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Calcium in PDB 8bav: Secretagogin (Human) in Complex with Its Target Peptide From Snap-25

Protein crystallography data

The structure of Secretagogin (Human) in Complex with Its Target Peptide From Snap-25, PDB code: 8bav 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) 41.36 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.544, 120.439, 124.066, 90, 90, 90
R / Rfree (%) 18.8 / 26.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Secretagogin (Human) in Complex with Its Target Peptide From Snap-25 (pdb code 8bav). 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 (Human) in Complex with Its Target Peptide From Snap-25, PDB code: 8bav:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8bav

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Calcium binding site 1 out of 8 in the Secretagogin (Human) in Complex with Its Target Peptide From Snap-25


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Secretagogin (Human) in Complex with Its Target Peptide From Snap-25 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:35.5
occ:1.00
OD1 C:ASP118 2.3 35.2 1.0
OD1 C:ASP120 2.3 34.4 1.0
OG C:SER122 2.4 32.9 1.0
O C:PHE124 2.5 31.0 1.0
OE2 C:GLU129 2.6 33.3 1.0
OE1 C:GLU129 2.6 29.7 1.0
CD C:GLU129 2.9 32.8 1.0
CG C:ASP120 3.2 37.2 1.0
OD2 C:ASP120 3.3 36.6 1.0
CB C:SER122 3.4 33.6 1.0
CG C:ASP118 3.5 35.4 1.0
C C:PHE124 3.7 32.6 1.0
N C:SER122 3.8 32.3 1.0
CA C:ASP118 4.0 34.1 1.0
CB C:ASP118 4.2 33.8 1.0
CA C:SER122 4.2 32.2 1.0
C C:ASP118 4.3 35.7 1.0
N C:PHE124 4.4 35.2 1.0
OD2 C:ASP118 4.4 36.5 1.0
CG C:GLU129 4.5 33.4 1.0
CA C:ILE125 4.5 31.3 1.0
N C:SER126 4.5 29.9 1.0
N C:ALA119 4.5 34.2 1.0
N C:ILE125 4.5 30.9 1.0
CB C:ASP120 4.6 35.9 1.0
N C:SER121 4.6 36.1 1.0
N C:ASP120 4.7 37.3 1.0
CA C:PHE124 4.7 35.8 1.0
N C:GLY123 4.8 29.7 1.0
CD1 C:PHE124 4.8 48.0 1.0
C C:SER122 4.8 30.1 1.0
O C:ASP118 4.8 38.4 1.0
CE1 C:PHE124 4.9 47.7 1.0
C C:ASP120 4.9 37.5 1.0
CG C:PHE124 4.9 44.5 1.0
C C:SER121 5.0 33.0 1.0
CA C:ASP120 5.0 35.3 1.0
C C:ILE125 5.0 29.5 1.0

Calcium binding site 2 out of 8 in 8bav

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Calcium binding site 2 out of 8 in the Secretagogin (Human) in Complex with Its Target Peptide From Snap-25


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Secretagogin (Human) in Complex with Its Target Peptide From Snap-25 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:45.8
occ:1.00
O C:HOH431 2.2 45.7 1.0
OD1 C:ASP162 2.2 36.1 1.0
O C:ARG168 2.3 30.4 1.0
OD1 C:ASN164 2.3 37.6 1.0
OD1 C:ASP166 2.4 41.5 1.0
CG C:ASP166 3.1 43.9 1.0
CG C:ASN164 3.3 43.7 1.0
OD2 C:ASP166 3.3 44.0 1.0
CG C:ASP162 3.3 35.5 1.0
C C:ARG168 3.4 35.1 1.0
ND2 C:ASN164 3.6 46.2 1.0
N C:ARG168 3.9 40.4 1.0
CA C:ARG168 4.0 39.8 1.0
OD2 C:ASP162 4.0 35.5 1.0
CB C:ARG168 4.1 45.8 1.0
N C:ASP166 4.2 42.2 1.0
OD2 C:ASP173 4.2 37.1 1.0
CA C:ASP162 4.3 37.3 1.0
CB C:ASP162 4.3 34.7 1.0
CB C:ASP166 4.5 45.5 1.0
N C:LEU169 4.5 30.9 1.0
C C:ASP162 4.6 39.4 1.0
N C:LYS165 4.6 43.8 1.0
N C:ASN164 4.6 42.0 1.0
CB C:ASN164 4.7 46.7 1.0
N C:ARG163 4.7 42.4 1.0
OD2 C:ASP170 4.7 65.1 1.0
CA C:ASP166 4.8 43.8 1.0
N C:GLY167 4.8 39.3 1.0
CA C:LEU169 4.8 31.1 1.0
C C:ASN164 4.9 44.0 1.0
CA C:ASN164 4.9 44.8 1.0
C C:ASP166 5.0 40.5 1.0

