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Calcium in PDB 2p6b: Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide

Protein crystallography data

The structure of Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide, PDB code: 2p6b was solved by H.Li, L.Zhang, A.Rao, S.C.Harrison, P.G.Hogan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.104, 89.155, 157.685, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 25.4

Other elements in 2p6b:

The structure of Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide 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 Human Calcineurin in Complex with Pvivit Peptide (pdb code 2p6b). 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 Human Calcineurin in Complex with Pvivit Peptide, PDB code: 2p6b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2p6b

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Calcium binding site 1 out of 8 in the Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide


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 Human Calcineurin in Complex with Pvivit Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:87.5
occ:1.00
 OG B:SER34 2.8 77.3 1.0
O B:SER36 2.9 64.8 1.0
OD1 B:ASP32 2.9 87.1 1.0
OE1 B:GLU41 3.0 66.5 1.0
OE2 B:GLU41 3.0 67.8 1.0
OD2 B:ASP32 3.1 87.6 1.0
CD B:GLU41 3.2 66.8 1.0
OD1 B:ASP30 3.4 66.8 1.0
CG B:ASP32 3.4 87.2 1.0
OE2 B:GLU68 3.7 66.9 1.0
C B:SER36 3.9 65.4 1.0
N B:SER38 4.0 64.2 1.0
CB B:SER34 4.0 77.0 1.0
OG B:SER36 4.0 68.4 1.0
CB B:SER38 4.1 64.2 1.0
OG B:SER38 4.1 63.0 1.0
CD B:GLU68 4.3 66.5 1.0
CG B:GLU41 4.3 67.2 1.0
OE1 B:GLU68 4.4 68.2 1.0
CA B:LEU37 4.5 64.1 1.0
CG B:ASP30 4.6 68.8 1.0
C B:LEU37 4.6 64.1 1.0
N B:LEU37 4.6 64.5 1.0
CA B:SER38 4.7 64.4 1.0
CA B:SER36 4.9 66.8 1.0
CB B:ASP32 4.9 85.2 1.0
N B:SER36 4.9 68.1 1.0
N B:SER34 5.0 79.8 1.0

Calcium binding site 2 out of 8 in 2p6b

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Calcium binding site 2 out of 8 in the Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide


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 Human Calcineurin in Complex with Pvivit Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:43.0
occ:1.00
 O B:GLU68 2.5 48.1 1.0
OD1 B:ASP62 2.6 40.2 1.0
OD1 B:ASN66 2.7 46.9 1.0
OE1 B:GLU73 2.8 39.0 1.0
OE2 B:GLU73 2.8 34.8 1.0
OD1 B:ASP64 2.8 45.7 1.0
O B:HOH530 2.8 47.1 1.0
OD2 B:ASP64 3.1 48.7 1.0
CD B:GLU73 3.2 38.2 1.0
CG B:ASP64 3.2 46.6 1.0
CG B:ASN66 3.5 44.8 1.0
C B:GLU68 3.7 50.5 1.0
CG B:ASP62 3.8 42.8 1.0
N B:ASN66 4.1 46.1 1.0
CB B:ASN66 4.2 45.4 1.0
ND2 B:ASN66 4.2 43.8 1.0
OD2 B:ASP70 4.2 47.0 1.0
CA B:ASP62 4.3 42.4 1.0
N B:ASP64 4.4 46.0 1.0
N B:GLU68 4.4 51.0 1.0
CA B:VAL69 4.4 48.2 1.0
N B:ASP70 4.5 48.2 1.0
N B:VAL69 4.5 48.9 1.0
CB B:ASP62 4.5 42.6 1.0
CB B:ASP64 4.6 45.3 1.0
N B:GLY65 4.6 46.1 1.0
C B:ASP62 4.6 43.0 1.0
CG B:GLU73 4.7 39.1 1.0
CA B:GLU68 4.7 52.9 1.0
CA B:ASN66 4.7 46.1 1.0
N B:THR63 4.8 43.9 1.0
CA B:ASP64 4.8 46.3 1.0
OD2 B:ASP62 4.8 45.9 1.0
N B:GLY67 4.8 47.9 1.0
C B:ASP64 4.8 46.1 1.0
CG B:ASP70 5.0 49.1 1.0

Calcium binding site 3 out of 8 in 2p6b

Go back to Calcium Binding Sites List in 2p6b
Calcium binding site 3 out of 8 in the Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide


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 Human Calcineurin in Complex with Pvivit Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:31.8
occ:1.00
 OD1 B:ASP99 2.5 21.4 1.0
O B:TYR105 2.5 31.5 1.0
O B:HOH521 2.5 19.7 1.0
OD1 B:ASP103 2.6 34.8 1.0
OD1 B:ASP101 2.7 35.6 1.0
OE1 B:GLU110 2.7 28.6 1.0
OE2 B:GLU110 2.8 30.9 1.0
CD B:GLU110 3.1 31.3 1.0
CG B:ASP103 3.2 34.0 1.0
CG B:ASP101 3.2 36.0 1.0
OD2 B:ASP101 3.3 36.6 1.0
OD2 B:ASP103 3.4 35.7 1.0
C B:TYR105 3.6 29.6 1.0
CG B:ASP99 3.7 27.7 1.0
N B:ASP103 4.0 31.7 1.0
N B:TYR105 4.1 26.9 1.0
N B:ASP101 4.2 34.3 1.0
CB B:ASP103 4.3 31.9 1.0
CB B:ASP101 4.4 35.0 1.0
N B:LYS102 4.4 32.9 1.0
O B:HOH509 4.4 30.5 1.0
CA B:TYR105 4.4 29.6 1.0
OD2 B:ASP99 4.5 28.2 1.0
CG B:GLU110 4.5 29.9 1.0
CA B:ASP99 4.5 27.6 1.0
CA B:ASP101 4.6 34.2 1.0
C B:ASP99 4.6 28.7 1.0
C B:ASP101 4.6 33.8 1.0
N B:ILE106 4.6 28.8 1.0
N B:SER107 4.6 24.2 1.0
CA B:ASP103 4.6 30.9 1.0
CB B:ASP99 4.7 27.2 1.0
CA B:ILE106 4.7 25.1 1.0
N B:MET100 4.7 30.5 1.0
N B:GLY104 4.7 27.8 1.0
O B:HOH518 4.8 31.1 1.0
CB B:TYR105 4.9 30.1 1.0
C B:ASP103 4.9 30.0 1.0
OG B:SER107 5.0 27.2 1.0
C B:LYS102 5.0 33.6 1.0
O B:ASP99 5.0 27.9 1.0

Calcium binding site 4 out of 8 in 2p6b

Go back to Calcium Binding Sites List in 2p6b
Calcium binding site 4 out of 8 in the Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide


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 Human Calcineurin in Complex with Pvivit Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:36.7
occ:1.00
 O B:ARG146 2.5 31.0 1.0
OD1 B:ASP140 2.6 36.6 1.0
OE1 B:GLU151 2.7 33.4 1.0
OD2 B:ASP142 2.7 49.3 1.0
OE2 B:GLU151 2.7 33.5 1.0
O B:HOH532 2.8 36.9 1.0
OD1 B:ASP144 2.8 46.7 1.0
CD B:GLU151 3.1 32.5 1.0
OD1 B:ASP142 3.1 49.8 1.0
CG B:ASP142 3.1 48.6 1.0
CG B:ASP144 3.3 44.7 1.0
OD2 B:ASP144 3.4 44.5 1.0
C B:ARG146 3.6 31.0 1.0
CG B:ASP140 3.7 36.0 1.0
N B:ARG146 4.1 33.1 1.0
N B:ASP144 4.3 41.3 1.0
CA B:ASP140 4.3 35.2 1.0
N B:ASP142 4.3 44.8 1.0
CB B:ASP142 4.4 46.7 1.0
CA B:ARG146 4.4 32.4 1.0
CB B:ASP140 4.5 34.7 1.0
N B:SER148 4.5 26.9 1.0
N B:ILE147 4.5 28.6 1.0
CB B:ASP144 4.5 41.5 1.0
CG B:GLU151 4.6 31.0 1.0
CA B:ILE147 4.6 28.0 1.0
OD2 B:ASP140 4.6 35.8 1.0
C B:ASP140 4.6 37.8 1.0
N B:GLY143 4.6 43.2 1.0
N B:GLY145 4.7 35.5 1.0
CA B:ASP142 4.7 45.1 1.0
O B:HOH514 4.7 33.4 1.0
N B:LYS141 4.8 40.2 1.0
CA B:ASP144 4.8 40.1 1.0
CB B:ARG146 4.8 33.9 1.0
C B:ASP142 4.9 44.2 1.0
C B:ASP144 5.0 38.0 1.0

Calcium binding site 5 out of 8 in 2p6b

Go back to Calcium Binding Sites List in 2p6b
Calcium binding site 5 out of 8 in the Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide


