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Calcium in PDB 8bbj: Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4

Protein crystallography data

The structure of Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4, PDB code: 8bbj was solved by R.Schnell, E.Szodorai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.29 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.409, 103.134, 121.656, 90, 90, 90
R / Rfree (%) 21.3 / 26.9

Other elements in 8bbj:

The structure of Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4 also contains other interesting chemical elements:

Arsenic (As) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4 (pdb code 8bbj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4, PDB code: 8bbj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8bbj

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Calcium binding site 1 out of 8 in the Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:64.5
occ:1.00
OD1 C:ASP118 2.3 58.3 1.0
OD1 C:ASP120 2.5 72.3 1.0
O C:PHE124 2.5 59.9 1.0
OE1 C:GLU129 2.6 65.5 1.0
OG C:SER122 2.7 57.7 1.0
OE2 C:GLU129 3.0 60.6 1.0
CD C:GLU129 3.2 65.2 1.0
CG C:ASP120 3.4 71.0 1.0
OD2 C:ASP120 3.5 74.7 1.0
CG C:ASP118 3.5 58.3 1.0
CB C:SER122 3.6 56.6 1.0
C C:PHE124 3.7 61.0 1.0
N C:SER122 4.1 63.5 1.0
OD2 C:ASP118 4.3 60.2 1.0
CA C:ASP118 4.3 64.1 1.0
N C:SER126 4.3 58.4 1.0
CA C:SER122 4.4 61.4 1.0
N C:PHE124 4.4 60.8 1.0
CA C:ILE125 4.4 59.6 1.0
N C:ILE125 4.5 58.6 1.0
CB C:ASP118 4.5 55.5 1.0
OG C:SER126 4.5 64.1 1.0
N C:ASP120 4.6 65.3 1.0
CA C:PHE124 4.6 62.6 1.0
CG C:GLU129 4.7 55.8 1.0
C C:ASP118 4.7 62.6 1.0
N C:ALA119 4.7 57.7 1.0
CB C:ASP120 4.7 61.0 1.0
C C:ILE125 4.8 55.4 1.0
N C:GLY123 4.9 60.1 1.0
C C:SER122 4.9 57.9 1.0
CB C:SER126 4.9 62.0 1.0
N C:SER121 4.9 64.5 1.0

Calcium binding site 2 out of 8 in 8bbj

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Calcium binding site 2 out of 8 in the Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:71.8
occ:1.00
OD1 C:ASN164 2.4 86.9 1.0
O C:ARG168 2.4 67.0 1.0
OD2 C:ASP166 2.6 75.6 1.0
OD1 C:ASP162 2.6 67.0 1.0
CG C:ASP166 3.3 75.8 1.0
CG C:ASN164 3.4 77.1 1.0
OD1 C:ASP166 3.5 80.0 1.0
OD2 C:ASP173 3.5 63.8 1.0
C C:ARG168 3.7 63.6 1.0
CG C:ASP162 3.8 71.4 1.0
ND2 C:ASN164 3.8 77.3 1.0
N C:ASN164 4.2 71.9 1.0
N C:LYS163 4.3 71.0 1.0
OD2 C:ASP162 4.4 75.3 1.0
N C:ARG168 4.5 73.3 1.0
N C:LEU169 4.6 59.7 1.0
CA C:ARG168 4.6 70.8 1.0
CA C:LEU169 4.6 61.2 1.0
CA C:ASP162 4.6 62.3 1.0
CB C:ASN164 4.7 75.2 1.0
CB C:ASP166 4.7 77.8 1.0
C C:ASP162 4.7 67.3 1.0
CG C:ASP173 4.7 66.2 1.0
N C:ASP166 4.7 74.4 1.0
N C:ASP170 4.8 57.5 1.0
CB C:ASP162 4.8 61.4 1.0
CA C:ASN164 4.8 73.2 1.0
CB C:ARG168 4.9 69.4 1.0
N C:LYS165 4.9 76.4 1.0
OD2 C:ASP170 5.0 76.7 1.0