Calcium binding site 3 out of 8 in 8bav

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Calcium binding site 3 out of 8 in the Secretagogin (Human) in Complex with Its Target Peptide From Snap-25


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Secretagogin (Human) in Complex with Its Target Peptide From Snap-25 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:54.9
occ:1.00
OD2 C:ASP210 2.3 34.9 1.0
O C:ALA216 2.3 39.1 1.0
OE1 C:GLU221 2.4 36.9 1.0
OG C:SER212 2.5 37.8 1.0
OG1 C:THR214 2.6 37.7 1.0
OE2 C:GLU218 2.8 51.8 1.0
CD C:GLU221 3.2 37.6 1.0
CG C:ASP210 3.4 36.0 1.0
OE2 C:GLU221 3.4 40.3 1.0
C C:ALA216 3.5 35.0 1.0
CB C:THR214 3.7 37.4 1.0
N C:THR214 3.8 37.4 1.0
CD C:GLU218 3.8 47.3 1.0
CB C:SER212 3.9 36.8 1.0
CG2 C:THR214 3.9 36.2 1.0
N C:LYS213 4.2 41.0 1.0
N C:ALA216 4.2 32.6 1.0
CA C:ASP210 4.2 34.6 1.0
OD1 C:ASP210 4.2 34.6 1.0
CB C:ASP210 4.3 35.3 1.0
OE1 C:GLU218 4.3 41.4 1.0
CA C:THR214 4.3 37.3 1.0
N C:SER212 4.3 41.2 1.0
CA C:LEU217 4.4 33.2 1.0
N C:GLU218 4.4 35.3 1.0
N C:LEU217 4.4 32.8 1.0
CA C:SER212 4.4 38.1 1.0
C C:SER212 4.4 39.7 1.0
CA C:ALA216 4.5 34.2 1.0
C C:ASP210 4.5 34.0 1.0
CG C:GLU221 4.7 34.8 1.0
N C:GLY215 4.7 33.6 1.0
C C:THR214 4.7 35.2 1.0
C C:LEU217 4.8 33.7 1.0
N C:VAL211 4.8 34.8 1.0
C C:LYS213 4.8 39.9 1.0
CG C:GLU218 4.9 40.3 1.0
CA C:LYS213 4.9 42.4 1.0

Calcium binding site 4 out of 8 in 8bav

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Calcium binding site 4 out of 8 in the Secretagogin (Human) in Complex with Its Target Peptide From Snap-25


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Secretagogin (Human) in Complex with Its Target Peptide From Snap-25 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:31.1
occ:1.00
OD2 C:ASP254 2.3 30.4 1.0
O C:LYS260 2.3 27.9 1.0
OE1 C:GLN262 2.3 30.1 1.0
OD1 C:ASN256 2.4 37.0 1.0
OE1 C:GLU265 2.4 30.3 1.0
OD1 C:ASP258 2.5 29.7 1.0
OE2 C:GLU265 2.6 29.5 1.0
CD C:GLU265 2.9 29.1 1.0
CG C:ASP258 3.2 32.9 1.0
CG C:ASN256 3.3 36.5 1.0
CG C:ASP254 3.4 29.0 1.0
OD2 C:ASP258 3.5 32.8 1.0
C C:LYS260 3.5 28.9 1.0
CD C:GLN262 3.5 31.0 1.0
ND2 C:ASN256 3.8 37.3 1.0
NE2 C:GLN262 4.0 33.5 1.0
N C:LYS260 4.1 36.5 1.0
N C:GLN262 4.2 28.7 1.0
N C:ASN256 4.2 31.5 1.0
N C:ASP258 4.2 39.5 1.0
OD1 C:ASP254 4.2 30.0 1.0
CA C:ASP254 4.2 29.1 1.0
CG C:GLU265 4.3 28.4 1.0
CA C:LYS260 4.3 33.1 1.0
CB C:ASP254 4.4 28.4 1.0
N C:ILE261 4.4 27.7 1.0
CB C:ASP258 4.4 32.4 1.0
C C:ASP254 4.4 29.3 1.0
N C:LYS257 4.5 39.7 1.0
CA C:ILE261 4.5 27.6 1.0
CB C:ASN256 4.5 34.5 1.0
N C:VAL255 4.5 30.8 1.0
CA C:ASN256 4.6 32.7 1.0
C C:ASN256 4.7 36.4 1.0
CB C:LYS260 4.7 35.6 1.0
CA C:ASP258 4.7 36.8 1.0
N C:GLY259 4.7 35.0 1.0
CG C:GLN262 4.8 28.5 1.0
O C:HOH442 4.8 24.8 1.0
C C:ILE261 4.8 29.1 1.0
CB C:GLN262 4.9 29.0 1.0
O C:ASP254 4.9 26.8 1.0
C C:ASP258 4.9 35.1 1.0

