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

Protein crystallography data

The structure of Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Hydroxypro-Arg-Pro-Amide, PDB code: 2hod 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 (°) 81.647, 47.069, 431.460, 90.00, 90.06, 90.00
R / Rfree (%) 26.8 / 34.7

Calcium Binding Sites:

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

Calcium binding site 1 out of 10 in 2hod

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


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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-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:86.2
occ:1.00
 O B:TRP385 2.6 79.6 1.0
OD2 B:ASP381 2.9 59.2 1.0
OD1 B:ASP383 2.9 68.6 1.0
OD1 B:ASP381 3.1 49.3 1.0
OD2 B:ASP383 3.2 58.4 1.0
CG B:ASP381 3.3 64.5 1.0
CG B:ASP383 3.5 75.7 1.0
C B:TRP385 3.6 79.8 1.0
N B:THR387 4.1 71.0 1.0
CA B:LEU386 4.1 70.8 1.0
N B:LEU386 4.3 74.7 1.0
O B:THR387 4.4 78.0 1.0
CD2 B:LEU386 4.5 58.2 1.0
C B:LEU386 4.6 71.2 1.0
CA B:TRP385 4.7 86.0 1.0
CB B:ASP381 4.7 73.3 1.0
CG B:GLN393 4.9 86.5 1.0
N B:TRP385 4.9 81.0 1.0
CG2 B:THR387 5.0 66.1 1.0
CB B:TRP385 5.0 96.4 1.0
CB B:ASP383 5.0 74.7 1.0

Calcium binding site 2 out of 10 in 2hod

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


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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-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:71.0
occ:1.00
 O C:PHE322 2.9 93.7 1.0
O C:GLY324 3.0 95.7 1.0
OD1 C:ASP318 3.0 0.6 1.0
CA C:GLY324 3.3 0.2 1.0
C C:GLY324 3.4 0.9 1.0
N C:GLY324 3.4 1.0 1.0
OD1 C:ASP320 3.8 70.0 1.0
C C:PHE322 3.8 94.7 1.0
CG C:ASP318 3.9 0.9 1.0
C C:GLU323 4.1 0.3 1.0
OD2 C:ASP318 4.1 0.1 1.0
N C:PHE322 4.1 85.9 1.0
CG C:ASP320 4.3 71.4 1.0
N C:ASN325 4.4 0.2 1.0
OD2 C:ASP320 4.4 62.5 1.0
CA C:PHE322 4.5 87.6 1.0
O C:ASP320 4.5 83.2 1.0
O C:GLU323 4.5 0.6 1.0
N C:GLU323 4.7 0.0 1.0
C C:ASP320 4.8 84.0 1.0
CB C:PHE322 4.8 81.0 1.0
CA C:GLU323 4.8 0.5 1.0

Calcium binding site 3 out of 10 in 2hod

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Calcium binding site 3 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Hydroxypro-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-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2

b:60.2
occ:1.00
 OD2 E:ASP381 2.8 73.6 1.0
O E:TRP385 2.8 76.4 1.0
OD1 E:ASP381 2.9 68.1 1.0
OD1 E:ASP383 2.9 86.3 1.0
C E:TRP385 3.2 74.4 1.0
CG E:ASP381 3.2 71.3 1.0
N E:LEU386 3.5 79.4 1.0
CA E:LEU386 3.7 81.9 1.0
CG E:ASP383 3.7 76.6 1.0
OD2 E:ASP383 3.8 77.2 1.0
CA E:TRP385 4.0 70.5 1.0
N E:TRP385 4.1 63.9 1.0
N E:THR387 4.1 91.0 1.0
CB E:TRP385 4.2 62.8 1.0
CD2 E:LEU386 4.3 76.0 1.0
O E:ASP383 4.3 46.5 1.0
C E:LEU386 4.4 86.0 1.0
O E:LYS392 4.5 66.0 1.0
CB E:ASP381 4.6 63.0 1.0
C E:ASP383 4.8 56.2 1.0
OG1 E:THR387 4.8 0.1 1.0
CB E:LEU386 4.9 73.3 1.0
CG E:LEU386 5.0 75.1 1.0

Calcium binding site 4 out of 10 in 2hod

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Calcium binding site 4 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Hydroxypro-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-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1

b:64.2
occ:1.00
 OD1 F:ASP320 2.7 58.8 1.0
OD1 F:ASP318 2.8 65.6 1.0
O F:PHE322 2.9 89.5 1.0
CG F:ASP318 3.2 72.2 1.0
OD2 F:ASP318 3.3 76.9 1.0
O F:GLY324 3.4 74.2 1.0
CG F:ASP320 3.7 66.0 1.0
C F:PHE322 3.8 88.2 1.0
C F:GLU323 3.9 79.9 1.0
CA F:GLU323 3.9 79.6 1.0
OD2 F:ASP320 4.0 62.7 1.0
O F:GLU323 4.1 74.5 1.0
C F:GLY324 4.2 74.2 1.0
N F:GLU323 4.3 86.4 1.0
N F:GLY324 4.3 78.3 1.0
CB F:ASP318 4.4 70.2 1.0
O F:ASP320 4.4 72.2 1.0
N F:PHE322 4.7 86.6 1.0
C F:ASP320 4.9 72.3 1.0
CA F:GLY324 4.9 73.0 1.0
N F:ASP320 4.9 69.0 1.0
CA F:PHE322 5.0 88.2 1.0
CB F:ASP320 5.0 67.5 1.0
N F:ASN325 5.0 74.7 1.0

