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Calcium in PDB 4wk2: Metal Ion and Ligand Binding of Integrin

Protein crystallography data

The structure of Metal Ion and Ligand Binding of Integrin, PDB code: 4wk2 was solved by W.Xia, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.57 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.980, 118.390, 170.290, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.4

Other elements in 4wk2:

The structure of Metal Ion and Ligand Binding of Integrin also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Metal Ion and Ligand Binding of Integrin (pdb code 4wk2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Metal Ion and Ligand Binding of Integrin, PDB code: 4wk2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4wk2

Go back to Calcium Binding Sites List in 4wk2
Calcium binding site 1 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Metal Ion and Ligand Binding of Integrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:87.1
occ:1.00
O A:THR245 2.3 86.7 1.0
OG A:SER241 2.3 0.2 1.0
OD1 A:ASP247 2.4 93.7 1.0
OE2 A:GLU239 2.4 93.7 1.0
OD1 A:ASP243 2.4 0.7 1.0
OD2 A:ASP247 2.4 97.6 1.0
OE1 A:GLU239 2.4 88.6 1.0
O A:HOH621 2.5 70.3 1.0
CG A:ASP247 2.6 93.8 1.0
CD A:GLU239 2.7 91.8 1.0
H A:SER241 3.2 1.0 1.0
CG A:ASP243 3.4 0.3 1.0
HB3 A:SER241 3.4 0.7 1.0
CB A:SER241 3.4 0.3 1.0
C A:THR245 3.5 96.9 1.0
H A:PHE240 3.6 97.0 1.0
OD2 A:ASP243 3.7 0.8 1.0
HA A:GLU239 3.7 0.5 1.0
H A:THR245 3.8 0.8 1.0
H A:ASP243 3.8 0.2 1.0
N A:SER241 3.9 0.8 1.0
HB A:THR245 4.0 0.6 1.0
CB A:ASP247 4.0 88.3 1.0
H A:GLY267 4.1 0.6 1.0
HA A:GLU246 4.1 0.9 1.0
N A:ASP247 4.1 86.9 1.0
H A:ASP247 4.1 0.3 1.0
HB2 A:SER241 4.1 0.7 1.0
CG A:GLU239 4.2 92.6 1.0
CA A:SER241 4.2 0.3 1.0
C A:GLU246 4.3 99.7 1.0
N A:THR245 4.3 0.7 1.0
N A:PHE240 4.3 80.9 1.0
CA A:THR245 4.4 0.4 1.0
N A:GLU246 4.4 0.9 1.0
H A:GLY242 4.4 0.0 1.0
OD1 A:ASN266 4.4 0.3 1.0
CA A:GLU246 4.5 0.7 1.0
HA A:ASP247 4.5 0.1 1.0
HG3 A:GLU239 4.5 0.1 1.0
CA A:ASP247 4.5 83.4 1.0
HB2 A:ASP247 4.5 0.0 1.0
CA A:GLU239 4.5 87.1 1.0
N A:ASP243 4.6 0.7 1.0
HB3 A:ASP247 4.6 0.0 1.0
CB A:THR245 4.6 0.4 1.0
C A:SER241 4.7 0.4 1.0
HG2 A:GLU239 4.7 0.1 1.0
N A:GLY242 4.7 95.8 1.0
CB A:ASP243 4.7 0.5 1.0
CB A:GLU239 4.8 90.9 1.0
O A:GLU246 4.8 99.8 1.0
HA A:ASN266 4.8 0.4 1.0
HB2 A:GLU239 4.9 0.0 1.0
N A:GLY267 4.9 0.4 1.0
HG22 A:THR245 4.9 0.8 1.0
C A:ASP243 4.9 0.1 1.0
O A:ASP243 4.9 0.9 1.0
C A:GLU239 5.0 88.2 1.0
CA A:ASP243 5.0 0.0 1.0