Calcium binding site 5 out of 8 in 8bav

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Calcium binding site 5 out of 8 in the Secretagogin (Human) in Complex with Its Target Peptide From Snap-25


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Secretagogin (Human) in Complex with Its Target Peptide From Snap-25 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:32.4
occ:1.00
OD1 D:ASP118 2.3 36.4 1.0
OD1 D:ASP120 2.3 37.4 1.0
O D:HOH440 2.3 42.4 1.0
O D:PHE124 2.3 28.3 1.0
OG D:SER122 2.5 30.6 1.0
OE2 D:GLU129 2.5 33.1 1.0
OE1 D:GLU129 2.7 30.0 1.0
CD D:GLU129 3.0 31.7 1.0
CG D:ASP120 3.2 39.8 1.0
OD2 D:ASP120 3.4 37.6 1.0
CG D:ASP118 3.5 35.3 1.0
CB D:SER122 3.5 32.4 1.0
C D:PHE124 3.6 32.3 1.0
N D:SER122 3.9 30.9 1.0
O D:HOH452 4.0 19.9 1.0
CA D:ASP118 4.2 34.9 1.0
CA D:SER122 4.3 31.3 1.0
N D:PHE124 4.3 34.0 1.0
CB D:ASP118 4.3 33.8 1.0
OD2 D:ASP118 4.3 37.1 1.0
N D:SER126 4.4 29.2 1.0
CG D:GLU129 4.5 32.7 1.0
N D:ILE125 4.5 34.7 1.0
CA D:ILE125 4.5 32.1 1.0
CA D:PHE124 4.5 32.4 1.0
C D:ASP118 4.5 38.1 1.0
CB D:ASP120 4.6 35.5 1.0
N D:ASP120 4.6 37.5 1.0
N D:GLY123 4.7 32.8 1.0
N D:SER121 4.7 38.9 1.0
OG D:SER126 4.8 39.1 1.0
C D:SER122 4.8 31.0 1.0
N D:ALA119 4.8 40.5 1.0
O D:HOH431 4.9 38.8 1.0
C D:ASP120 4.9 38.0 1.0
CA D:ASP120 4.9 34.6 1.0
C D:ILE125 4.9 30.0 1.0

Calcium binding site 6 out of 8 in 8bav

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Calcium binding site 6 out of 8 in the Secretagogin (Human) in Complex with Its Target Peptide From Snap-25


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Secretagogin (Human) in Complex with Its Target Peptide From Snap-25 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:43.2
occ:1.00
O D:ARG168 2.3 30.6 1.0
OD1 D:ASP162 2.4 37.6 1.0
OD1 D:ASP166 2.4 53.9 1.0
O D:HOH404 2.7 38.7 1.0
OD1 D:ASN164 2.8 76.4 1.0
CG D:ASP166 3.4 51.1 1.0
O D:ASN164 3.5 80.5 1.0
CG D:ASN164 3.5 65.0 1.0
C D:ARG168 3.5 34.5 1.0
CG D:ASP162 3.6 39.0 1.0
ND2 D:ASN164 3.6 64.4 1.0
OD2 D:ASP166 3.9 54.6 1.0
OD2 D:ASP173 4.1 31.6 1.0
N D:ARG168 4.2 33.3 1.0
OD2 D:ASP162 4.2 40.9 1.0
CA D:ARG168 4.4 35.7 1.0
N D:LEU169 4.4 31.9 1.0
N D:ASP166 4.4 44.7 1.0
CA D:ASP162 4.5 43.7 1.0
CA D:LEU169 4.5 33.1 1.0
CB D:ASP166 4.5 42.2 1.0
N D:ARG163 4.6 57.4 1.0
CG D:ARG168 4.6 43.1 1.0
N D:ASN164 4.6 73.3 1.0
C D:ASN164 4.6 71.9 1.0
CB D:ASP162 4.6 44.4 1.0
C D:ASP162 4.7 47.2 1.0
N D:ASP170 4.7 34.1 1.0
CB D:ASN164 4.8 65.5 1.0
CA D:ASP166 4.9 41.0 1.0
N D:GLY167 4.9 35.1 1.0
C D:LEU169 4.9 32.2 1.0

Calcium binding site 7 out of 8 in 8bav

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Calcium binding site 7 out of 8 in the Secretagogin (Human) in Complex with Its Target Peptide From Snap-25


