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Calcium in PDB 6ynu: Cam-P458 Complex (Crystal Form 1)

Protein crystallography data

The structure of Cam-P458 Complex (Crystal Form 1), PDB code: 6ynu was solved by A.E.Mechaly, A.Voegele, A.Haouz, A.Chenal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.60 / 3.12
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 73.341, 174.344, 97.843, 90, 90, 90
R / Rfree (%) 24.6 / 29.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Cam-P458 Complex (Crystal Form 1) (pdb code 6ynu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Cam-P458 Complex (Crystal Form 1), PDB code: 6ynu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6ynu

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Calcium binding site 1 out of 9 in the Cam-P458 Complex (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cam-P458 Complex (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:97.6
occ:1.00
OD1 A:ASP58 2.1 172.0 1.0
OD1 A:ASN60 2.2 136.4 1.0
OD1 A:ASP56 2.4 137.0 1.0
OE1 A:GLU67 2.4 114.5 1.0
OD2 A:ASP58 2.5 142.3 1.0
O A:THR62 2.5 114.6 1.0
CG A:ASP58 2.6 138.9 1.0
OE2 A:GLU67 2.7 111.5 1.0
CG A:ASN60 2.8 133.6 1.0
ND2 A:ASN60 2.9 150.7 1.0
CD A:GLU67 2.9 106.7 1.0
C A:THR62 3.5 114.1 1.0
CG A:ASP56 3.6 139.2 1.0
OD2 A:ASP64 3.7 112.1 1.0
CB A:ASP58 4.0 129.9 1.0
CB A:ASN60 4.1 120.6 1.0
N A:THR62 4.2 152.1 1.0
OG1 A:THR62 4.2 123.1 1.0
OD2 A:ASP56 4.3 152.1 1.0
N A:ASP64 4.3 107.2 1.0
N A:ASN60 4.3 135.4 1.0
CG A:GLU67 4.4 105.6 1.0
N A:ILE63 4.4 113.1 1.0
N A:ASP58 4.4 108.5 1.0
CG A:ASP64 4.4 109.9 1.0
CA A:THR62 4.4 130.6 1.0
CA A:ILE63 4.4 116.9 1.0
CA A:ASN60 4.6 130.8 1.0
CA A:ASP56 4.6 106.3 1.0
CA A:ASP58 4.7 121.7 1.0
CB A:ASP56 4.7 109.3 1.0
N A:GLY59 4.7 141.9 1.0
C A:ILE63 4.8 112.1 1.0
C A:ASN60 4.8 134.3 1.0
CB A:THR62 4.9 120.6 1.0
CB A:ASP64 5.0 109.6 1.0
C A:ASP56 5.0 122.7 1.0

Calcium binding site 2 out of 9 in 6ynu

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Calcium binding site 2 out of 9 in the Cam-P458 Complex (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cam-P458 Complex (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:130.8
occ:1.00
OE1 A:GLU140 2.2 150.1 1.0
OD1 A:ASP131 2.2 164.0 1.0
OD1 A:ASP133 2.3 143.4 1.0
O A:GLN135 2.5 119.7 1.0
OE2 A:GLU140 2.5 137.8 1.0
OD1 A:ASP129 2.5 121.1 1.0
OD2 A:ASP131 2.5 161.4 1.0
CD A:GLU140 2.7 127.4 1.0
CG A:ASP131 2.7 162.8 1.0
CG A:ASP133 3.1 140.2 1.0
OD2 A:ASP133 3.3 144.7 1.0
C A:GLN135 3.5 119.3 1.0
CG A:ASP129 3.7 141.1 1.0
N A:ASN137 3.8 104.2 1.0
CA A:VAL136 4.1 111.5 1.0
CG A:ASN137 4.1 106.4 1.0
CG A:GLU140 4.1 111.5 1.0
CB A:ASP131 4.2 145.9 1.0
ND2 A:ASN137 4.2 109.1 1.0
N A:VAL136 4.2 122.8 1.0
OD2 A:ASP129 4.3 121.8 1.0
CB A:ASN137 4.4 105.0 1.0
C A:VAL136 4.4 100.3 1.0
OD1 A:ASN137 4.4 105.5 1.0
CB A:ASP133 4.5 132.4 1.0
N A:ASP131 4.6 144.8 1.0
N A:ASP133 4.6 156.1 1.0
CA A:GLN135 4.6 108.6 1.0
N A:GLN135 4.7 133.7 1.0
CA A:ASN137 4.8 102.2 1.0
CD1 A:TYR99 4.8 143.2 1.0
CA A:ASP129 4.8 112.8 1.0
CB A:ASP129 4.8 131.2 1.0
CE1 A:TYR99 4.8 156.3 1.0
N A:GLY132 4.9 147.6 1.0
CA A:ASP131 4.9 155.8 1.0
N A:ILE130 4.9 138.8 1.0
CB A:GLN135 4.9 127.7 1.0
CB A:GLU140 5.0 111.7 1.0

