Calcium in PDB 6om2: Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide

Protein crystallography data

The structure of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide, PDB code: 6om2 was solved by J.C.Wang, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.43 / 2.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 161.190, 53.850, 176.620, 90.00, 111.47, 90.00
R / Rfree (%) 25.1 / 28.2

Other elements in 6om2:

The structure of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide (pdb code 6om2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide, PDB code: 6om2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 6om2

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Calcium binding site 1 out of 10 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:69.9
occ:1.00
OD1 A:ASP234 2.3 77.9 1.0
OD1 A:ASN232 2.3 71.8 1.0
OD1 A:ASP238 2.4 74.3 1.0
OD2 A:ASP238 2.4 74.2 1.0
O A:ILE236 2.4 69.4 1.0
OD1 A:ASP230 2.4 84.6 1.0
OD2 A:ASP234 2.5 77.9 1.0
CG A:ASP238 2.7 72.5 1.0
CG A:ASP234 2.7 80.0 1.0
HD21 A:ASN232 2.8 86.0 1.0
CG A:ASN232 3.1 71.7 1.0
ND2 A:ASN232 3.2 71.7 1.0
H A:PHE231 3.4 83.3 1.0
HA A:ASP230 3.5 92.1 1.0
HB A:ILE236 3.5 89.9 1.0
H A:ASN232 3.5 82.2 1.0
CG A:ASP230 3.5 84.9 1.0
C A:ILE236 3.6 70.5 1.0
H A:ASP234 3.7 0.5 1.0
OD1 A:ASP257 3.9 80.2 1.0
H A:ILE236 3.9 89.1 1.0
HD22 A:ASN232 4.0 86.0 1.0
H A:GLY258 4.1 0.4 1.0
CB A:ASP238 4.1 68.5 1.0
CB A:ASP234 4.1 85.2 1.0
N A:PHE231 4.2 69.5 1.0
N A:ASN232 4.2 68.5 1.0
N A:ILE236 4.2 74.2 1.0
CA A:ILE236 4.3 73.4 1.0
OD2 A:ASP230 4.3 89.0 1.0
CA A:ASP230 4.3 76.7 1.0
HB3 A:ASP234 4.3 0.2 1.0
N A:ASP238 4.3 67.9 1.0
CB A:ILE236 4.3 74.9 1.0
H A:ASP238 4.4 81.5 1.0
HB2 A:ASP238 4.4 82.2 1.0
CB A:ASN232 4.4 71.8 1.0
CB A:ASP230 4.4 80.5 1.0
N A:ASP234 4.5 84.6 1.0
H A:GLY235 4.5 97.4 1.0
C A:ASP237 4.5 81.7 1.0
HG22 A:ILE236 4.6 89.1 1.0
CA A:ASP238 4.7 67.0 1.0
N A:ASP237 4.7 87.5 1.0
HA A:ASP238 4.7 80.3 1.0
HA A:ASP237 4.7 99.6 1.0
H A:GLY233 4.7 93.2 1.0
HB3 A:ASP238 4.7 82.2 1.0
HB2 A:ASP234 4.7 0.2 1.0
HB2 A:ASP230 4.7 96.6 1.0
CA A:ASN232 4.7 70.9 1.0
CA A:ASP234 4.8 87.3 1.0
HB3 A:ASN232 4.8 86.2 1.0
C A:ASP230 4.8 77.3 1.0
N A:GLY235 4.8 81.1 1.0
HA A:ASP257 4.8 87.5 1.0
O A:ASP237 4.9 82.5 1.0
CA A:ASP237 4.9 83.0 1.0
N A:GLY233 4.9 77.6 1.0
HD11 A:LEU264 4.9 95.9 1.0
N A:GLY258 4.9 87.0 1.0
C A:ASN232 5.0 72.7 1.0
C A:PHE231 5.0 73.5 1.0