Calcium binding site 2 out of 6 in 4wk2

Go back to Calcium Binding Sites List in 4wk2
Calcium binding site 2 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Metal Ion and Ligand Binding of Integrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:73.9
occ:1.00
O A:LEU299 2.3 83.3 1.0
OD1 A:ASN295 2.4 84.2 1.0
OD1 A:ASP293 2.4 84.1 1.0
OD1 A:ASP301 2.4 88.8 1.0
OD1 A:ASP297 2.4 89.0 1.0
OD2 A:ASP301 2.4 89.8 1.0
O A:HOH601 2.5 93.1 1.0
CG A:ASP301 2.7 87.0 1.0
HB2 A:LEU299 3.2 0.8 1.0
CG A:ASP297 3.3 94.7 1.0
HA A:ASP293 3.4 0.0 1.0
C A:LEU299 3.4 84.9 1.0
OD2 A:ASP297 3.4 98.3 1.0
CG A:ASN295 3.4 84.8 1.0
HD21 A:ASN295 3.5 0.2 1.0
H A:LEU299 3.5 0.8 1.0
CG A:ASP293 3.5 85.2 1.0
H A:ASN295 3.7 0.6 1.0
H A:VAL294 3.8 99.1 1.0
ND2 A:ASN295 3.8 86.8 1.0
H A:ASP297 3.9 0.4 1.0
CB A:LEU299 4.0 92.3 1.0
CA A:LEU299 4.0 86.9 1.0
N A:LEU299 4.0 86.5 1.0
H A:GLN329 4.1 85.5 1.0
CA A:ASP293 4.1 85.9 1.0
HB2 A:ASP293 4.2 0.6 1.0
CB A:ASP301 4.2 81.9 1.0
CB A:ASP293 4.2 86.3 1.0
HB3 A:GLN329 4.2 88.1 1.0
HD22 A:LEU328 4.3 93.5 1.0
HB3 A:LEU299 4.3 0.8 1.0
N A:VAL294 4.4 82.5 1.0
H A:ASP301 4.4 99.9 1.0
N A:ASP301 4.4 83.3 1.0
O A:GLN329 4.4 79.4 1.0
N A:ASN295 4.5 83.9 1.0
OD2 A:ASP293 4.5 87.2 1.0
N A:ASP300 4.5 99.0 1.0
HB2 A:ASP301 4.5 98.3 1.0
C A:ASP300 4.6 92.1 1.0
HA A:ASP300 4.6 0.5 1.0
HG22 A:VAL294 4.6 99.3 1.0
C A:ASP293 4.6 86.2 1.0
CB A:ASP297 4.7 96.4 1.0
H A:GLY298 4.7 98.0 1.0
HD22 A:ASN295 4.7 0.2 1.0
N A:ASP297 4.7 96.2 1.0
N A:GLN329 4.8 71.2 1.0
CB A:ASN295 4.8 84.5 1.0
HB3 A:ASP301 4.8 98.3 1.0
CA A:ASP301 4.8 77.5 1.0
HA A:LEU328 4.8 89.2 1.0
CA A:ASP300 4.8 97.1 1.0
HA A:ASP301 4.8 93.0 1.0
HB3 A:LEU328 4.8 96.0 1.0
H A:GLY296 4.9 0.8 1.0
HA A:LEU299 4.9 0.3 1.0
CA A:ASN295 5.0 86.1 1.0
N A:GLY298 5.0 81.7 1.0

