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Calcium in PDB 6psd: Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide

Protein crystallography data

The structure of Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide, PDB code: 6psd was solved by R.Dominguez, I.G.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.35 / 2.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.290, 161.990, 56.900, 90.00, 104.01, 90.00
R / Rfree (%) 19.7 / 23.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide (pdb code 6psd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide, PDB code: 6psd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6psd

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Calcium binding site 1 out of 8 in the Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:36.8
occ:1.00
OD1 E:ASP97 2.2 50.5 1.0
O E:TYR103 2.3 43.6 1.0
OD1 E:ASP99 2.4 68.8 1.0
OE2 E:GLU108 2.4 32.6 1.0
OE1 E:GLU108 2.5 36.7 1.0
CD E:GLU108 2.8 36.7 1.0
OD1 E:ASN101 3.0 82.1 1.0
CG E:ASP97 3.1 54.6 1.0
CG E:ASP99 3.2 67.3 1.0
OD2 E:ASP99 3.3 67.8 1.0
OD2 E:ASP97 3.4 55.2 1.0
CB E:ASN101 3.5 68.2 1.0
CG E:ASN101 3.5 76.3 1.0
C E:TYR103 3.5 46.0 1.0
N E:ASN101 4.0 70.4 1.0
CG E:GLU108 4.3 36.1 1.0
N E:TYR103 4.4 49.1 1.0
CA E:ASN101 4.4 65.1 1.0
CA E:TYR103 4.4 48.7 1.0
CB E:ASP97 4.4 52.4 1.0
N E:LEU104 4.5 47.4 1.0
CB E:TYR103 4.5 46.8 1.0
CB E:ASP99 4.6 65.7 1.0
ND2 E:ASN101 4.6 82.5 1.0
CA E:LEU104 4.6 47.6 1.0
OG1 E:THR105 4.7 32.7 1.0
N E:THR105 4.7 43.3 1.0
CA E:ASP97 4.7 51.5 1.0
CG2 E:THR105 4.7 36.7 1.0
N E:ASP99 4.8 61.6 1.0
N E:GLY100 4.8 68.7 1.0
C E:ASP97 5.0 49.1 1.0

Calcium binding site 2 out of 8 in 6psd

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Calcium binding site 2 out of 8 in the Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:64.8
occ:1.00
OD1 C:ASP97 2.3 86.4 1.0
OD1 C:ASP99 2.3 0.4 1.0
O C:TYR103 2.4 69.0 1.0
CB C:ASN101 2.7 0.6 1.0
OE2 C:GLU108 2.9 91.0 1.0
CG C:ASP99 3.3 0.6 1.0
N C:ASN101 3.3 0.2 1.0
CG C:ASP97 3.4 91.3 1.0
CA C:ASN101 3.4 0.4 1.0
OD2 C:ASP99 3.5 0.8 1.0
C C:TYR103 3.6 69.9 1.0
CG C:ASN101 3.7 1.0 1.0
CD C:GLU108 3.8 97.5 1.0
OD1 C:ASN101 3.8 0.2 1.0
C C:ASN101 3.8 0.7 1.0
OD2 C:ASP97 3.8 97.7 1.0
OE1 C:GLU108 3.9 0.8 1.0
N C:TYR103 4.0 77.9 1.0
O C:ASN101 4.2 0.1 1.0
N C:GLY102 4.3 97.3 1.0
CA C:TYR103 4.4 75.6 1.0
N C:GLY100 4.4 0.4 1.0
C C:GLY100 4.5 0.6 1.0
CB C:ASP97 4.6 94.1 1.0
CB C:ASP99 4.6 0.7 1.0
N C:LEU104 4.6 73.1 1.0
N C:ASP99 4.6 0.7 1.0
CA C:ASP97 4.7 92.0 1.0
CA C:LEU104 4.8 73.5 1.0
C C:ASP99 4.8 0.7 1.0
CB C:TYR103 4.8 77.4 1.0
CA C:ASP99 4.9 0.1 1.0
ND2 C:ASN101 4.9 0.9 1.0
C C:ASP97 4.9 98.5 1.0
CA C:GLY100 5.0 0.3 1.0
CG2 C:THR105 5.0 74.5 1.0