Calcium binding site 2 out of 10 in 6om2

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Calcium binding site 2 out of 10 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:70.2
occ:1.00
OD1 A:ASP288 2.3 80.3 1.0
OD2 A:ASP292 2.3 61.3 1.0
O A:TYR290 2.3 62.8 1.0
OD1 A:ASP292 2.4 61.7 1.0
OD1 A:ASN286 2.4 72.5 1.0
O A:HOH2101 2.4 77.2 1.0
OD1 A:ASP284 2.4 72.5 1.0
OD2 A:ASP288 2.4 79.3 1.0
CG A:ASP292 2.6 61.0 1.0
CG A:ASP288 2.6 80.7 1.0
HA A:ASP284 3.1 81.1 1.0
H A:ILE285 3.3 83.0 1.0
H A:TYR290 3.4 84.7 1.0
C A:TYR290 3.5 64.9 1.0
CG A:ASN286 3.5 72.3 1.0
HB2 A:TYR290 3.5 87.8 1.0
CG A:ASP284 3.5 73.2 1.0
H A:ASN286 3.6 83.6 1.0
HD21 A:ASN286 3.7 88.4 1.0
H A:ASP288 3.9 94.1 1.0
CA A:ASP284 4.0 67.6 1.0
N A:ILE285 4.0 69.2 1.0
ND2 A:ASN286 4.0 73.7 1.0
N A:TYR290 4.1 70.6 1.0
CB A:ASP288 4.1 82.7 1.0
CB A:ASP292 4.1 60.2 1.0
CA A:TYR290 4.1 70.4 1.0
CB A:ASP284 4.2 71.1 1.0
CB A:TYR290 4.3 73.1 1.0
HG22 A:ILE285 4.3 82.9 1.0
N A:ASN286 4.3 69.7 1.0
HB3 A:ASP288 4.3 99.2 1.0
HG A:LEU319 4.4 87.5 1.0
H A:GLN320 4.4 82.7 1.0
C A:ASP284 4.4 65.6 1.0
C A:ALA291 4.4 61.9 1.0
HB2 A:ASP284 4.4 85.3 1.0
N A:ASP292 4.4 59.9 1.0
OD2 A:ASP284 4.5 75.8 1.0
HB2 A:ASP292 4.5 72.2 1.0
O A:ALA291 4.6 64.4 1.0
HA A:LEU319 4.6 89.2 1.0
HB3 A:TYR290 4.6 87.8 1.0
N A:ALA291 4.6 67.9 1.0
H A:ASP289 4.6 0.3 1.0
N A:ASP288 4.6 78.4 1.0
HB3 A:LEU319 4.6 89.2 1.0
HB3 A:GLN320 4.6 91.1 1.0
H A:ASP292 4.6 71.9 1.0
HB3 A:ASP292 4.7 72.2 1.0
HA A:ALA291 4.7 76.0 1.0
HB2 A:ASP288 4.7 99.2 1.0
CA A:ASP292 4.7 59.7 1.0
CB A:ASN286 4.8 71.1 1.0
HA A:ASP292 4.8 71.7 1.0
CA A:ALA291 4.8 63.3 1.0
CA A:ASP288 4.8 83.3 1.0
HD22 A:ASN286 4.9 88.4 1.0
O A:GLN320 4.9 75.8 1.0
N A:ASP289 4.9 0.2 1.0
N A:GLN320 4.9 69.0 1.0
CA A:ASN286 5.0 70.8 1.0
HD23 A:LEU319 5.0 88.9 1.0