Calcium binding site 3 out of 6 in 4wk2

Go back to Calcium Binding Sites List in 4wk2
Calcium binding site 3 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Metal Ion and Ligand Binding of Integrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:66.2
occ:1.00
OD1 A:ASP362 2.3 97.8 1.0
O A:TYR366 2.4 73.9 1.0
OD1 A:ASP360 2.4 93.5 1.0
OD1 A:ASP364 2.4 94.9 1.0
OD2 A:ASP368 2.5 73.6 1.0
OD1 A:ASP368 2.5 76.0 1.0
O A:HOH608 2.5 47.8 1.0
CG A:ASP368 2.8 72.9 1.0
O A:HOH623 3.1 62.9 1.0
H A:ASP362 3.2 1.0 1.0
H A:LEU361 3.4 98.7 1.0
CG A:ASP364 3.4 95.6 1.0
CG A:ASP362 3.4 0.4 1.0
HA A:ASP360 3.5 0.9 1.0
C A:TYR366 3.6 77.2 1.0
CG A:ASP360 3.7 98.9 1.0
H A:ASP364 3.8 0.1 1.0
H A:TYR366 3.8 0.7 1.0
OD2 A:ASP364 3.9 97.3 1.0
N A:LEU361 3.9 82.3 1.0
HB2 A:TYR366 3.9 99.1 1.0
OD2 A:ASP362 3.9 0.1 1.0
N A:ASP362 4.0 98.3 1.0
H A:GLY389 4.1 90.8 1.0
CA A:ASP360 4.2 95.8 1.0
HA A:ASN367 4.3 90.3 1.0
CB A:ASP368 4.3 69.5 1.0
C A:ASP360 4.4 91.1 1.0
H A:GLN363 4.4 0.6 1.0
C A:ASN367 4.4 70.7 1.0
HB3 A:LEU361 4.4 1.0 1.0
CA A:TYR366 4.4 84.2 1.0
N A:ASP368 4.5 69.0 1.0
N A:TYR366 4.5 86.4 1.0
OD2 A:ASP360 4.5 0.8 1.0
HB2 A:LEU361 4.5 1.0 1.0
N A:ASN367 4.5 77.2 1.0
CB A:ASP360 4.6 98.4 1.0
H A:ASP368 4.6 82.8 1.0
N A:ASP364 4.6 96.8 1.0
CB A:ASP364 4.6 95.2 1.0
CB A:TYR366 4.6 82.6 1.0
CA A:ASN367 4.6 75.2 1.0
CB A:ASP362 4.6 0.5 1.0
HB3 A:ASP364 4.7 0.2 1.0
HB2 A:ASP368 4.7 83.5 1.0
HA A:PRO388 4.7 95.5 1.0
CA A:LEU361 4.7 83.1 1.0
O A:ASN367 4.8 67.9 1.0
HB3 A:ASP368 4.8 83.5 1.0
CA A:ASP362 4.8 0.6 1.0
N A:GLN363 4.8 0.0 1.0
CB A:LEU361 4.8 85.8 1.0
N A:GLY389 4.8 75.7 1.0
CA A:ASP368 4.9 71.3 1.0
C A:LEU361 4.9 88.0 1.0
HA A:ASP368 4.9 85.5 1.0
O A:GLY389 5.0 82.2 1.0
HB3 A:TYR366 5.0 99.1 1.0
HB3 A:ASP362 5.0 0.7 1.0