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Secretagogin (Human) in Complex with Its Target Peptide From Snap-25 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:52.5
occ:1.00
OE1 D:GLU221 2.3 32.9 1.0
O D:ALA216 2.3 28.1 1.0
OD1 D:ASP210 2.4 34.3 1.0
OG1 D:THR214 2.6 32.2 1.0
OG D:SER212 2.6 39.8 1.0
CD D:GLU221 3.1 33.0 1.0
OE2 D:GLU221 3.2 37.1 1.0
OE1 D:GLU218 3.3 43.4 1.0
CG D:ASP210 3.5 33.9 1.0
C D:ALA216 3.5 29.7 1.0
CB D:THR214 3.7 34.5 1.0
CG2 D:THR214 3.9 36.1 1.0
N D:THR214 3.9 36.4 1.0
CB D:SER212 4.0 37.5 1.0
CD D:GLU218 4.0 47.0 1.0
OD2 D:ASP210 4.2 36.0 1.0
CA D:ASP210 4.3 32.4 1.0
N D:GLU218 4.3 34.5 1.0
CA D:LEU217 4.3 31.9 1.0
N D:SER212 4.3 37.9 1.0
CA D:THR214 4.3 34.7 1.0
N D:LEU217 4.3 31.9 1.0
N D:ALA216 4.4 32.6 1.0
N D:LYS213 4.4 39.2 1.0
CB D:ASP210 4.4 33.3 1.0
CA D:SER212 4.5 38.8 1.0
CG D:GLU218 4.5 44.1 1.0
C D:SER212 4.5 38.0 1.0
CG D:GLU221 4.5 30.4 1.0
CA D:ALA216 4.6 30.0 1.0
C D:ASP210 4.6 35.0 1.0
C D:LEU217 4.7 33.3 1.0
CB D:GLU218 4.8 39.0 1.0
OE2 D:GLU218 4.8 59.5 1.0
N D:GLY215 4.8 31.0 1.0
C D:THR214 4.9 33.5 1.0
N D:VAL211 4.9 35.9 1.0

Calcium binding site 8 out of 8 in 8bav

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Calcium binding site 8 out of 8 in the Secretagogin (Human) in Complex with Its Target Peptide From Snap-25


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Secretagogin (Human) in Complex with Its Target Peptide From Snap-25 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca304

b:30.3
occ:1.00
OE1 D:GLN262 2.2 29.7 1.0
OD2 D:ASP254 2.2 24.0 1.0
OD1 D:ASN256 2.3 29.1 1.0
O D:LYS260 2.4 27.5 1.0
OD1 D:ASP258 2.5 30.6 1.0
OE2 D:GLU265 2.5 31.9 1.0
OE1 D:GLU265 2.6 32.2 1.0
CD D:GLU265 2.9 33.5 1.0
CG D:ASP258 3.3 33.4 1.0
CD D:GLN262 3.3 31.1 1.0
CG D:ASN256 3.4 30.5 1.0
CG D:ASP254 3.4 27.5 1.0
C D:LYS260 3.5 29.1 1.0
OD2 D:ASP258 3.6 29.2 1.0
NE2 D:GLN262 3.9 33.3 1.0
ND2 D:ASN256 3.9 31.6 1.0
N D:GLN262 4.1 29.6 1.0
OD1 D:ASP254 4.1 30.5 1.0
N D:LYS260 4.2 29.8 1.0
N D:ASP258 4.3 36.4 1.0
CA D:LYS260 4.3 30.3 1.0
N D:ILE261 4.3 27.7 1.0
CA D:ASP254 4.4 29.3 1.0
CA D:ILE261 4.4 27.6 1.0
N D:ASN256 4.4 34.7 1.0
CG D:GLU265 4.4 33.1 1.0
CB D:ASP254 4.4 28.5 1.0
N D:LYS257 4.5 38.7 1.0
CB D:ASP258 4.5 32.1 1.0
C D:ASP254 4.6 30.1 1.0
CB D:ASN256 4.6 30.6 1.0
CB D:LYS260 4.6 31.9 1.0
CG D:GLN262 4.6 30.2 1.0
N D:VAL255 4.6 31.6 1.0
C D:ILE261 4.7 28.7 1.0
CA D:ASN256 4.8 33.7 1.0
O D:HOH461 4.8 29.2 1.0
CB D:GLN262 4.8 31.4 1.0
CA D:ASP258 4.8 34.4 1.0
C D:ASN256 4.8 35.7 1.0
N D:GLY259 4.9 35.4 1.0

Reference:

R.Schnell, E.Szodorai. Calmodulin Type Regulator (Homo Sapiens) with Peptide Ligand To Be Published.
Page generated: Fri Jul 19 07:15:39 2024

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