Calcium binding site 3 out of 10 in 6om2

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Calcium binding site 3 out of 10 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:73.1
occ:1.00
OD1 A:ASP351 2.3 84.4 1.0
OD1 A:ASP349 2.4 82.2 1.0
OD1 A:ASP357 2.4 72.9 1.0
O A:PHE355 2.4 67.2 1.0
OD1 A:ASP353 2.4 73.8 1.0
OD2 A:ASP357 2.4 73.6 1.0
O A:HOH2112 2.5 69.5 1.0
CG A:ASP357 2.7 72.9 1.0
CG A:ASP353 3.3 74.9 1.0
CG A:ASP351 3.4 86.0 1.0
HD22 A:ASN377 3.4 95.7 1.0
HA A:ASP349 3.5 98.3 1.0
C A:PHE355 3.5 66.3 1.0
CG A:ASP349 3.5 82.5 1.0
H A:PHE355 3.6 81.8 1.0
H A:ASP351 3.6 0.9 1.0
OD2 A:ASP353 3.6 74.8 1.0
OD2 A:ASP351 3.7 86.3 1.0
HB2 A:PHE355 3.7 80.1 1.0
H A:ASP353 3.8 91.9 1.0
H A:GLY378 3.8 83.2 1.0
H A:LEU350 4.1 93.2 1.0
HB3 A:ASN377 4.1 94.2 1.0
O A:ASN356 4.2 65.5 1.0
C A:ASN356 4.2 65.6 1.0
ND2 A:ASN377 4.2 79.8 1.0
CB A:ASP357 4.2 72.1 1.0
N A:PHE355 4.2 68.2 1.0
CA A:ASP349 4.3 81.9 1.0
CA A:PHE355 4.3 66.8 1.0
OD2 A:ASP349 4.3 83.0 1.0
HA A:ASN356 4.3 78.8 1.0
N A:ASP351 4.4 85.7 1.0
N A:LEU350 4.4 77.7 1.0
N A:ASN356 4.5 66.1 1.0
CB A:PHE355 4.5 66.8 1.0
CB A:ASP349 4.5 82.5 1.0
N A:ASP357 4.6 70.0 1.0
HA A:ASN377 4.6 91.8 1.0
CA A:ASN356 4.6 65.7 1.0
CB A:ASP353 4.6 76.6 1.0
C A:ASP349 4.6 83.6 1.0
H A:GLN352 4.6 89.6 1.0
N A:ASP353 4.6 76.6 1.0
N A:GLY378 4.7 69.3 1.0
HB2 A:ASP357 4.7 86.5 1.0
HD21 A:ASN377 4.7 95.7 1.0
O A:GLY378 4.7 70.5 1.0
HB3 A:ASP353 4.7 91.9 1.0
CB A:ASP351 4.7 88.0 1.0
HB3 A:ASP357 4.7 86.5 1.0
H A:GLY354 4.8 90.5 1.0
CA A:ASP357 4.9 70.4 1.0
CB A:ASN377 4.9 78.5 1.0
HB3 A:LEU350 4.9 95.1 1.0
HA A:ASP357 4.9 84.5 1.0
HB3 A:PHE355 4.9 80.1 1.0
H A:ASP357 4.9 84.0 1.0
HD2 A:PHE355 4.9 82.8 1.0
N A:GLN352 5.0 74.7 1.0
CA A:ASP351 5.0 87.5 1.0

Calcium binding site 4 out of 10 in 6om2

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Calcium binding site 4 out of 10 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2004

b:78.9
occ:1.00
OD1 A:ASP414 2.3 87.8 1.0
OD1 A:ASP416 2.4 95.0 1.0
OD1 A:ASP422 2.4 0.2 1.0
O A:TYR420 2.4 82.6 1.0
OD1 A:ASN418 2.4 0.1 1.0
OD2 A:ASP422 2.4 0.4 1.0
O A:HOH2102 2.4 83.9 1.0
CG A:ASP422 2.7 0.7 1.0
CG A:ASP416 3.3 98.1 1.0
HA A:ASP414 3.3 0.9 1.0
CG A:ASN418 3.3 0.3 1.0
H A:TYR420 3.4 0.7 1.0
CG A:ASP414 3.5 87.0 1.0
HD21 A:ASN418 3.5 0.4 1.0
C A:TYR420 3.6 80.6 1.0
OD2 A:ASP416 3.6 98.9 1.0
H A:ALA438 3.6 0.7 1.0
HB3 A:ALA438 3.6 0.0 1.0
H A:ASP416 3.7 0.7 1.0
ND2 A:ASN418 3.8 0.1 1.0
HB2 A:TYR420 3.8 99.1 1.0
H A:ASN418 3.8 0.1 1.0
H A:ILE415 3.9 0.1 1.0
CA A:ASP414 4.0 84.1 1.0
N A:TYR420 4.1 83.9 1.0
CB A:ASP422 4.1 0.5 1.0
CB A:ASP414 4.2 84.1 1.0
HB2 A:ASP414 4.2 0.9 1.0
CA A:TYR420 4.2 81.5 1.0
N A:ASP422 4.3 96.5 1.0
H A:GLY419 4.3 0.5 1.0
N A:ILE415 4.3 96.8 1.0
H A:ASP422 4.3 0.8 1.0
N A:ALA438 4.4 88.1 1.0
C A:PRO421 4.4 79.3 1.0
N A:ASP416 4.4 97.3 1.0
CB A:TYR420 4.5 82.6 1.0
OD2 A:ASP414 4.5 88.6 1.0
C A:ASP414 4.5 87.5 1.0
HB2 A:ASP422 4.5 0.8 1.0
CB A:ASN418 4.5 0.8 1.0
O A:ALA438 4.5 90.1 1.0
CB A:ALA438 4.5 83.4 1.0
HB3 A:ASN418 4.5 0.8 1.0
HG22 A:ILE415 4.6 0.0 1.0
HD22 A:ASN418 4.6 0.4 1.0
HA A:PRO421 4.6 93.8 1.0
CB A:ASP416 4.6 0.5 1.0
N A:PRO421 4.6 79.0 1.0
H A:LYS417 4.6 0.8 1.0
N A:ASN418 4.6 0.2 1.0
HA A:ASP422 4.6 0.8 1.0
CA A:ASP422 4.6 98.2 1.0
HA A:ARG437 4.7 0.9 1.0
HB3 A:ARG437 4.7 0.6 1.0
HB3 A:ASP422 4.7 0.8 1.0
CA A:PRO421 4.8 78.2 1.0
HB2 A:ALA438 4.8 0.0 1.0
O A:PRO421 4.8 79.4 1.0
HB3 A:ASP416 4.8 0.8 1.0
HB3 A:TYR420 4.8 99.1 1.0
N A:GLY419 4.9 89.6 1.0
N A:LYS417 4.9 0.8 1.0
CA A:ASP416 4.9 0.9 1.0
CA A:ALA438 4.9 86.5 1.0

