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Calcium in PDB 2hpc: Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.

Protein crystallography data

The structure of Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide., PDB code: 2hpc was solved by R.F.Doolittle, J.M.Kollman, A.Chen, L.Pandi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.90
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.677, 46.069, 429.901, 90.00, 89.99, 90.00
R / Rfree (%) 27.5 / 36

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. (pdb code 2hpc). 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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide., PDB code: 2hpc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 2hpc

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Calcium binding site 1 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.


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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:90.2
occ:1.00
 O B:TRP385 2.8 82.1 1.0
OD1 B:ASP383 2.8 61.6 1.0
OD2 B:ASP381 3.1 59.2 1.0
OD1 B:ASP381 3.1 64.5 1.0
OD2 B:ASP383 3.2 57.9 1.0
CG B:ASP383 3.4 66.8 1.0
CG B:ASP381 3.5 64.6 1.0
N B:THR387 3.7 76.8 1.0
CA B:LEU386 3.7 73.7 1.0
C B:TRP385 3.8 81.0 1.0
O B:THR387 4.0 86.2 1.0
C B:LEU386 4.2 69.5 1.0
N B:LEU386 4.2 77.9 1.0
CD2 B:LEU386 4.2 69.1 1.0
CG2 B:THR387 4.7 74.0 1.0
C B:THR387 4.8 87.2 1.0
CG B:GLN393 4.8 59.1 1.0
CA B:THR387 4.8 82.8 1.0
CB B:LEU386 4.9 75.0 1.0
CB B:ASP383 4.9 71.1 1.0
O B:ASP383 4.9 75.6 1.0
O B:LYS392 4.9 76.5 1.0

Calcium binding site 2 out of 10 in 2hpc

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Calcium binding site 2 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.


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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:78.7
occ:1.00
 O C:PHE322 2.7 0.4 1.0
O C:GLY324 2.8 93.0 1.0
OD1 C:ASP318 3.1 82.6 1.0
N C:GLY324 3.4 100.0 1.0
C C:PHE322 3.4 0.5 1.0
OD1 C:ASP320 3.6 81.4 1.0
C C:GLY324 3.6 96.9 1.0
OD2 C:ASP320 3.8 76.3 1.0
N C:PHE322 3.8 90.8 1.0
CG C:ASP320 3.9 82.4 1.0
O C:ASP320 3.9 88.3 1.0
CA C:GLY324 3.9 99.2 1.0
CA C:PHE322 4.0 98.5 1.0
CB C:PHE322 4.1 0.0 1.0
N C:GLU323 4.2 0.9 1.0
O C:ASP318 4.3 90.9 1.0
C C:GLU323 4.4 0.6 1.0
CG C:ASP318 4.4 87.8 1.0
C C:ASP320 4.5 87.8 1.0
CA C:GLU323 4.5 1.0 1.0
N C:ASN325 4.8 97.4 1.0
N C:ASP320 4.8 78.5 1.0
CD2 C:PHE322 4.9 0.5 1.0
CG C:PHE322 5.0 0.9 1.0
CB C:ASP320 5.0 83.3 1.0

Calcium binding site 3 out of 10 in 2hpc

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Calcium binding site 3 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.


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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2

b:57.2
occ:1.00
 O E:TRP385 2.7 78.2 1.0
OD2 E:ASP381 2.7 43.8 1.0
OD1 E:ASP383 2.8 75.2 1.0
OD1 E:ASP381 3.1 48.8 1.0
C E:TRP385 3.2 74.3 1.0
CG E:ASP381 3.2 47.8 1.0
N E:LEU386 3.5 73.0 1.0
CA E:LEU386 3.6 73.6 1.0
CG E:ASP383 3.7 60.3 1.0
OD2 E:ASP383 3.9 57.4 1.0
N E:THR387 3.9 77.1 1.0
CA E:TRP385 4.1 69.6 1.0
C E:LEU386 4.1 78.2 1.0
N E:TRP385 4.2 62.4 1.0
OG1 E:THR387 4.2 68.4 1.0
CB E:TRP385 4.3 55.1 1.0
O E:LYS392 4.5 58.5 1.0
O E:ASP383 4.6 33.1 1.0
CB E:ASP381 4.7 45.2 1.0
CB E:LEU386 4.9 72.2 1.0
CD2 E:LEU386 4.9 71.5 1.0

Calcium binding site 4 out of 10 in 2hpc

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Calcium binding site 4 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.