Calcium binding site 3 out of 8 in 6psd

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Calcium binding site 3 out of 8 in the Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:41.4
occ:1.00
O A:TYR103 2.2 56.5 1.0
OE2 A:GLU108 2.3 50.5 1.0
OD1 A:ASP99 2.4 60.2 1.0
OE1 A:GLU108 2.4 52.2 1.0
OD1 A:ASP97 2.6 70.2 1.0
CD A:GLU108 2.7 50.0 1.0
OD1 A:ASN101 2.7 83.7 1.0
O A:HOH302 3.1 37.4 1.0
CG A:ASP99 3.1 58.7 1.0
OD2 A:ASP99 3.1 56.5 1.0
CG A:ASN101 3.3 86.3 1.0
C A:TYR103 3.5 57.0 1.0
CG A:ASP97 3.6 64.3 1.0
CB A:ASN101 3.7 74.2 1.0
CG A:GLU108 4.2 46.9 1.0
OD2 A:ASP97 4.2 67.2 1.0
N A:ASN101 4.2 67.2 1.0
N A:LEU104 4.3 57.3 1.0
ND2 A:ASN101 4.4 92.4 1.0
CA A:LEU104 4.4 58.0 1.0
N A:THR105 4.4 57.4 1.0
CA A:TYR103 4.4 56.5 1.0
N A:TYR103 4.5 57.0 1.0
CB A:ASP99 4.5 59.9 1.0
CA A:ASP97 4.5 52.9 1.0
N A:ASP99 4.5 60.0 1.0
OG1 A:THR105 4.5 51.5 1.0
CA A:ASN101 4.5 66.0 1.0
CB A:ASP97 4.6 55.6 1.0
CG2 A:THR105 4.6 58.6 1.0
CB A:TYR103 4.7 54.2 1.0
C A:ASP97 4.7 53.5 1.0
N A:ALA98 4.8 50.3 1.0
N A:GLY100 4.8 56.1 1.0
C A:LEU104 4.9 56.8 1.0
CA A:ASP99 4.9 60.0 1.0
CB A:GLU108 5.0 46.4 1.0

Calcium binding site 4 out of 8 in 6psd

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Calcium binding site 4 out of 8 in the Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:54.5
occ:1.00
O G:TYR103 2.2 61.9 1.0
OD1 G:ASP97 2.4 79.7 1.0
OE2 G:GLU108 2.4 59.7 1.0
OD1 G:ASP99 2.4 64.9 1.0
OE1 G:GLU108 2.5 65.8 1.0
CD G:GLU108 2.7 67.3 1.0
OD1 G:ASN101 2.8 97.6 1.0
C G:TYR103 3.3 68.3 1.0
CG G:ASP99 3.4 78.5 1.0
CB G:ASN101 3.6 92.0 1.0
CG G:ASN101 3.6 92.8 1.0
CG G:ASP97 3.6 81.4 1.0
OD2 G:ASP99 3.6 72.4 1.0
N G:ASN101 4.0 81.2 1.0
N G:TYR103 4.1 72.3 1.0
CA G:TYR103 4.2 70.1 1.0
CG G:GLU108 4.2 66.9 1.0
N G:LEU104 4.3 64.4 1.0
OD2 G:ASP97 4.3 80.2 1.0
CA G:ASP97 4.3 81.0 1.0
CA G:ASN101 4.4 88.4 1.0
CB G:TYR103 4.4 65.6 1.0
CA G:LEU104 4.4 66.4 1.0
CB G:ASP97 4.6 82.1 1.0
N G:THR105 4.6 67.5 1.0
N G:ASP99 4.6 91.2 1.0
C G:ASP97 4.7 85.3 1.0
N G:GLY100 4.7 90.5 1.0
CB G:ASP99 4.8 81.4 1.0
N G:ALA98 4.8 93.2 1.0
CG2 G:THR105 4.8 71.4 1.0
ND2 G:ASN101 4.9 93.6 1.0
OG1 G:THR105 4.9 65.4 1.0
C G:LEU104 5.0 62.7 1.0
N G:GLY102 5.0 90.7 1.0