Calcium binding site 5 out of 10 in 6om2

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Calcium binding site 5 out of 10 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2002

b:94.1
occ:1.00
O B:PRO211 2.1 94.4 1.0
OD1 B:ASN207 2.3 89.7 1.0
OD1 B:ASP209 2.3 80.5 1.0
OE1 B:GLU212 2.4 84.9 1.0
O B:ASP209 2.4 83.0 1.0
OD2 B:ASP151 2.4 0.4 1.0
HA B:GLU212 2.8 99.2 1.0
C B:PRO211 3.1 96.0 1.0
CG B:ASN207 3.3 89.7 1.0
CD B:GLU212 3.3 87.0 1.0
HD21 B:ASN207 3.3 0.5 1.0
HB2 B:ASP151 3.4 0.9 1.0
CG B:ASP151 3.4 0.9 1.0
CG B:ASP209 3.5 82.6 1.0
C B:ASP209 3.6 85.7 1.0
CA B:GLU212 3.6 82.7 1.0
ND2 B:ASN207 3.7 90.4 1.0
N B:GLU212 3.8 86.2 1.0
O B:THR210 3.8 94.2 1.0
CB B:ASP151 3.9 0.2 1.0
OE2 B:GLU212 3.9 89.0 1.0
C B:THR210 4.0 95.9 1.0
HE2 B:HIS247 4.1 1.0 1.0
OD2 B:ASP209 4.2 82.5 1.0
HB3 B:ASP151 4.2 0.9 1.0
CG B:GLU212 4.2 87.7 1.0
N B:PRO211 4.3 0.4 1.0
H B:ASP209 4.3 0.0 1.0
CA B:PRO211 4.3 0.1 1.0
HG2 B:GLU212 4.3 0.2 1.0
CA B:ASP209 4.3 85.8 1.0
CB B:GLU212 4.4 84.2 1.0
N B:ASP209 4.4 83.3 1.0
HB3 B:GLU212 4.5 0.1 1.0
CB B:ASP209 4.5 86.1 1.0
NE2 B:HIS247 4.5 87.5 1.0
HD22 B:ASN207 4.5 0.5 1.0
OD1 B:ASP151 4.5 1.0 1.0
N B:THR210 4.5 95.0 1.0
HD2 B:HIS247 4.6 0.6 1.0
H B:GLY213 4.6 0.1 1.0
CB B:ASN207 4.6 90.1 1.0
HB2 B:ASN207 4.6 0.1 1.0
H B:GLU212 4.6 0.5 1.0
HB3 B:TYR157 4.7 0.7 1.0
CD2 B:HIS247 4.8 85.5 1.0
CA B:THR210 4.8 97.4 1.0
C B:GLU212 4.8 80.4 1.0
HG2 B:PRO211 4.8 0.3 1.0
H B:ILE208 4.8 0.4 1.0
HA B:THR210 4.8 0.8 1.0
O B:VAL150 4.9 0.3 1.0
HB2 B:ASP209 4.9 0.3 1.0
HA B:PRO211 5.0 0.3 1.0
N B:GLY213 5.0 0.1 1.0