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 Human Calcineurin in Complex with Pvivit Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca505

b:68.4
occ:1.00
 O D:SER36 2.7 56.2 1.0
OE1 D:GLU41 2.9 71.6 1.0
OD1 D:ASP32 2.9 70.6 1.0
OD1 D:ASP30 2.9 62.7 1.0
OG D:SER34 3.0 66.2 1.0
O D:HOH533 3.0 62.2 1.0
OE2 D:GLU41 3.1 73.2 1.0
OD2 D:ASP32 3.1 70.8 1.0
CD D:GLU41 3.3 72.0 1.0
CG D:ASP32 3.3 70.7 1.0
CG D:ASP30 3.7 61.9 1.0
C D:SER36 3.8 57.6 1.0
CB D:SER34 3.9 67.0 1.0
OD2 D:ASP30 4.0 60.9 1.0
N D:SER34 4.0 68.6 1.0
OE2 D:GLU68 4.3 58.8 1.0
CA D:LEU37 4.5 57.2 1.0
N D:ASN33 4.5 69.5 1.0
CA D:SER34 4.5 66.5 1.0
N D:SER38 4.6 59.8 1.0
N D:LEU37 4.6 57.4 1.0
CA D:ASP30 4.6 64.7 1.0
CG D:GLU41 4.6 71.6 1.0
N D:SER36 4.6 60.0 1.0
N D:ASP32 4.6 69.4 1.0
OG D:SER36 4.7 59.9 1.0
CB D:ASP32 4.7 70.4 1.0
CB D:ASP30 4.7 63.1 1.0
CA D:SER36 4.8 59.3 1.0
OG D:SER38 4.9 59.3 1.0
C D:ASP30 4.9 66.5 1.0
C D:ASP32 5.0 70.0 1.0
N D:GLY35 5.0 63.6 1.0
C D:ASN33 5.0 69.7 1.0
CA D:ASP32 5.0 69.9 1.0
C D:LEU37 5.0 58.2 1.0

Calcium binding site 6 out of 8 in 2p6b

Go back to Calcium Binding Sites List in 2p6b
Calcium binding site 6 out of 8 in the Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide


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 Human Calcineurin in Complex with Pvivit Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca506

b:48.5
occ:1.00
 O D:GLU68 2.7 49.0 1.0
OD1 D:ASN66 2.7 56.0 1.0
OE2 D:GLU73 2.8 45.3 1.0
OE1 D:GLU73 2.8 43.8 1.0
OD1 D:ASP62 2.8 55.4 1.0
O D:HOH528 2.9 44.6 1.0
OD1 D:ASP64 2.9 62.7 1.0
OD2 D:ASP64 3.0 62.7 1.0
CD D:GLU73 3.1 44.2 1.0
CG D:ASP64 3.2 61.1 1.0
CG D:ASN66 3.4 56.5 1.0
C D:GLU68 3.7 48.5 1.0
CG D:ASP62 3.9 54.7 1.0
N D:ASN66 4.0 55.1 1.0
CB D:ASN66 4.1 55.5 1.0
ND2 D:ASN66 4.1 55.3 1.0
N D:ASP64 4.2 57.9 1.0
CA D:ASP62 4.2 52.2 1.0
CA D:VAL69 4.4 45.0 1.0
CB D:ASP64 4.4 58.9 1.0
N D:VAL69 4.5 46.5 1.0
N D:GLU68 4.5 51.3 1.0
N D:GLY65 4.5 57.1 1.0
CB D:ASP62 4.5 53.2 1.0
C D:ASP62 4.5 53.2 1.0
CA D:ASN66 4.5 55.5 1.0
N D:ASP70 4.5 43.2 1.0
N D:THR63 4.6 54.4 1.0
CA D:GLU68 4.6 50.8 1.0
CG D:GLU73 4.6 43.3 1.0
CA D:ASP64 4.7 58.2 1.0
C D:ASP64 4.8 57.2 1.0
N D:GLY67 4.9 54.9 1.0
C D:ASN66 5.0 55.6 1.0
OD2 D:ASP62 5.0 56.3 1.0

Calcium binding site 7 out of 8 in 2p6b

Go back to Calcium Binding Sites List in 2p6b
Calcium binding site 7 out of 8 in the Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide


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 Human Calcineurin in Complex with Pvivit Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca507

b:38.4
occ:1.00
 O D:TYR105 2.5 39.0 1.0
OD1 D:ASP99 2.6 36.8 1.0
OE1 D:GLU110 2.7 37.3 1.0
O D:HOH523 2.7 30.7 1.0
OD1 D:ASP101 2.8 38.2 1.0
OD1 D:ASP103 2.9 41.1 1.0
OE2 D:GLU110 3.0 39.2 1.0
OD2 D:ASP103 3.1 44.6 1.0
CD D:GLU110 3.1 38.8 1.0
CG D:ASP103 3.2 42.2 1.0
CG D:ASP101 3.3 37.0 1.0
OD2 D:ASP101 3.4 37.2 1.0
C D:TYR105 3.6 38.6 1.0
CG D:ASP99 3.8 39.7 1.0
N D:ASP103 4.1 38.2 1.0
N D:TYR105 4.2 39.3 1.0
CA D:TYR105 4.3 39.8 1.0
O D:HOH522 4.3 55.0 1.0
N D:ASP101 4.4 39.1 1.0
CB D:ASP103 4.4 40.1 1.0
N D:SER107 4.4 31.0 1.0
N D:ILE106 4.5 37.6 1.0
CG D:GLU110 4.5 36.6 1.0
CB D:TYR105 4.5 40.6 1.0
CB D:ASP101 4.5 36.6 1.0
CA D:ILE106 4.6 33.6 1.0
OD2 D:ASP99 4.6 40.8 1.0
N D:LYS102 4.6 39.1 1.0
CA D:ASP99 4.6 38.0 1.0
CA D:ASP103 4.7 38.7 1.0
CB D:ASP99 4.7 38.6 1.0
N D:MET100 4.8 39.8 1.0
CA D:ASP101 4.8 38.5 1.0
OG D:SER107 4.9 32.4 1.0
C D:ASP99 4.9 39.2 1.0
C D:ASP101 4.9 38.8 1.0
N D:GLY104 5.0 38.6 1.0
C D:ILE106 5.0 32.1 1.0

Calcium binding site 8 out of 8 in 2p6b

Go back to Calcium Binding Sites List in 2p6b
Calcium binding site 8 out of 8 in the Crystal Structure of Human Calcineurin in Complex with Pvivit Peptide


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 Human Calcineurin in Complex with Pvivit Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca508

b:38.1
occ:1.00
 OD1 D:ASP140 2.5 35.7 1.0
OE1 D:GLU151 2.7 35.6 1.0
O D:ARG146 2.7 36.4 1.0
OD1 D:ASP144 2.7 35.8 1.0
O D:HOH530 2.7 42.9 1.0
OD2 D:ASP142 2.7 45.9 1.0
OE2 D:GLU151 2.8 38.1 1.0
CD D:GLU151 3.0 35.8 1.0
CG D:ASP144 3.3 33.8 1.0
CG D:ASP142 3.4 41.8 1.0
OD2 D:ASP144 3.5 34.1 1.0
OD1 D:ASP142 3.6 43.1 1.0
C D:ARG146 3.7 35.4 1.0
CG D:ASP140 3.7 36.1 1.0
CA D:ASP140 4.3 36.7 1.0
N D:ARG146 4.3 33.8 1.0
CB D:ASP140 4.4 37.5 1.0
N D:ASP142 4.4 38.1 1.0
N D:ILE147 4.4 34.8 1.0
CA D:ILE147 4.4 34.2 1.0
N D:ASP144 4.4 33.2 1.0
N D:SER148 4.5 34.6 1.0
CG D:GLU151 4.5 35.0 1.0
CA D:ARG146 4.5 35.5 1.0
CB D:ASP142 4.6 38.7 1.0
CB D:ASP144 4.6 33.1 1.0
CG D:ARG146 4.6 43.1 1.0
C D:ASP140 4.7 36.9 1.0
OD2 D:ASP140 4.7 35.9 1.0
N D:LYS141 4.7 37.3 1.0
N D:GLY143 4.8 34.2 1.0
OG D:SER148 4.9 35.0 1.0
C D:ILE147 4.9 35.5 1.0
CA D:ASP142 4.9 37.0 1.0
CA D:ASP144 5.0 33.3 1.0

Reference:

H.Li, L.Zhang, A.Rao, S.C.Harrison, P.G.Hogan. Structure of Calcineurin in Complex with Pvivit Peptide: Portrait of A Low-Affinity Signalling Interaction J.Mol.Biol. V. 369 1296 2007.
ISSN: ISSN 0022-2836
PubMed: 17498738
DOI: 10.1016/J.JMB.2007.04.032
Page generated: Fri Jul 12 15:01:08 2024

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