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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1

b:54.6
occ:1.00
 O F:PHE322 2.6 82.8 1.0
OD2 F:ASP320 2.7 51.6 1.0
OD1 F:ASP318 2.7 46.0 1.0
OD2 F:ASP318 3.0 62.9 1.0
CG F:ASP318 3.1 55.7 1.0
O F:GLY324 3.5 79.2 1.0
C F:PHE322 3.6 81.1 1.0
CG F:ASP320 3.7 70.9 1.0
CA F:GLU323 4.0 76.1 1.0
C F:GLU323 4.0 78.4 1.0
C F:GLY324 4.1 78.9 1.0
O F:ASP320 4.1 62.8 1.0
OD1 F:ASP320 4.1 73.6 1.0
N F:GLU323 4.2 80.5 1.0
N F:GLY324 4.2 79.7 1.0
N F:PHE322 4.4 72.5 1.0
O F:GLU323 4.4 75.6 1.0
C F:ASP320 4.5 60.9 1.0
CB F:ASP318 4.5 49.8 1.0
N F:ASN325 4.6 75.6 1.0
CA F:ASN325 4.6 65.3 1.0
CA F:PHE322 4.6 80.2 1.0
N F:ASP320 4.7 62.8 1.0
CB F:ASP320 4.8 65.0 1.0
CA F:GLY324 4.9 76.5 1.0
C F:LYS321 4.9 61.1 1.0
CA F:ASP320 4.9 59.2 1.0

Calcium binding site 5 out of 10 in 2hpc

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Calcium binding site 5 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.


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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca2

b:83.0
occ:1.00
 O H:TRP385 2.7 85.0 1.0
OD1 H:ASP383 2.7 64.3 1.0
OD2 H:ASP381 3.1 64.3 1.0
OD2 H:ASP383 3.2 61.4 1.0
OD1 H:ASP381 3.2 64.5 1.0
CG H:ASP383 3.3 66.0 1.0
CG H:ASP381 3.6 67.0 1.0
CA H:LEU386 3.6 75.4 1.0
C H:TRP385 3.7 84.0 1.0
N H:THR387 3.7 75.0 1.0
CD2 H:LEU386 4.1 71.9 1.0
N H:LEU386 4.1 78.9 1.0
O H:THR387 4.1 79.2 1.0
C H:LEU386 4.1 70.1 1.0
CG2 H:THR387 4.7 72.0 1.0
CB H:LEU386 4.7 76.7 1.0
O H:ASP383 4.8 67.5 1.0
CA H:THR387 4.8 78.9 1.0
CB H:ASP383 4.8 70.0 1.0
C H:THR387 4.8 81.8 1.0
CG H:GLN393 4.9 61.2 1.0
CA H:TRP385 5.0 86.5 1.0

Calcium binding site 6 out of 10 in 2hpc

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Calcium binding site 6 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.


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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca1

b:76.6
occ:1.00
 O I:PHE322 2.8 99.8 1.0
O I:GLY324 2.8 87.8 1.0
OD1 I:ASP318 3.1 95.3 1.0
C I:PHE322 3.5 0.4 1.0
OD1 I:ASP320 3.5 76.4 1.0
N I:GLY324 3.5 98.1 1.0
OD2 I:ASP320 3.7 78.5 1.0
C I:GLY324 3.7 91.1 1.0
O I:ASP320 3.8 87.0 1.0
CG I:ASP320 3.8 82.4 1.0
N I:PHE322 3.8 91.0 1.0
CA I:PHE322 4.1 96.8 1.0
CA I:GLY324 4.1 94.0 1.0
O I:ASP318 4.2 88.4 1.0
CB I:PHE322 4.2 0.7 1.0
CG I:ASP318 4.3 93.4 1.0
N I:GLU323 4.3 0.2 1.0
C I:ASP320 4.3 88.0 1.0
C I:GLU323 4.5 0.9 1.0
N I:ASP320 4.6 81.3 1.0
CA I:GLU323 4.6 0.3 1.0
CA I:ASP320 4.9 85.6 1.0
CB I:ASP320 4.9 82.5 1.0
N I:ASN325 4.9 93.3 1.0
C I:ASP318 5.0 85.3 1.0

Calcium binding site 7 out of 10 in 2hpc

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Calcium binding site 7 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.