Calcium binding site 3 out of 9 in 6ynu

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Calcium binding site 3 out of 9 in the Cam-P458 Complex (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cam-P458 Complex (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:139.9
occ:1.00
O A:TYR99 2.1 146.2 1.0
OE1 A:GLU104 2.2 133.3 1.0
OD1 A:ASP95 2.2 134.3 1.0
OD1 A:ASN97 2.3 114.4 1.0
OD1 A:ASP93 2.4 105.2 1.0
OE2 A:GLU104 2.6 125.3 1.0
CD A:GLU104 2.7 125.9 1.0
CG A:ASP95 2.9 125.9 1.0
OD2 A:ASP95 2.9 144.5 1.0
CG A:ASN97 3.1 117.1 1.0
C A:TYR99 3.3 103.7 1.0
ND2 A:ASN97 3.4 141.4 1.0
CG A:ASP93 3.7 103.8 1.0
CG A:GLU104 4.1 112.1 1.0
N A:SER101 4.1 111.8 1.0
N A:ILE100 4.2 100.4 1.0
CA A:ILE100 4.2 98.5 1.0
CB A:ASP95 4.3 118.4 1.0
N A:TYR99 4.3 139.2 1.0
CA A:TYR99 4.3 118.3 1.0
N A:ASP95 4.3 111.5 1.0
CB A:ASN97 4.4 119.0 1.0
CA A:ASP93 4.5 96.9 1.0
OD2 A:ASP93 4.5 107.1 1.0
C A:ILE100 4.6 106.8 1.0
CB A:ASP93 4.6 98.5 1.0
CB A:TYR99 4.6 113.2 1.0
C A:ASP93 4.6 107.9 1.0
OG A:SER101 4.7 118.0 1.0
N A:ASN97 4.7 127.2 1.0
CB A:SER101 4.7 109.8 1.0
CA A:ASP95 4.8 115.8 1.0
N A:LYS94 4.8 116.9 1.0
CB A:GLU104 4.9 101.0 1.0

Calcium binding site 4 out of 9 in 6ynu

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Calcium binding site 4 out of 9 in the Cam-P458 Complex (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cam-P458 Complex (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:133.5
occ:1.00
O A:THR26 2.3 131.3 1.0
OE1 A:GLU31 2.3 134.4 1.0
OD1 A:ASP24 2.4 133.6 1.0
OD1 A:ASP22 2.4 174.7 1.0
OD1 A:ASP20 2.4 126.5 1.0
OE2 A:GLU31 2.5 137.1 1.0
CD A:GLU31 2.7 136.4 1.0
OD2 A:ASP22 2.9 140.2 1.0
CG A:ASP22 3.0 139.7 1.0
CG A:ASP24 3.2 134.3 1.0
OD2 A:ASP24 3.3 146.4 1.0
C A:THR26 3.5 133.1 1.0
CG A:ASP20 3.6 124.4 1.0
CA A:ASP20 4.1 131.4 1.0
CG2 A:THR28 4.2 156.9 1.0
CG A:GLU31 4.2 148.1 1.0
CB A:ASP20 4.3 129.4 1.0
OG1 A:THR26 4.3 128.9 1.0
CA A:ILE27 4.4 124.8 1.0
N A:THR28 4.4 129.5 1.0
N A:ILE27 4.4 124.0 1.0
CB A:ASP22 4.4 136.9 1.0
N A:THR26 4.4 134.0 1.0
CB A:ASP24 4.5 134.5 1.0
CA A:THR26 4.5 135.7 1.0
C A:ASP20 4.6 127.3 1.0
N A:ASP24 4.6 131.3 1.0
OD2 A:ASP20 4.6 123.3 1.0
N A:ASP22 4.7 147.7 1.0
C A:ILE27 4.9 126.1 1.0
N A:GLY23 4.9 130.3 1.0
N A:LYS21 4.9 128.0 1.0

Calcium binding site 5 out of 9 in 6ynu

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Calcium binding site 5 out of 9 in the Cam-P458 Complex (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cam-P458 Complex (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:137.4
occ:1.00
OE2 A:GLU54 2.3 168.2 1.0
CD A:GLU54 3.3 153.1 1.0
CG A:GLU54 3.7 141.7 1.0
OD2 A:ASP50 3.9 178.4 1.0
OD1 A:ASP50 3.9 170.5 1.0
CG A:ASP50 4.3 172.8 1.0
OE1 A:GLU54 4.5 119.8 1.0