Calcium binding site 6 out of 10 in 6om2

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Calcium binding site 6 out of 10 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:73.5
occ:1.00
OD1 C:ASP234 2.3 79.0 1.0
OD1 C:ASN232 2.3 71.9 1.0
OD2 C:ASP238 2.4 81.4 1.0
OD1 C:ASP238 2.4 83.5 1.0
OD2 C:ASP234 2.4 81.2 1.0
OD1 C:ASP230 2.4 92.3 1.0
O C:ILE236 2.5 72.3 1.0
CG C:ASP238 2.6 80.1 1.0
CG C:ASP234 2.6 82.7 1.0
HA C:ASP230 3.3 97.8 1.0
HD21 C:ASN232 3.3 97.1 1.0
CG C:ASN232 3.3 76.2 1.0
H C:PHE231 3.4 92.5 1.0
CG C:ASP230 3.4 91.4 1.0
H C:ASP234 3.5 0.1 1.0
H C:ASN232 3.6 81.3 1.0
ND2 C:ASN232 3.7 80.9 1.0
C C:ILE236 3.7 73.2 1.0
HB C:ILE236 3.9 0.0 1.0
CB C:ASP238 3.9 74.6 1.0
OD1 C:ASP257 3.9 91.4 1.0
CB C:ASP234 4.0 89.2 1.0
H C:GLY258 4.0 0.7 1.0
CA C:ASP230 4.1 81.5 1.0
N C:ASP238 4.1 74.1 1.0
H C:ASP238 4.1 88.9 1.0
N C:PHE231 4.2 77.1 1.0
HB2 C:ASP238 4.2 89.5 1.0
OD2 C:ASP230 4.2 95.5 1.0
H C:ILE236 4.2 0.5 1.0
HB3 C:ASP234 4.2 0.1 1.0
CB C:ASP230 4.3 85.5 1.0
N C:ASN232 4.3 67.8 1.0
N C:ASP234 4.3 83.4 1.0
C C:ASP237 4.3 93.8 1.0
N C:ILE236 4.4 83.8 1.0
CA C:ASP238 4.5 73.1 1.0
CA C:ILE236 4.5 80.1 1.0
HA C:ASP237 4.5 0.8 1.0
HD22 C:ASN232 4.5 97.1 1.0
HA C:ASP238 4.5 87.8 1.0
HB2 C:ASP230 4.5 0.6 1.0
H C:GLY233 4.6 0.0 1.0
H C:GLY235 4.6 0.9 1.0
HB3 C:ASP238 4.6 89.5 1.0
CB C:ASN232 4.6 76.5 1.0
HB2 C:ASP234 4.6 0.1 1.0
HA C:ASP257 4.6 97.2 1.0
CB C:ILE236 4.7 83.4 1.0
N C:ASP237 4.7 0.7 1.0
C C:ASP230 4.7 80.5 1.0
CA C:ASP234 4.7 89.1 1.0
O C:ASP237 4.7 95.6 1.0
CA C:ASP237 4.7 94.8 1.0
HD11 C:LEU264 4.8 0.5 1.0
HG22 C:ILE236 4.9 95.2 1.0
N C:GLY233 4.9 96.7 1.0
N C:GLY258 4.9 89.8 1.0
CA C:ASN232 4.9 73.2 1.0
N C:GLY235 4.9 91.6 1.0

