Calcium in PDB 8t2u: Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide

Other elements in 8t2u:

The structure of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide (pdb code 8t2u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide, PDB code: 8t2u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8t2u

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Calcium binding site 1 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1102

b:234.8
occ:1.00
 O A:ASP247 2.3 229.4 1.0
OD1 A:ASP245 2.3 265.5 1.0
OE2 A:GLU252 2.3 205.5 1.0
O A:THR250 2.4 233.0 1.0
OG1 A:THR250 2.4 193.4 1.0
OE1 A:GLU252 2.4 192.3 1.0
CD A:GLU252 2.6 193.8 1.0
OD2 A:ASP245 2.9 238.3 1.0
CG A:ASP245 3.0 240.8 1.0
C A:THR250 3.0 212.3 1.0
CB A:THR250 3.4 181.4 1.0
C A:ASP247 3.4 231.6 1.0
CA A:THR250 3.5 200.9 1.0
N A:THR250 3.7 202.2 1.0
CB A:ASP247 3.7 251.0 1.0
CA A:ASP247 3.9 243.2 1.0
N A:THR251 4.0 196.1 1.0
CG A:GLU252 4.0 183.3 1.0
N A:ASP247 4.1 238.3 1.0
CB A:ASP245 4.4 201.7 1.0
CA A:THR251 4.5 168.0 1.0
N A:LEU248 4.6 220.8 1.0
C A:THR251 4.6 150.2 1.0
CG2 A:THR250 4.7 184.1 1.0
N A:GLU252 4.7 147.0 1.0
CG A:GLU243 4.9 188.5 1.0
CA A:LEU248 5.0 228.0 1.0
N A:ASP245 5.0 214.6 1.0
C A:ASN249 5.0 232.0 1.0

Calcium binding site 2 out of 6 in 8t2u

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Calcium binding site 2 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1103

b:218.2
occ:1.00
 O A:TYR371 2.3 185.5 1.0
OD1 A:ASP365 2.4 198.1 1.0
OD1 A:ASP367 2.4 291.2 1.0
OD2 A:ASP373 2.4 194.3 1.0
OD1 A:ASP373 2.4 156.4 1.0
OD1 A:ASP369 2.6 263.7 1.0
CG A:ASP373 2.8 158.1 1.0
C A:TYR371 3.2 180.8 1.0
CG A:ASP365 3.4 198.6 1.0
CG A:ASP367 3.4 315.6 1.0
CB A:TYR371 3.5 246.8 1.0
CA A:TYR371 3.6 215.9 1.0
N A:TYR371 3.6 223.0 1.0
OD2 A:ASP367 3.7 320.2 1.0
CG A:ASP369 3.8 277.6 1.0
CD1 A:TYR371 3.9 276.8 1.0
OD2 A:ASP365 4.0 219.4 1.0
CG A:TYR371 4.1 270.9 1.0
N A:LEU366 4.2 236.8 1.0
N A:ASP367 4.3 303.3 1.0
CB A:ASP373 4.3 144.6 1.0
CB A:ASP365 4.4 190.0 1.0
OD2 A:ASP369 4.5 265.8 1.0
N A:ASN372 4.5 148.3 1.0
CA A:ASP365 4.5 177.5 1.0
N A:GLY370 4.6 273.4 1.0
C A:GLY370 4.7 236.7 1.0
CB A:ASP367 4.7 312.9 1.0
C A:ASP365 4.8 205.8 1.0
N A:ASP373 4.8 132.2 1.0
C A:ASN372 4.8 149.6 1.0
CD1 A:LEU393 4.9 204.6 1.0
CB A:ASP369 4.9 288.0 1.0
CA A:ASP367 5.0 312.1 1.0