Calcium binding site 3 out of 8 in 8bbj

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Calcium binding site 3 out of 8 in the Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:96.3
occ:1.00
O C:ALA216 2.2 75.0 1.0
OD1 C:ASP210 2.4 75.1 1.0
OG C:SER212 2.4 85.8 1.0
OG1 C:THR214 2.6 81.3 1.0
OE1 C:GLU221 2.7 77.6 1.0
OE1 C:GLU218 2.9 93.3 1.0
OE2 C:GLU221 3.2 80.7 1.0
C C:ALA216 3.3 68.5 1.0
CG C:ASP210 3.3 74.2 1.0
CD C:GLU221 3.3 83.7 1.0
CB C:THR214 3.6 78.5 1.0
N C:ALA216 3.7 70.9 1.0
CB C:SER212 3.8 80.4 1.0
CD C:GLU218 3.8 91.0 1.0
CG2 C:THR214 3.8 81.7 1.0
N C:THR214 3.9 79.5 1.0
OD2 C:ASP210 3.9 73.8 1.0
CG C:GLU218 4.0 89.1 1.0
CA C:ALA216 4.1 71.5 1.0
CA C:THR214 4.2 76.7 1.0
N C:LEU217 4.2 64.1 1.0
CB C:ASP210 4.3 73.9 1.0
N C:GLY215 4.3 76.3 1.0
CA C:LEU217 4.3 73.0 1.0
CA C:ASP210 4.4 70.4 1.0
C C:THR214 4.5 81.2 1.0
N C:LYS213 4.5 80.6 1.0
N C:SER212 4.5 76.7 1.0
CA C:SER212 4.6 76.3 1.0
C C:SER212 4.7 81.6 1.0
N C:GLU218 4.7 68.9 1.0
CD2 C:LEU217 4.7 69.6 1.0
CG C:GLU221 4.8 74.5 1.0
C C:GLY215 4.9 69.5 1.0
C C:LEU217 4.9 72.4 1.0
C C:ASP210 4.9 74.8 1.0
CB C:ALA216 4.9 66.1 1.0
OE2 C:GLU218 5.0 92.2 1.0

Calcium binding site 4 out of 8 in 8bbj

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Calcium binding site 4 out of 8 in the Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:75.6
occ:1.00
OD1 C:ASN256 2.3 79.2 1.0
OE1 C:GLU265 2.4 76.9 1.0
O C:LYS260 2.4 75.3 1.0
OD2 C:ASP254 2.4 75.3 1.0
OD1 C:ASP258 2.5 79.7 1.0
OE1 C:GLN262 2.5 74.3 1.0
OE2 C:GLU265 2.6 78.1 1.0
CD C:GLU265 2.8 76.8 1.0
CG C:ASP258 3.2 80.0 1.0
CG C:ASN256 3.3 75.5 1.0
OD2 C:ASP258 3.4 85.7 1.0
CG C:ASP254 3.4 78.0 1.0
CD C:GLN262 3.5 75.4 1.0
C C:LYS260 3.6 77.1 1.0
ND2 C:ASN256 3.7 86.5 1.0
NE2 C:GLN262 3.9 75.8 1.0
OD1 C:ASP254 4.0 84.7 1.0
N C:GLN262 4.2 68.0 1.0
CA C:ASP254 4.3 75.4 1.0
CG C:GLU265 4.3 74.6 1.0
N C:ASP258 4.3 80.3 1.0
CB C:ASP254 4.4 72.2 1.0
N C:ASN256 4.4 86.8 1.0
CA C:ILE261 4.4 70.8 1.0
N C:LYS260 4.4 74.9 1.0
N C:ILE261 4.5 68.8 1.0
CB C:ASP258 4.5 81.4 1.0
N C:LYS257 4.5 81.1 1.0
CB C:ASN256 4.5 74.2 1.0
N C:VAL255 4.6 73.6 1.0
CA C:LYS260 4.6 77.3 1.0
C C:ASP254 4.7 75.7 1.0
CG C:GLN262 4.8 71.1 1.0
CA C:ASN256 4.8 79.9 1.0
C C:ILE261 4.9 67.9 1.0
CA C:ASP258 4.9 78.5 1.0
C C:ASN256 4.9 83.7 1.0
N C:GLY259 4.9 83.2 1.0
CB C:GLN262 4.9 70.2 1.0
CB C:GLU265 5.0 65.6 1.0