Calcium binding site 7 out of 10 in 6om2

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Calcium binding site 7 out of 10 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:61.7
occ:1.00
O C:TYR290 2.3 63.7 1.0
OD1 C:ASP288 2.3 85.1 1.0
OD1 C:ASN286 2.3 75.5 1.0
OD2 C:ASP292 2.4 66.7 1.0
OD1 C:ASP292 2.4 69.5 1.0
OD1 C:ASP284 2.4 70.5 1.0
O C:HOH701 2.5 67.4 1.0
OD2 C:ASP288 2.5 84.5 1.0
CG C:ASP292 2.7 67.5 1.0
CG C:ASP288 2.7 85.2 1.0
H C:TYR290 3.2 83.9 1.0
HB2 C:TYR290 3.2 84.6 1.0
HA C:ASP284 3.3 81.5 1.0
C C:TYR290 3.4 66.4 1.0
H C:ILE285 3.4 74.3 1.0
CG C:ASN286 3.5 75.2 1.0
H C:ASN286 3.5 86.9 1.0
CG C:ASP284 3.6 71.6 1.0
HD21 C:ASN286 3.6 91.9 1.0
H C:ASP288 3.9 99.2 1.0
N C:TYR290 3.9 69.9 1.0
CB C:TYR290 3.9 70.5 1.0
CA C:TYR290 4.0 69.9 1.0
ND2 C:ASN286 4.0 76.6 1.0
H C:GLN320 4.1 76.7 1.0
CA C:ASP284 4.1 67.9 1.0
N C:ILE285 4.1 61.9 1.0
CB C:ASP292 4.2 66.2 1.0
HB3 C:TYR290 4.2 84.6 1.0
CB C:ASP288 4.2 86.3 1.0
HG22 C:ILE285 4.3 73.1 1.0
CB C:ASP284 4.3 71.0 1.0
H C:ASP292 4.3 82.4 1.0
N C:ASN286 4.3 72.4 1.0
HG C:LEU319 4.3 87.4 1.0
HB2 C:ASP284 4.3 85.1 1.0
N C:ASP292 4.4 68.7 1.0
H C:ASP289 4.4 0.4 1.0
HB3 C:GLN320 4.5 81.6 1.0
OD2 C:ASP284 4.5 73.3 1.0
HB2 C:ASP292 4.5 79.4 1.0
HB3 C:ASP288 4.6 0.6 1.0
N C:ALA291 4.6 76.3 1.0
C C:ASP284 4.6 65.7 1.0
HA C:LEU319 4.6 90.2 1.0
C C:ALA291 4.6 71.3 1.0
N C:ASP288 4.7 82.7 1.0
CB C:ASN286 4.7 73.3 1.0
HB3 C:ASP292 4.7 79.4 1.0
HB2 C:ASP288 4.7 0.6 1.0
HB3 C:LEU319 4.7 89.8 1.0
HA C:ALA291 4.8 87.7 1.0
CA C:ASP292 4.8 67.5 1.0
N C:GLN320 4.8 63.9 1.0
HD22 C:ASN286 4.8 91.9 1.0
N C:ASP289 4.8 89.5 1.0
O C:GLN320 4.8 68.3 1.0
HA C:ASP292 4.8 81.0 1.0
HA C:TYR290 4.9 83.9 1.0
CA C:ALA291 4.9 73.1 1.0
CA C:ASP288 4.9 86.2 1.0
CA C:ASN286 4.9 72.9 1.0
HD2 C:TYR290 5.0 90.1 1.0