Calcium binding site 3 out of 6 in 8t2u

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Calcium binding site 3 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1104

b:143.3
occ:1.00
 OD1 A:ASN430 2.3 166.3 1.0
O A:TYR432 2.3 150.4 1.0
OD1 A:ASP434 2.4 101.5 1.0
OD1 A:ASP426 2.4 170.2 1.0
OD2 A:ASP434 2.4 108.8 1.0
OD1 A:ASP428 2.4 187.7 1.0
CG A:ASP434 2.7 88.6 1.0
CG A:ASN430 2.8 205.5 1.0
CG A:ASP426 2.9 181.5 1.0
ND2 A:ASN430 2.9 209.5 1.0
OD2 A:ASP426 3.2 190.2 1.0
C A:TYR432 3.4 133.9 1.0
CG A:ASP428 3.6 211.5 1.0
CB A:ASP426 3.9 163.0 1.0
CA A:ASP426 3.9 139.3 1.0
N A:ILE427 4.0 136.2 1.0
N A:TYR432 4.1 185.6 1.0
OD2 A:ASP428 4.1 207.9 1.0
CB A:ASP434 4.1 86.9 1.0
CA A:TYR432 4.2 165.0 1.0
N A:ASN430 4.2 240.2 1.0
CB A:ASN430 4.2 217.3 1.0
N A:ASP428 4.3 167.8 1.0
C A:PRO433 4.3 115.0 1.0
N A:ASP434 4.4 104.7 1.0
C A:ASP426 4.4 147.7 1.0
CB A:TYR432 4.4 181.7 1.0
N A:PRO433 4.5 119.3 1.0
O A:PRO433 4.5 134.6 1.0
N A:ASP429 4.6 236.6 1.0
CA A:PRO433 4.6 114.9 1.0
CA A:ASP434 4.7 92.4 1.0
CA A:ASN430 4.7 229.2 1.0
CB A:ASP428 4.8 217.6 1.0
N A:GLY431 4.9 235.6 1.0
CA A:ASP428 4.9 208.1 1.0

Calcium binding site 4 out of 6 in 8t2u

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Calcium binding site 4 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1105

b:165.6
occ:1.00
 O A:ARG303 1.8 164.9 1.0
OD1 A:ASN299 1.9 159.8 1.0
OD1 A:ASP305 2.2 116.8 1.0
OD1 A:ASP301 2.4 147.0 1.0
OD1 A:ASP297 2.5 178.7 1.0
CG A:ASN299 2.7 176.9 1.0
CG A:ASP305 2.9 119.7 1.0
OD2 A:ASP305 2.9 120.9 1.0
C A:ARG303 3.0 147.5 1.0
ND2 A:ASN299 3.0 190.2 1.0
CG A:ASP301 3.2 166.1 1.0
CG A:ASP297 3.3 189.1 1.0
OD2 A:ASP301 3.4 179.2 1.0
CB A:ARG303 3.6 198.8 1.0
CA A:ARG303 3.6 170.4 1.0
OD2 A:ASP297 3.6 187.2 1.0
N A:ARG303 3.7 175.9 1.0
N A:HIS304 4.1 154.3 1.0
CB A:ASN299 4.1 167.3 1.0
C A:HIS304 4.1 142.2 1.0
O A:HIS304 4.3 142.3 1.0
N A:ASP305 4.3 140.4 1.0
CB A:ASP305 4.3 109.8 1.0
CB A:GLN333 4.4 184.3 1.0
O A:GLN333 4.4 179.4 1.0
CB A:ASP297 4.5 173.0 1.0
CA A:HIS304 4.5 159.9 1.0
NH2 A:ARG303 4.5 232.3 1.0
N A:ASP301 4.5 179.2 1.0
CA A:ASP297 4.5 150.3 1.0
CZ A:ARG303 4.5 237.7 1.0
CB A:ASP301 4.6 180.7 1.0
N A:GLN333 4.6 158.5 1.0
NE A:ARG303 4.7 231.3 1.0
CG A:ARG303 4.8 224.8 1.0
CA A:ASP305 4.8 112.9 1.0
N A:GLY300 4.8 159.6 1.0
N A:GLY302 4.9 201.7 1.0
NH1 A:ARG303 4.9 240.1 1.0
C A:GLY302 4.9 199.8 1.0
CA A:GLN333 5.0 177.7 1.0
CA A:ASP301 5.0 184.8 1.0
CD2 A:LEU332 5.0 107.3 1.0
N A:ASN299 5.0 149.7 1.0