Calcium binding site 6 out of 9 in 6ynu

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Calcium binding site 6 out of 9 in the Cam-P458 Complex (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cam-P458 Complex (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:132.3
occ:1.00
O C:TYR99 2.0 194.8 1.0
OE1 C:GLU104 2.4 149.0 1.0
OD1 C:ASN97 2.4 149.2 1.0
OD1 C:ASP95 2.5 129.6 1.0
OD1 C:ASP93 2.5 151.7 1.0
OE2 C:GLU104 2.6 150.0 1.0
CD C:GLU104 2.8 153.1 1.0
OD2 C:ASP95 2.8 156.9 1.0
CG C:ASP95 3.0 150.6 1.0
C C:TYR99 3.2 159.8 1.0
CG C:ASN97 3.3 147.5 1.0
ND2 C:ASN97 3.7 152.9 1.0
CG C:ASP93 3.7 145.9 1.0
N C:ILE100 4.1 150.0 1.0
CA C:ILE100 4.1 151.8 1.0
N C:SER101 4.1 160.3 1.0
CA C:TYR99 4.2 157.3 1.0
N C:TYR99 4.2 146.9 1.0
CG C:GLU104 4.2 164.2 1.0
CB C:ASP95 4.4 144.9 1.0
N C:ASP95 4.5 142.4 1.0
CA C:ASP93 4.5 131.9 1.0
C C:ILE100 4.6 158.5 1.0
OD2 C:ASP93 4.6 130.0 1.0
CB C:ASN97 4.6 152.7 1.0
CB C:TYR99 4.6 163.4 1.0
CB C:ASP93 4.6 145.6 1.0
OG C:SER101 4.7 154.8 1.0
C C:ASP93 4.7 127.6 1.0
NE2 C:GLN135 4.8 159.8 1.0
N C:ASN97 4.8 140.4 1.0
N C:LYS94 4.8 135.3 1.0
CB C:SER101 4.9 163.6 1.0
CA C:ASP95 5.0 145.8 1.0

Calcium binding site 7 out of 9 in 6ynu

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Calcium binding site 7 out of 9 in the Cam-P458 Complex (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cam-P458 Complex (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:145.8
occ:1.00
OD1 C:ASP58 2.1 205.8 1.0
OD1 C:ASN60 2.2 173.3 1.0
O C:THR62 2.3 150.7 1.0
OD1 C:ASP56 2.3 200.6 1.0
OE1 C:GLU67 2.5 154.2 1.0
CG C:ASP58 2.9 178.6 1.0
OD2 C:ASP58 3.0 203.6 1.0
OE2 C:GLU67 3.2 170.4 1.0
CD C:GLU67 3.2 154.8 1.0
CG C:ASN60 3.4 162.1 1.0
C C:THR62 3.5 154.9 1.0
CG C:ASP56 3.6 193.9 1.0
N C:ASN60 3.9 165.6 1.0
O C:ASN60 4.1 147.6 1.0
OD2 C:ASP56 4.3 193.8 1.0
ND2 C:ASN60 4.3 148.8 1.0
OD2 C:ASP64 4.3 169.6 1.0
CB C:ASP58 4.3 150.9 1.0
N C:GLY59 4.3 166.2 1.0
N C:ILE63 4.3 155.4 1.0
CA C:ILE63 4.3 152.9 1.0
CA C:ASP56 4.4 158.4 1.0
N C:ASP58 4.4 167.4 1.0
N C:THR62 4.4 154.4 1.0
CB C:ASN60 4.4 144.3 1.0
C C:ASN60 4.5 168.7 1.0
CA C:ASN60 4.5 158.5 1.0
CA C:THR62 4.6 160.5 1.0
N C:ASP64 4.6 145.2 1.0
CB C:ASP56 4.6 170.7 1.0
CG C:GLU67 4.7 154.1 1.0
CA C:ASP58 4.7 157.4 1.0
C C:ASP56 4.8 159.1 1.0
C C:ASP58 4.8 164.3 1.0
C C:GLY59 4.9 179.3 1.0
C C:ILE63 4.9 148.2 1.0
OG1 C:THR62 4.9 191.6 1.0
CG C:ASP64 4.9 166.7 1.0
N C:ALA57 5.0 158.9 1.0