Calcium binding site 5 out of 8 in 6psd

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Calcium binding site 5 out of 8 in the Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca201

b:51.4
occ:1.00
OD1 I:ASP97 2.1 52.5 1.0
OE2 I:GLU108 2.3 64.0 1.0
OD1 I:ASP99 2.4 45.1 1.0
O I:TYR103 2.4 38.4 1.0
OE1 I:GLU108 2.5 66.7 1.0
OD1 I:ASN101 2.5 88.8 1.0
CD I:GLU108 2.6 60.6 1.0
CG I:ASN101 3.3 73.3 1.0
CG I:ASP99 3.3 52.0 1.0
CG I:ASP97 3.4 49.5 1.0
CB I:ASN101 3.4 69.2 1.0
C I:TYR103 3.6 42.6 1.0
OD2 I:ASP99 3.6 53.2 1.0
N I:ASN101 4.0 53.7 1.0
CG I:GLU108 4.1 57.8 1.0
CA I:ASP97 4.2 45.7 1.0
OD2 I:ASP97 4.2 48.3 1.0
CB I:ASP97 4.2 46.0 1.0
CA I:LEU104 4.3 50.1 1.0
CA I:ASN101 4.3 59.9 1.0
N I:LEU104 4.4 45.4 1.0
N I:THR105 4.4 52.9 1.0
C I:ASP97 4.4 43.0 1.0
N I:ASP99 4.5 52.5 1.0
N I:ALA98 4.6 42.5 1.0
N I:TYR103 4.6 40.8 1.0
ND2 I:ASN101 4.6 77.2 1.0
CA I:TYR103 4.6 44.5 1.0
CB I:ASP99 4.7 55.1 1.0
N I:GLY100 4.7 50.1 1.0
CG2 I:THR105 4.7 53.5 1.0
C I:LEU104 4.7 52.6 1.0
OG1 I:THR105 4.8 47.8 1.0
CB I:GLU108 4.9 52.9 1.0
CA I:ASP99 5.0 54.0 1.0
O I:ASP97 5.0 36.8 1.0

Calcium binding site 6 out of 8 in 6psd

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Calcium binding site 6 out of 8 in the Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca201

b:30.7
occ:1.00
OD1 K:ASP97 2.0 42.8 1.0
O K:TYR103 2.2 34.3 1.0
OD1 K:ASP99 2.2 41.8 1.0
OE2 K:GLU108 2.5 29.3 1.0
OE1 K:GLU108 2.6 33.4 1.0
CD K:GLU108 2.8 31.8 1.0
CG K:ASP99 2.9 40.2 1.0
OD2 K:ASP99 3.0 40.9 1.0
OD1 K:ASN101 3.1 59.7 1.0
CG K:ASP97 3.1 44.0 1.0
C K:TYR103 3.3 33.9 1.0
OD2 K:ASP97 3.5 48.5 1.0
CG K:ASN101 3.6 47.9 1.0
CB K:ASN101 3.6 43.3 1.0
N K:ASN101 4.2 44.6 1.0
CG K:GLU108 4.3 34.8 1.0
CA K:TYR103 4.3 34.3 1.0
N K:LEU104 4.3 37.7 1.0
N K:TYR103 4.3 33.8 1.0
CB K:ASP97 4.3 42.0 1.0
CB K:ASP99 4.4 42.8 1.0
CB K:TYR103 4.5 39.0 1.0
CA K:LEU104 4.5 39.5 1.0
CA K:ASN101 4.5 42.3 1.0
CA K:ASP97 4.6 39.4 1.0
N K:THR105 4.6 38.5 1.0
CG2 K:THR105 4.6 45.0 1.0
N K:ASP99 4.6 46.1 1.0
ND2 K:ASN101 4.6 51.8 1.0
OG1 K:THR105 4.7 52.9 1.0
N K:GLY100 4.8 40.2 1.0
CA K:ASP99 4.9 43.6 1.0
C K:ASP97 4.9 40.9 1.0
C K:ASP99 4.9 43.9 1.0