Calcium binding site 5 out of 8 in 8bbj

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Calcium binding site 5 out of 8 in the Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:61.9
occ:1.00
OD2 D:ASP120 2.3 62.8 1.0
O D:HOH405 2.3 56.6 1.0
OG D:SER122 2.5 59.1 1.0
OE2 D:GLU129 2.5 60.6 1.0
OE1 D:GLU129 2.6 65.8 1.0
OD1 D:ASP118 2.6 57.5 1.0
O D:PHE124 2.6 55.8 1.0
CD D:GLU129 2.9 61.7 1.0
CG D:ASP120 3.2 62.7 1.0
OD1 D:ASP120 3.5 62.6 1.0
CB D:SER122 3.6 54.2 1.0
C D:PHE124 3.7 56.7 1.0
CG D:ASP118 3.8 56.4 1.0
O D:HOH407 4.0 58.6 1.0
N D:SER122 4.1 62.7 1.0
CA D:ASP118 4.3 60.2 1.0
CG D:GLU129 4.4 57.3 1.0
CA D:SER122 4.4 58.5 1.0
N D:SER126 4.4 60.1 1.0
N D:PHE124 4.5 56.7 1.0
CA D:ILE125 4.5 60.6 1.0
N D:ILE125 4.5 57.6 1.0
N D:ASP120 4.5 66.6 1.0
CB D:ASP118 4.5 58.8 1.0
OG D:SER126 4.6 64.9 1.0
C D:ASP118 4.6 58.2 1.0
CB D:ASP120 4.6 63.2 1.0
N D:ALA119 4.6 61.7 1.0
CA D:PHE124 4.7 59.3 1.0
OD2 D:ASP118 4.7 54.1 1.0
N D:SER121 4.9 60.8 1.0
C D:ILE125 4.9 60.4 1.0
N D:GLY123 5.0 54.8 1.0
CA D:ASP120 5.0 57.0 1.0

Calcium binding site 6 out of 8 in 8bbj

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Calcium binding site 6 out of 8 in the Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:73.0
occ:1.00
OD1 D:ASP162 2.3 70.7 1.0
OD1 D:ASN164 2.4 80.1 1.0
OD2 D:ASP166 2.4 67.0 1.0
O D:ARG168 2.5 66.6 1.0
CG D:ASN164 3.5 75.2 1.0
CG D:ASP166 3.5 72.9 1.0
CG D:ASP162 3.5 71.3 1.0
C D:ARG168 3.6 59.1 1.0
OD2 D:ASP173 3.8 58.5 1.0
ND2 D:ASN164 4.1 70.2 1.0
OD1 D:ASP166 4.1 76.1 1.0
OD2 D:ASP162 4.2 71.5 1.0
N D:ARG168 4.2 73.3 1.0
N D:ASN164 4.3 71.7 1.0
N D:ASP166 4.3 75.8 1.0
N D:LYS163 4.4 69.2 1.0
CA D:ARG168 4.4 65.4 1.0
CA D:ASP162 4.4 67.3 1.0
CB D:ASP162 4.5 66.4 1.0
N D:LEU169 4.6 54.1 1.0
CB D:ASP166 4.6 73.1 1.0
C D:ASP162 4.6 66.8 1.0
N D:LYS165 4.6 78.1 1.0
CB D:ASN164 4.7 75.6 1.0
CA D:LEU169 4.7 56.5 1.0
CB D:ARG168 4.7 65.3 1.0
C D:ASN164 4.8 79.7 1.0
CA D:ASN164 4.8 67.4 1.0
N D:ASP170 4.8 57.5 1.0
CA D:ASP166 4.9 74.9 1.0
C D:LEU169 5.0 56.7 1.0
N D:GLY167 5.0 68.1 1.0