Calcium binding site 8 out of 9 in 6ynu

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Calcium binding site 8 out of 9 in the Cam-P458 Complex (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cam-P458 Complex (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:174.8
occ:1.00
OE2 C:GLU140 2.3 182.9 1.0
OD1 C:ASP131 2.3 178.5 1.0
OD1 C:ASP133 2.4 167.9 1.0
O C:GLN135 2.4 164.5 1.0
OD1 C:ASP129 2.5 184.3 1.0
CD C:GLU140 2.9 182.9 1.0
CG C:ASP131 2.9 175.7 1.0
OD2 C:ASP131 3.0 181.4 1.0
OE1 C:GLU140 3.1 187.6 1.0
CG C:ASP133 3.3 164.6 1.0
C C:GLN135 3.5 169.5 1.0
OD2 C:ASP133 3.6 164.3 1.0
CG C:ASP129 3.7 183.9 1.0
N C:ASN137 3.8 166.5 1.0
CA C:VAL136 4.0 162.7 1.0
N C:VAL136 4.2 168.8 1.0
CG C:GLU140 4.2 175.7 1.0
OD2 C:ASP129 4.4 177.4 1.0
C C:VAL136 4.4 158.7 1.0
CB C:ASP131 4.4 172.4 1.0
CG C:ASN137 4.4 165.9 1.0
N C:ASP131 4.5 176.5 1.0
CA C:GLN135 4.6 169.4 1.0
N C:ASP133 4.6 173.4 1.0
CB C:ASN137 4.6 169.1 1.0
CB C:ASP133 4.6 165.8 1.0
N C:GLN135 4.6 177.7 1.0
OD1 C:ASN137 4.6 156.6 1.0
ND2 C:ASN137 4.7 176.7 1.0
N C:GLY132 4.7 183.6 1.0
CA C:ASP129 4.8 177.7 1.0
N C:ILE130 4.8 186.5 1.0
CB C:ASP129 4.8 181.4 1.0
CA C:ASN137 4.8 166.3 1.0
CA C:ASP131 4.9 179.1 1.0
CB C:GLN135 4.9 169.3 1.0
CD1 C:TYR99 5.0 168.1 1.0

Calcium binding site 9 out of 9 in 6ynu

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Calcium binding site 9 out of 9 in the Cam-P458 Complex (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cam-P458 Complex (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:157.4
occ:1.00
O C:THR26 2.2 157.6 1.0
OE1 C:GLU31 2.4 171.7 1.0
OD1 C:ASP24 2.4 168.0 1.0
OD1 C:ASP22 2.4 171.0 1.0
OD1 C:ASP20 2.5 152.6 1.0
OE2 C:GLU31 3.0 173.9 1.0
CD C:GLU31 3.0 174.5 1.0
CG C:ASP24 3.1 171.5 1.0
CG C:ASP22 3.2 175.8 1.0
OD2 C:ASP22 3.2 162.8 1.0
OD2 C:ASP24 3.3 174.8 1.0
C C:THR26 3.5 154.8 1.0
CG C:ASP20 3.7 154.9 1.0
CG2 C:THR28 3.8 167.8 1.0
OG1 C:THR26 4.1 164.4 1.0
CA C:ASP20 4.3 158.0 1.0
N C:THR28 4.3 166.2 1.0
N C:THR26 4.3 164.5 1.0
CB C:ASP20 4.4 154.1 1.0
N C:ILE27 4.4 159.0 1.0
CA C:THR26 4.4 161.2 1.0
CA C:ILE27 4.5 170.2 1.0
CG C:GLU31 4.5 181.4 1.0
CB C:ASP24 4.5 162.4 1.0
CB C:ASP22 4.6 176.6 1.0
N C:ASP24 4.7 181.1 1.0
OD2 C:ASP20 4.7 147.4 1.0
C C:ASP20 4.7 163.5 1.0
N C:ASP22 4.8 176.6 1.0
C C:ILE27 4.9 165.3 1.0
CB C:THR26 4.9 159.9 1.0
N C:GLY23 5.0 153.6 1.0

Reference:

A.Voegele, M.Sadi, D.P.O'brien, P.Gehan, D.Raoux‐Barbot, M.Davi, S.Hoos, S.Brule, B.Raynal, P.Weber, A.E.Mechaly, A.Haouz, N.Rodriguez, P.Vachette, D.Durand, S.Brier, D.Ladant, A.Chenal. A High-Affinity Calmodulin-Binding Site in the Cyaa Toxin Translocation Domain Is Essential For Invasion of Eukaryotic Cells Adv Sci 2021.
ISSN: ESSN 2198-3844
DOI: 10.1002/ADVS.202003630
Page generated: Thu Jul 18 22:25:51 2024

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