Calcium binding site 4 out of 6 in 4wk2

Go back to Calcium Binding Sites List in 4wk2
Calcium binding site 4 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Metal Ion and Ligand Binding of Integrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:81.3
occ:1.00
O A:TYR430 2.3 95.8 1.0
OD1 A:ASP426 2.3 0.2 1.0
OD1 A:ASP424 2.3 0.1 1.0
OD1 A:ASP432 2.4 82.2 1.0
OD1 A:ASN428 2.4 0.8 1.0
OD2 A:ASP432 2.4 80.9 1.0
O A:HOH610 2.5 61.8 1.0
CG A:ASP432 2.7 80.7 1.0
CG A:ASP426 3.4 0.1 1.0
H A:ASP426 3.4 0.8 1.0
CG A:ASN428 3.4 0.5 1.0
H A:LEU425 3.5 0.2 1.0
CG A:ASP424 3.5 0.9 1.0
C A:TYR430 3.5 90.9 1.0
HA A:ASP424 3.6 0.7 1.0
HD21 A:ASN428 3.6 0.1 1.0
H A:ASN428 3.7 0.4 1.0
OD2 A:ASP426 3.8 0.1 1.0
H A:TYR430 3.8 0.6 1.0
H A:GLY448 3.8 0.9 1.0
HB2 A:TYR430 3.9 0.8 1.0
ND2 A:ASN428 3.9 0.8 1.0
N A:LEU425 4.1 0.4 1.0
CB A:ASP432 4.2 74.9 1.0
H A:GLY427 4.2 1.0 1.0
OD2 A:ASP424 4.2 0.6 1.0
N A:ASP426 4.2 0.5 1.0
HA A:PRO431 4.3 88.2 1.0
CA A:TYR430 4.3 94.5 1.0
CA A:ASP424 4.3 88.9 1.0
C A:PRO431 4.3 72.9 1.0
HG2 A:ARG447 4.3 0.9 1.0
N A:TYR430 4.3 94.6 1.0
CB A:ASP424 4.4 96.0 1.0
O A:GLY448 4.4 0.4 1.0
CB A:TYR430 4.5 94.0 1.0
N A:ASP432 4.5 81.9 1.0
N A:PRO431 4.5 75.3 1.0
N A:ASN428 4.5 0.4 1.0
O A:PRO431 4.5 75.7 1.0
N A:GLY448 4.5 99.1 1.0
HB2 A:ASP432 4.6 89.9 1.0
CA A:PRO431 4.6 73.5 1.0
HB3 A:ARG447 4.6 99.9 1.0
C A:ASP424 4.6 85.0 1.0
CB A:ASN428 4.6 0.3 1.0
HB3 A:TYR430 4.6 0.8 1.0
HA A:ARG447 4.6 90.3 1.0
CB A:ASP426 4.7 0.1 1.0
HB2 A:ASP424 4.7 0.2 1.0
N A:GLY427 4.7 0.2 1.0
HB3 A:ASN428 4.7 0.5 1.0
HD22 A:ASN428 4.7 0.1 1.0
H A:ASP432 4.7 98.2 1.0
HB3 A:ASP432 4.7 89.9 1.0
CA A:ASP432 4.8 76.6 1.0
HA A:ASP432 4.8 92.0 1.0
HB3 A:LEU425 4.8 0.7 1.0
H A:GLY429 4.8 0.8 1.0
CA A:ASP426 4.9 0.6 1.0
HA3 A:GLY448 5.0 0.2 1.0

Calcium binding site 5 out of 6 in 4wk2

Go back to Calcium Binding Sites List in 4wk2
Calcium binding site 5 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Metal Ion and Ligand Binding of Integrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:0.4
occ:1.00
OD1 B:ASP138 2.4 0.6 1.0
OD1 B:ASP137 2.4 0.8 1.0
O B:SER134 2.4 81.6 1.0
O B:HOH614 2.4 59.3 1.0
O B:HOH680 2.5 0.5 1.0
HA B:MET135 3.0 1.0 1.0
CG B:ASP137 3.4 0.4 1.0
C B:SER134 3.5 90.0 1.0
CG B:ASP138 3.6 0.4 1.0
OD2 B:ASP137 3.6 0.8 1.0
O B:HOH670 3.8 80.5 1.0
CA B:MET135 3.9 0.6 1.0
H B:ASP138 3.9 0.7 1.0
H B:ASP137 4.0 0.8 1.0
OD2 B:ASP259 4.1 85.9 1.0
N B:MET135 4.1 0.3 1.0
H B:LYS136 4.3 0.1 1.0
O B:ALA342 4.3 0.3 1.0
OD2 B:ASP138 4.3 0.3 1.0
C B:MET135 4.4 0.2 1.0
O B:HOH629 4.4 67.9 1.0
N B:LYS136 4.5 0.8 1.0
N B:ASP138 4.5 0.1 1.0
HB2 B:ASP138 4.6 0.6 1.0
N B:ASP137 4.6 0.1 1.0
SD B:MET135 4.6 77.8 1.0
CB B:ASP138 4.7 0.5 1.0
HA B:ASN343 4.7 0.1 1.0
HB2 B:SER134 4.7 0.1 1.0
HA B:SER134 4.7 0.9 1.0
CB B:ASP137 4.7 0.1 1.0
CA B:SER134 4.7 95.7 1.0
HB3 B:ASN343 4.8 1.0 1.0
HB3 B:ASP259 4.8 92.1 1.0
CG B:ASP259 4.9 80.5 1.0
H B:MET135 5.0 0.1 1.0