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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca2

b:60.8
occ:1.00
 O K:TRP385 2.7 75.9 1.0
OD2 K:ASP381 2.8 46.8 1.0
OD1 K:ASP383 2.8 71.7 1.0
OD1 K:ASP381 3.0 45.8 1.0
C K:TRP385 3.1 72.6 1.0
CG K:ASP381 3.2 46.1 1.0
N K:LEU386 3.5 72.3 1.0
CA K:LEU386 3.5 72.1 1.0
CG K:ASP383 3.7 56.9 1.0
N K:THR387 3.9 73.1 1.0
OD2 K:ASP383 3.9 61.7 1.0
CA K:TRP385 4.1 67.7 1.0
C K:LEU386 4.1 75.3 1.0
N K:TRP385 4.1 60.9 1.0
CB K:TRP385 4.3 58.4 1.0
OG1 K:THR387 4.4 63.5 1.0
O K:ASP383 4.6 39.2 1.0
CB K:ASP381 4.6 45.5 1.0
O K:LYS392 4.7 56.5 1.0
CB K:LEU386 4.7 70.2 1.0
CD2 K:LEU386 4.8 60.3 1.0
C K:ASP383 4.9 40.5 1.0

Calcium binding site 8 out of 10 in 2hpc

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Calcium binding site 8 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.


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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1

b:58.9
occ:1.00
 O L:PHE322 2.6 82.0 1.0
OD2 L:ASP320 2.8 44.6 1.0
OD1 L:ASP318 2.8 48.4 1.0
OD2 L:ASP318 3.0 67.4 1.0
CG L:ASP318 3.2 58.5 1.0
O L:GLY324 3.3 77.9 1.0
C L:PHE322 3.5 80.3 1.0
CG L:ASP320 3.8 63.1 1.0
C L:GLU323 3.9 79.1 1.0
C L:GLY324 3.9 75.2 1.0
CA L:GLU323 3.9 74.9 1.0
N L:GLY324 4.1 79.7 1.0
N L:GLU323 4.1 80.2 1.0
O L:ASP320 4.2 58.4 1.0
OD1 L:ASP320 4.2 62.4 1.0
O L:GLU323 4.3 76.8 1.0
N L:ASN325 4.4 72.7 1.0
CA L:ASN325 4.4 62.7 1.0
N L:PHE322 4.5 73.3 1.0
CB L:ASP318 4.5 50.3 1.0
C L:ASP320 4.6 58.1 1.0
CA L:PHE322 4.7 79.8 1.0
CA L:GLY324 4.7 73.2 1.0
N L:ASP320 4.8 57.1 1.0
C L:LYS321 4.9 63.1 1.0
CB L:ASP320 5.0 58.8 1.0

Calcium binding site 9 out of 10 in 2hpc

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Calcium binding site 9 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.


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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca3

b:90.1
occ:1.00
 O E:GLY263 2.7 34.5 1.0
OE2 F:GLU132 2.8 71.1 1.0
CD F:GLU132 3.0 63.6 1.0
OD2 E:ASP261 3.3 70.6 1.0
OE1 F:GLU132 3.4 67.0 1.0
CG F:GLU132 3.7 48.0 1.0
CE2 E:TYR378 3.7 79.1 1.0
C E:GLY263 3.8 34.5 1.0
OH E:TYR378 3.8 67.0 1.0
CG E:ASP261 4.2 62.0 1.0
CZ E:TYR378 4.3 79.5 1.0
OD1 E:ASP261 4.4 71.3 1.0
N E:ARG264 4.6 31.5 1.0
CA E:GLY263 4.6 32.3 1.0
CA E:ARG264 4.6 34.5 1.0
NE2 F:GLN136 4.8 47.9 1.0
CD2 E:TYR378 4.8 78.3 1.0

Calcium binding site 10 out of 10 in 2hpc

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Calcium binding site 10 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide.


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 Fragment D From Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca3

b:89.1
occ:1.00
 O K:GLY263 2.9 32.6 1.0
CD L:GLU132 2.9 71.9 1.0
OE2 L:GLU132 3.0 73.8 1.0
OE1 L:GLU132 3.2 75.9 1.0
CE2 K:TYR378 3.5 77.9 1.0
OH K:TYR378 3.5 75.4 1.0
CG L:GLU132 3.6 54.1 1.0
OD2 K:ASP261 3.6 67.7 1.0
C K:GLY263 4.0 32.1 1.0
CZ K:TYR378 4.0 79.2 1.0
CG K:ASP261 4.6 63.4 1.0
CD2 K:TYR378 4.6 77.0 1.0
OD1 K:ASP261 4.7 68.2 1.0
CA K:ARG264 4.7 34.8 1.0
N K:ARG264 4.8 28.4 1.0
CA K:GLY263 4.8 27.6 1.0

Reference:

R.F.Doolittle, J.M.Kollman, A.Chen, L.Pandi. N/A N/A.
Page generated: Fri Jul 12 12:47:22 2024

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