Calcium binding site 8 out of 10 in 6om2

Go back to Calcium Binding Sites List in 6om2
Calcium binding site 8 out of 10 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:66.7
occ:1.00
O C:PHE355 2.2 71.1 1.0
OD1 C:ASP351 2.3 79.8 1.0
O C:HOH713 2.4 74.3 1.0
OD1 C:ASP353 2.4 83.6 1.0
OD1 C:ASP357 2.4 85.5 1.0
OD1 C:ASP349 2.4 75.4 1.0
OD2 C:ASP357 2.5 86.2 1.0
CG C:ASP357 2.7 85.3 1.0
H C:ASP351 3.2 96.7 1.0
HD22 C:ASN377 3.2 93.7 1.0
HA C:ASP349 3.3 91.0 1.0
CG C:ASP353 3.4 84.7 1.0
CG C:ASP351 3.4 81.3 1.0
C C:PHE355 3.4 71.2 1.0
H C:PHE355 3.5 87.5 1.0
H C:LEU350 3.5 81.0 1.0
H C:ASP353 3.6 0.8 1.0
CG C:ASP349 3.7 77.5 1.0
OD2 C:ASP353 3.8 84.5 1.0
HB2 C:PHE355 3.9 84.3 1.0
OD2 C:ASP351 3.9 81.9 1.0
N C:LEU350 4.0 67.5 1.0
ND2 C:ASN377 4.0 78.1 1.0
N C:ASP351 4.0 80.6 1.0
CA C:ASP349 4.0 75.8 1.0
HA C:ASN356 4.2 90.3 1.0
N C:PHE355 4.2 72.9 1.0
CB C:ASP357 4.2 84.4 1.0
C C:ASP349 4.2 75.5 1.0
CA C:PHE355 4.3 72.0 1.0
C C:ASN356 4.3 73.1 1.0
H C:GLY378 4.3 80.8 1.0
H C:GLN352 4.3 87.0 1.0
HD21 C:ASN377 4.3 93.7 1.0
HB3 C:ASN377 4.4 92.7 1.0
N C:ASP353 4.4 86.5 1.0
N C:ASN356 4.4 76.7 1.0
N C:ASP357 4.4 85.6 1.0
CB C:ASP349 4.5 78.1 1.0
HB3 C:LEU350 4.5 81.2 1.0
CA C:ASN356 4.5 75.3 1.0
O C:ASN356 4.5 72.6 1.0
OD2 C:ASP349 4.5 79.3 1.0
CB C:ASP353 4.5 86.7 1.0
CB C:PHE355 4.5 70.3 1.0
N C:GLN352 4.6 72.5 1.0
HB2 C:ASP357 4.6 0.3 1.0
HB3 C:ASP353 4.6 0.0 1.0
H C:ASP357 4.7 0.7 1.0
CB C:ASP351 4.7 82.7 1.0
CA C:ASP351 4.7 82.5 1.0
HB3 C:ASP357 4.7 0.3 1.0
CA C:ASP357 4.8 84.3 1.0
H C:GLY354 4.8 86.6 1.0
HA C:ASN377 4.8 90.7 1.0
HA C:ASP357 4.9 0.2 1.0
O C:GLY348 4.9 81.6 1.0
C C:ASP351 4.9 83.4 1.0
CA C:LEU350 4.9 68.5 1.0
CA C:ASP353 4.9 87.1 1.0
HB3 C:PHE355 4.9 84.3 1.0
C C:LEU350 5.0 70.4 1.0

Calcium binding site 9 out of 10 in 6om2

Go back to Calcium Binding Sites List in 6om2
Calcium binding site 9 out of 10 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca605

b:82.1
occ:1.00
O C:TYR420 2.3 80.0 1.0
OD1 C:ASP414 2.3 77.8 1.0
OD1 C:ASP416 2.3 80.7 1.0
OD1 C:ASN418 2.4 85.5 1.0
OD1 C:ASP422 2.4 80.2 1.0
O C:HOH722 2.4 60.9 1.0
OD2 C:ASP422 2.5 82.9 1.0
CG C:ASP422 2.7 80.5 1.0
HA C:ASP414 3.3 89.3 1.0
CG C:ASP416 3.4 82.8 1.0
CG C:ASN418 3.4 86.4 1.0
H C:TYR420 3.4 99.9 1.0
C C:TYR420 3.5 78.6 1.0
HB2 C:TYR420 3.5 94.6 1.0
CG C:ASP414 3.5 77.6 1.0
H C:ALA438 3.6 91.3 1.0
H C:ASP416 3.7 97.2 1.0
HD21 C:ASN418 3.7 0.2 1.0
OD2 C:ASP416 3.7 83.8 1.0
HB3 C:ALA438 3.8 88.9 1.0
H C:ASN418 3.9 0.3 1.0
ND2 C:ASN418 3.9 84.3 1.0
H C:ILE415 4.0 1.0 1.0
CA C:ASP414 4.0 74.4 1.0
N C:TYR420 4.1 83.2 1.0
CA C:TYR420 4.1 79.7 1.0
CB C:ASP422 4.2 78.2 1.0
CB C:ASP414 4.2 75.3 1.0
CB C:TYR420 4.2 78.8 1.0
HB2 C:ASP414 4.3 90.4 1.0
N C:ASP422 4.3 75.8 1.0
N C:ILE415 4.4 85.0 1.0
C C:PRO421 4.4 71.8 1.0
N C:ALA438 4.4 76.1 1.0
O C:ALA438 4.4 79.2 1.0
H C:ASP422 4.4 91.0 1.0
C C:ASP414 4.4 76.2 1.0
N C:ASP416 4.5 81.0 1.0
HA C:PRO421 4.5 87.7 1.0
HB3 C:TYR420 4.5 94.6 1.0
OD2 C:ASP414 4.5 79.4 1.0
HG22 C:ILE415 4.5 0.8 1.0
N C:PRO421 4.5 74.1 1.0
HB2 C:ASP422 4.6 93.8 1.0
CB C:ASN418 4.6 90.1 1.0
HB3 C:ARG437 4.6 95.8 1.0
HA C:ARG437 4.6 92.6 1.0
HB3 C:ASN418 4.6 0.1 1.0
CB C:ASP416 4.6 84.3 1.0
CA C:PRO421 4.7 73.1 1.0
N C:ASN418 4.7 93.6 1.0
CA C:ASP422 4.7 75.5 1.0
CB C:ALA438 4.7 74.1 1.0
HA C:ASP422 4.7 90.6 1.0
HB3 C:ASP422 4.7 93.8 1.0
H C:LYS417 4.7 0.8 1.0
O C:PRO421 4.8 70.7 1.0
HD22 C:ASN418 4.8 0.2 1.0
HB3 C:ASP416 4.9 0.2 1.0
H C:GLY419 5.0 0.3 1.0
CA C:ALA438 5.0 75.9 1.0