Calcium binding site 7 out of 8 in 6psd

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Calcium binding site 7 out of 8 in the Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca201

b:47.2
occ:1.00
O M:TYR103 2.0 59.3 1.0
OD1 M:ASP99 2.1 71.7 1.0
OD1 M:ASN101 2.2 98.0 1.0
OD1 M:ASP97 2.3 67.5 1.0
OE1 M:GLU108 2.5 63.0 1.0
OE2 M:GLU108 2.7 56.5 1.0
CG M:ASN101 2.8 86.9 1.0
CD M:GLU108 2.9 61.8 1.0
CG M:ASP99 3.0 79.7 1.0
CB M:ASN101 3.0 78.9 1.0
OD2 M:ASP99 3.2 77.9 1.0
C M:TYR103 3.2 60.8 1.0
CG M:ASP97 3.5 65.9 1.0
N M:ASN101 3.5 80.0 1.0
ND2 M:ASN101 3.8 94.8 1.0
CA M:ASN101 3.9 78.0 1.0
N M:TYR103 4.0 65.4 1.0
CA M:TYR103 4.1 63.6 1.0
OD2 M:ASP97 4.1 65.5 1.0
N M:LEU104 4.3 64.7 1.0
CB M:ASP99 4.3 85.1 1.0
N M:ASP99 4.4 89.4 1.0
CG M:GLU108 4.4 58.9 1.0
N M:GLY100 4.5 89.3 1.0
CA M:LEU104 4.5 62.2 1.0
CA M:ASP97 4.5 66.8 1.0
CB M:TYR103 4.5 64.7 1.0
CB M:ASP97 4.6 64.9 1.0
CG2 M:THR105 4.7 60.8 1.0
CA M:ASP99 4.7 88.6 1.0
C M:GLY100 4.7 81.2 1.0
C M:ASN101 4.7 73.2 1.0
N M:THR105 4.7 61.3 1.0
C M:ASP99 4.7 91.5 1.0
C M:ASP97 4.8 67.4 1.0
N M:GLY102 4.8 64.0 1.0
N M:ALA98 4.9 72.8 1.0

Calcium binding site 8 out of 8 in 6psd

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Calcium binding site 8 out of 8 in the Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca201

b:69.2
occ:1.00
OE2 O:GLU108 2.0 67.6 1.0
O O:TYR103 2.2 78.9 1.0
OD1 O:ASP99 2.2 88.4 1.0
OD1 O:ASP97 2.4 76.2 1.0
OD2 O:ASP99 2.6 0.2 1.0
OE1 O:GLU108 2.6 68.5 1.0
CD O:GLU108 2.6 64.0 1.0
CG O:ASP99 2.7 96.7 1.0
CB O:ASN101 3.1 85.1 1.0
C O:TYR103 3.4 72.4 1.0
CG O:ASP97 3.6 74.6 1.0
CG O:ASN101 4.0 83.2 1.0
OD1 O:ASN101 4.1 83.3 1.0
CG O:GLU108 4.1 63.7 1.0
N O:ASN101 4.1 81.7 1.0
CB O:ASP99 4.2 94.0 1.0
CA O:ASN101 4.2 84.4 1.0
N O:TYR103 4.2 84.7 1.0
CA O:ASP97 4.3 74.7 1.0
N O:LEU104 4.3 65.2 1.0
CA O:TYR103 4.3 79.9 1.0
CA O:LEU104 4.4 59.3 1.0
OD2 O:ASP97 4.4 76.8 1.0
N O:THR105 4.4 56.5 1.0
N O:ASP99 4.5 83.6 1.0
CB O:ASP97 4.5 74.0 1.0
C O:ASP97 4.5 74.9 1.0
CG2 O:THR105 4.5 65.9 1.0
CB O:TYR103 4.6 81.2 1.0
N O:ALA98 4.8 77.3 1.0
CA O:ASP99 4.8 86.2 1.0
CB O:GLU108 4.8 62.7 1.0
OG1 O:THR105 4.8 61.3 1.0
C O:LEU104 4.9 55.0 1.0
C O:ASN101 4.9 83.3 1.0
N O:GLY102 4.9 86.5 1.0

Reference:

R.Dominguez, I.G.Lee. Complex of CRACR2A with A Dynein Light Intermediate Chain Peptide To Be Published.
Page generated: Tue Jul 16 12:58:36 2024

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