0 1.0
CA F:TYR105 4.4 0.0 1.0
OG F:SER107 4.5 97.0 1.0
CB F:ASP99 4.6 93.3 1.0
CA F:ASP103 4.7 98.1 1.0
CB F:ASP101 4.7 99.8 1.0
C F:ILE106 4.8 100.0 1.0
N F:LYS102 4.9 0.0 1.0
N F:ASP101 4.9 0.0 1.0
CB F:TYR105 4.9 99.7 1.0
CA F:ASP99 4.9 94.6 1.0
C F:ASP103 5.0 98.8 1.0

Calcium binding site 8 out of 8 in 1m63

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Calcium binding site 8 out of 8 in the Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca503

b:99.0
occ:1.00
 OE2 F:GLU151 1.9 90.1 1.0
OE1 F:GLU151 2.4 92.8 1.0
CD F:GLU151 2.4 91.5 1.0
O F:ARG146 2.4 95.3 1.0
OD1 F:ASP144 2.4 0.0 1.0
OD1 F:ASP140 2.4 0.0 1.0
OD1 F:ASP142 2.5 0.0 1.0
CG F:ASP144 3.1 0.0 1.0
OD2 F:ASP144 3.1 99.5 1.0
CG F:ASP142 3.6 99.9 1.0
CG F:ASP140 3.6 99.7 1.0
C F:ARG146 3.6 96.5 1.0
OD2 F:ASP142 3.9 97.8 1.0
CG F:GLU151 3.9 91.0 1.0
CA F:ILE147 3.9 97.9 1.0
N F:SER148 4.0 99.7 1.0
N F:ILE147 4.2 96.3 1.0
OD2 F:ASP140 4.2 97.1 1.0
CB F:ASP144 4.5 0.0 1.0
C F:ILE147 4.5 99.5 1.0
OG F:SER148 4.6 93.3 1.0
CB F:ASP140 4.6 0.0 1.0
CG1 F:ILE147 4.7 97.4 1.0
CB F:GLU151 4.7 89.6 1.0
CA F:ASP140 4.7 0.0 1.0
N F:ARG146 4.8 0.0 1.0
CA F:ARG146 4.8 98.1 1.0
N F:ASP144 4.8 94.9 1.0
CB F:SER148 4.8 96.6 1.0
CB F:ASP142 4.9 99.7 1.0
CB F:ILE147 4.9 97.0 1.0

Reference:

Q.Huai, H.-Y.Kim, Y.Liu, Y.Zhao, A.Mondragon, J.O.Liu, H.Ke. Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes Proc.Natl.Acad.Sci.Usa V. 99 12037 2002.
ISSN: ISSN 0027-8424
PubMed: 12218175
DOI: 10.1073/PNAS.192206699
Page generated: Thu Jul 11 12:16:48 2024

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