Calcium binding site 10 out of 10 in 6om2

Go back to Calcium Binding Sites List in 6om2
Calcium binding site 10 out of 10 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca3204

b:92.5
occ:1.00
O D:PRO211 2.1 90.7 1.0
OD1 D:ASN207 2.3 94.4 1.0
OD1 D:ASP209 2.3 71.5 1.0
OE1 D:GLU212 2.4 0.9 1.0
O D:ASP209 2.4 73.5 1.0
OD2 D:ASP151 2.4 0.2 1.0
HA D:GLU212 2.9 0.2 1.0
C D:PRO211 3.2 89.8 1.0
HD21 D:ASN207 3.3 0.6 1.0
CG D:ASN207 3.3 93.4 1.0
CD D:GLU212 3.3 0.2 1.0
HB2 D:ASP151 3.5 0.8 1.0
CG D:ASP209 3.5 74.7 1.0
CG D:ASP151 3.5 0.4 1.0
C D:ASP209 3.6 78.2 1.0
ND2 D:ASN207 3.7 92.2 1.0
CA D:GLU212 3.7 99.3 1.0
N D:GLU212 3.9 0.1 1.0
O D:THR210 3.9 85.1 1.0
OE2 D:GLU212 4.0 0.4 1.0
CB D:ASP151 4.0 0.2 1.0
HE2 D:HIS247 4.1 1.0 1.0
C D:THR210 4.1 89.4 1.0
OD2 D:ASP209 4.2 73.7 1.0
H D:ASP209 4.2 94.8 1.0
HB3 D:ASP151 4.3 0.8 1.0
N D:PRO211 4.3 98.8 1.0
CG D:GLU212 4.3 0.7 1.0
CA D:ASP209 4.3 81.3 1.0
N D:ASP209 4.3 79.0 1.0
CA D:PRO211 4.3 94.4 1.0
CB D:GLU212 4.4 98.9 1.0
HG2 D:GLU212 4.4 0.2 1.0
CB D:ASP209 4.5 81.0 1.0
HD22 D:ASN207 4.5 0.6 1.0
HB3 D:GLU212 4.5 0.7 1.0
NE2 D:HIS247 4.5 88.3 1.0
HB3 D:TYR157 4.5 0.7 1.0
OD1 D:ASP151 4.6 0.2 1.0
N D:THR210 4.6 95.8 1.0
HD2 D:HIS247 4.6 0.6 1.0
CB D:ASN207 4.6 94.0 1.0
HB2 D:ASN207 4.6 0.8 1.0
H D:GLY213 4.7 0.0 1.0
H D:GLU212 4.7 0.7 1.0
H D:ILE208 4.8 95.4 1.0
HG2 D:PRO211 4.8 0.6 1.0
CD2 D:HIS247 4.8 83.8 1.0
CA D:THR210 4.8 94.1 1.0
C D:GLU212 4.9 95.9 1.0
HA D:THR210 4.9 1.0 1.0
HB2 D:ASP209 4.9 97.2 1.0
O D:VAL150 4.9 0.1 1.0

Reference:

J.C.Wang, R.E.Iacob, J.R.Engen, T.A.Springer. Crystal Structure of Atypical Integrin Alphav BETA8 Nat Commun 2019.
ISSN: ESSN 2041-1723
Page generated: Sat Dec 12 07:24:18 2020

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