Calcium binding site 7 out of 8 in 8bbj

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Calcium binding site 7 out of 8 in the Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:84.1
occ:1.00
OD1 D:ASP210 2.3 69.7 1.0
O D:ALA216 2.4 66.5 1.0
OE2 D:GLU218 2.5 102.5 1.0
OG1 D:THR214 2.7 70.8 1.0
OE1 D:GLU221 3.0 71.9 1.0
CG D:ASP210 3.0 66.0 1.0
OG D:SER212 3.1 71.7 1.0
CD D:GLU218 3.3 88.8 1.0
OE1 D:GLU218 3.4 102.2 1.0
N D:THR214 3.5 74.0 1.0
OD2 D:ASP210 3.5 64.0 1.0
OE2 D:GLU221 3.6 75.5 1.0
C D:ALA216 3.6 62.3 1.0
CB D:THR214 3.6 75.1 1.0
CG2 D:THR214 3.6 71.9 1.0
CD D:GLU221 3.7 71.2 1.0
N D:ALA216 4.0 63.1 1.0
CA D:THR214 4.0 71.8 1.0
CB D:ASP210 4.0 65.0 1.0
N D:LYS213 4.1 71.8 1.0
N D:GLY215 4.1 71.8 1.0
CA D:ASP210 4.2 60.6 1.0
CB D:SER212 4.3 74.1 1.0
N D:SER212 4.4 67.5 1.0
C D:THR214 4.4 66.2 1.0
CA D:ALA216 4.4 62.6 1.0
C D:SER212 4.4 71.6 1.0
N D:LEU217 4.6 68.0 1.0
CA D:SER212 4.6 73.7 1.0
C D:LYS213 4.6 76.3 1.0
CA D:LEU217 4.7 61.9 1.0
C D:ASP210 4.7 61.6 1.0
CA D:LYS213 4.7 71.9 1.0
CG D:GLU218 4.7 82.8 1.0
N D:VAL211 4.9 60.4 1.0
N D:GLU218 4.9 69.9 1.0
C D:GLY215 4.9 57.4 1.0

Calcium binding site 8 out of 8 in 8bbj

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Calcium binding site 8 out of 8 in the Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Secretagogin (Mouse) in Complex with Its Target Peptide From Syntaxin- 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca304

b:51.7
occ:1.00
O D:LYS260 2.3 63.5 1.0
OD2 D:ASP254 2.3 59.7 1.0
OE1 D:GLN262 2.4 57.5 1.0
OE2 D:GLU265 2.4 71.1 1.0
OD1 D:ASN256 2.5 67.6 1.0
OD2 D:ASP258 2.5 70.4 1.0
OE1 D:GLU265 2.8 67.2 1.0
CD D:GLU265 2.9 67.0 1.0
CG D:ASP258 3.4 64.0 1.0
CG D:ASP254 3.4 60.9 1.0
CG D:ASN256 3.4 65.7 1.0
C D:LYS260 3.5 61.0 1.0
CD D:GLN262 3.5 55.9 1.0
OD1 D:ASP258 3.7 64.3 1.0
ND2 D:ASN256 3.9 67.3 1.0
NE2 D:GLN262 4.0 57.2 1.0
N D:GLN262 4.1 57.8 1.0
CA D:ASP254 4.2 62.9 1.0
OD1 D:ASP254 4.2 61.1 1.0
CG D:GLU265 4.3 60.5 1.0
CB D:ASP254 4.3 60.6 1.0
N D:LYS260 4.3 67.7 1.0
N D:ILE261 4.3 59.8 1.0
CA D:ILE261 4.3 60.5 1.0
CA D:LYS260 4.4 60.7 1.0
N D:VAL255 4.4 63.0 1.0
N D:ASP258 4.4 68.6 1.0
N D:ASN256 4.5 66.2 1.0
C D:ASP254 4.6 67.9 1.0
CB D:ASP258 4.6 63.7 1.0
N D:LYS257 4.6 67.0 1.0
CB D:ASN256 4.7 54.8 1.0
CG D:GLN262 4.7 47.9 1.0
C D:ILE261 4.8 62.4 1.0
CB D:GLN262 4.8 58.5 1.0
CB D:LYS260 4.8 59.9 1.0
N D:GLY259 4.9 61.3 1.0
CA D:ASN256 4.9 54.8 1.0
CA D:ASP258 5.0 62.1 1.0
C D:ASN256 5.0 64.6 1.0

Reference:

R.Schnell, E.Szodorai. Calcium Binding Protein in Complex with Its 2ND Peptide Ligand To Be Published.
Page generated: Fri Jul 19 07:17:13 2024

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