Calcium binding site 5 out of 6 in 8t2u

Go back to Calcium Binding Sites List in 8t2u
Calcium binding site 5 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2002

b:105.6
occ:1.00
 O B:PRO219 2.2 100.5 1.0
OD1 B:ASN215 2.3 103.4 1.0
O B:ASP217 2.4 74.4 1.0
OD2 B:ASP158 2.4 88.0 1.0
OD1 B:ASP217 2.4 80.0 1.0
OE1 B:GLU220 2.4 104.7 1.0
CG B:ASN215 2.8 67.7 1.0
ND2 B:ASN215 2.9 75.0 1.0
CD B:GLU220 3.2 80.8 1.0
C B:ASP217 3.4 71.6 1.0
C B:PRO219 3.4 68.0 1.0
CG B:ASP217 3.4 68.2 1.0
CG B:ASP158 3.6 93.4 1.0
NE2 B:HIS255 3.6 74.3 1.0
OE2 B:GLU220 3.8 95.1 1.0
CD2 B:HIS255 3.9 86.8 1.0
N B:ASP217 4.0 70.3 1.0
CA B:ASP217 4.1 67.9 1.0
CB B:ASN215 4.1 57.7 1.0
CA B:GLU220 4.1 64.6 1.0
CB B:ASP158 4.2 79.1 1.0
N B:GLU220 4.2 63.3 1.0
O B:ALA218 4.2 65.3 1.0
C B:ALA218 4.2 72.5 1.0
OD2 B:ASP217 4.2 79.9 1.0
CG B:GLU220 4.2 71.5 1.0
CB B:ASP217 4.3 70.9 1.0
N B:PRO219 4.3 48.6 1.0
N B:ALA218 4.3 70.5 1.0
CA B:PRO219 4.5 57.3 1.0
OD1 B:ASP158 4.6 53.6 1.0
CB B:GLU220 4.7 68.6 1.0
CA B:ALA218 4.7 80.9 1.0
CE1 B:HIS255 4.8 92.2 1.0
CD B:PRO219 4.9 46.1 1.0
N B:ARG216 4.9 68.2 1.0
C B:ARG216 4.9 83.0 1.0

Calcium binding site 6 out of 6 in 8t2u

Go back to Calcium Binding Sites List in 8t2u
Calcium binding site 6 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Eptifibatide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:158.6
occ:1.00
 OD2 B:ASP251 2.4 152.5 1.0
O B:SER123 2.4 93.8 1.0
OD1 B:ASP126 2.4 192.6 1.0
OD2 B:ASP127 2.4 223.2 1.0
CG B:ASP126 2.6 207.3 1.0
CG B:ASP251 2.7 127.4 1.0
CB B:ASP126 2.9 177.7 1.0
OD1 B:ASP251 3.0 96.3 1.0
C B:SER123 3.5 76.7 1.0
OD2 B:ASP126 3.5 239.6 1.0
N B:ASP126 3.5 141.5 1.0
CG B:ASP127 3.5 226.2 1.0
CA B:ASP126 3.6 157.3 1.0
CB B:ASP251 3.6 126.8 1.0
N B:ASP127 3.7 173.5 1.0
O B:MET124 3.8 101.5 1.0
C B:MET124 3.9 84.4 1.0
CA B:MET124 4.0 87.1 1.0
C B:ASP126 4.1 169.0 1.0
N B:MET124 4.2 77.0 1.0
CB B:ASP127 4.4 202.7 1.0
OD1 B:ASP127 4.4 227.6 1.0
N B:LYS125 4.4 76.8 1.0
CA B:SER123 4.5 72.1 1.0
C B:LYS125 4.5 128.5 1.0
OG B:SER123 4.6 54.7 1.0
CA B:ASP127 4.7 187.3 1.0
CB B:SER123 4.8 53.6 1.0
CE B:MET124 4.9 123.9 1.0

Reference:

B.D.Adair, J.P.Xiong, M.Yeager, M.A.Arnaout. Cryo-Em Structures of Full-Length Integrin Alpha Iib Beta 3 in Native Lipids. Nat Commun V. 14 4168 2023.
ISSN: ESSN 2041-1723
PubMed: 37443315
DOI: 10.1038/S41467-023-39763-0
Page generated: Fri Jul 19 11:59:32 2024

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