Calcium binding site 6 out of 6 in 4wk2

Go back to Calcium Binding Sites List in 4wk2
Calcium binding site 6 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Metal Ion and Ligand Binding of Integrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:66.8
occ:1.00
O B:PRO228 2.2 70.4 1.0
OD1 B:ASN224 2.2 69.1 1.0
OD1 B:ASP226 2.3 76.6 1.0
OE1 B:GLU169 2.3 60.8 1.0
O B:ASP226 2.4 73.7 1.0
OE2 B:GLU229 2.4 67.4 1.0
HA B:GLU229 2.7 70.5 1.0
C B:PRO228 3.1 61.7 1.0
HD21 B:ASN224 3.2 84.4 1.0
CG B:ASN224 3.2 67.7 1.0
HE2 B:HIS263 3.4 72.6 1.0
C B:ASP226 3.4 74.0 1.0
CD B:GLU229 3.4 64.1 1.0
CG B:ASP226 3.4 76.5 1.0
CD B:GLU169 3.4 60.6 1.0
HG2 B:GLU169 3.5 75.4 1.0
CA B:GLU229 3.6 58.7 1.0
ND2 B:ASN224 3.6 70.3 1.0
HB2 B:GLU169 3.7 72.4 1.0
N B:GLU229 3.7 58.0 1.0
CG B:GLU169 3.9 62.8 1.0
C B:SER227 4.0 66.9 1.0
H B:ASP226 4.0 90.5 1.0
OE1 B:GLU229 4.1 67.9 1.0
O B:SER227 4.1 65.7 1.0
NE2 B:HIS263 4.1 60.5 1.0
N B:PRO228 4.1 66.8 1.0
HD2 B:HIS263 4.1 69.8 1.0
OD2 B:ASP226 4.2 79.1 1.0
CA B:ASP226 4.2 76.6 1.0
CA B:PRO228 4.2 64.7 1.0
N B:ASP226 4.3 75.4 1.0
CB B:GLU169 4.3 60.4 1.0
N B:SER227 4.3 70.9 1.0
CB B:ASP226 4.4 75.8 1.0
CG B:GLU229 4.4 62.8 1.0
CB B:GLU229 4.4 59.3 1.0
HD22 B:ASN224 4.4 84.4 1.0
HD2 B:PRO228 4.4 85.3 1.0
CD2 B:HIS263 4.5 58.2 1.0
HB2 C:ASP5003 4.5 1.0 1.0
HG2 B:GLU229 4.5 75.4 1.0
OE2 B:GLU169 4.5 61.2 1.0
H B:GLU229 4.5 69.6 1.0
HB3 B:GLU229 4.6 71.2 1.0
CA B:SER227 4.6 71.5 1.0
CB B:ASN224 4.6 66.4 1.0
HA B:SER227 4.6 85.8 1.0
C B:GLU229 4.6 55.4 1.0
HB2 B:ASN224 4.6 79.7 1.0
HB2 B:ASP226 4.7 90.9 1.0
H B:LEU225 4.7 89.5 1.0
HB3 B:TYR175 4.8 74.7 1.0
HG3 B:GLU169 4.8 75.4 1.0
HB2 B:PRO228 4.9 79.0 1.0
CD B:PRO228 4.9 71.1 1.0
H B:GLY230 4.9 49.8 1.0
HB3 B:GLU169 4.9 72.4 1.0
HA B:PRO228 4.9 77.7 1.0
HB3 B:ASN224 5.0 79.7 1.0
O B:VAL168 5.0 61.1 1.0

Reference:

W.Xia, T.A.Springer. Metal Ion and Ligand Binding of Integrin ALPHA5BETA1 at High Resolution To Be Published.
Page generated: Sun Jul 14 14:09:28 2024

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