Calcium binding site 5 out of 10 in 2hod

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Calcium binding site 5 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Hydroxypro-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-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca2

b:87.8
occ:1.00
 O H:TRP385 2.6 74.3 1.0
OD1 H:ASP383 2.8 66.8 1.0
OD2 H:ASP381 2.9 52.1 1.0
OD1 H:ASP381 2.9 52.5 1.0
OD2 H:ASP383 3.2 52.0 1.0
CG H:ASP381 3.2 62.8 1.0
CG H:ASP383 3.4 73.3 1.0
C H:TRP385 3.6 78.0 1.0
N H:THR387 4.1 74.5 1.0
CA H:LEU386 4.1 72.0 1.0
N H:LEU386 4.3 75.0 1.0
O H:THR387 4.4 78.9 1.0
CD2 H:LEU386 4.6 57.7 1.0
CA H:TRP385 4.7 84.1 1.0
C H:LEU386 4.7 74.2 1.0
CB H:ASP381 4.7 73.5 1.0
N H:TRP385 4.9 80.1 1.0
CG H:GLN393 4.9 84.5 1.0
CB H:ASP383 4.9 74.1 1.0
O H:ASP381 5.0 82.1 1.0
CB H:TRP385 5.0 95.7 1.0

Calcium binding site 6 out of 10 in 2hod

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Calcium binding site 6 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Hydroxypro-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-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca1

b:69.4
occ:1.00
 O I:PHE322 2.9 91.2 1.0
O I:GLY324 2.9 96.6 1.0
OD1 I:ASP318 3.0 98.3 1.0
C I:GLY324 3.3 0.8 1.0
CA I:GLY324 3.3 0.8 1.0
N I:GLY324 3.4 0.7 1.0
OD1 I:ASP320 3.7 72.1 1.0
C I:PHE322 3.8 94.2 1.0
CG I:ASP318 3.8 0.4 1.0
OD2 I:ASP318 4.0 0.3 1.0
N I:PHE322 4.0 84.6 1.0
C I:GLU323 4.1 0.3 1.0
CG I:ASP320 4.2 71.3 1.0
OD2 I:ASP320 4.3 60.8 1.0
N I:ASN325 4.4 0.8 1.0
CA I:PHE322 4.4 86.8 1.0
O I:ASP320 4.4 83.3 1.0
O I:GLU323 4.6 0.3 1.0
N I:GLU323 4.6 0.2 1.0
CB I:PHE322 4.7 82.2 1.0
C I:ASP320 4.7 83.5 1.0
CA I:GLU323 4.8 0.9 1.0
N I:ASP320 5.0 81.6 1.0

Calcium binding site 7 out of 10 in 2hod

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Calcium binding site 7 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Hydroxypro-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-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca2

b:60.3
occ:1.00
 OD2 K:ASP381 2.8 73.1 1.0
OD1 K:ASP381 2.9 75.8 1.0
OD1 K:ASP383 2.9 85.5 1.0
O K:TRP385 2.9 76.9 1.0
CG K:ASP381 3.2 73.4 1.0
C K:TRP385 3.2 73.4 1.0
N K:LEU386 3.5 77.8 1.0
CA K:LEU386 3.7 78.6 1.0
CG K:ASP383 3.7 76.4 1.0
OD2 K:ASP383 3.9 71.8 1.0
CA K:TRP385 4.1 69.5 1.0
N K:THR387 4.1 88.4 1.0
N K:TRP385 4.1 62.4 1.0
CB K:TRP385 4.3 64.2 1.0
CD2 K:LEU386 4.3 74.6 1.0
C K:LEU386 4.4 82.7 1.0
O K:LYS392 4.4 63.1 1.0
O K:ASP383 4.4 47.2 1.0
CB K:ASP381 4.6 63.9 1.0
OG1 K:THR387 4.7 0.7 1.0
CB K:LEU386 4.9 70.3 1.0
C K:ASP383 4.9 53.7 1.0
CA K:GLN393 5.0 66.0 1.0
CG K:LEU386 5.0 71.4 1.0

Calcium binding site 8 out of 10 in 2hod

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Calcium binding site 8 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Hydroxypro-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-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1

b:62.4
occ:1.00
 OD1 L:ASP320 2.8 57.4 1.0
OD1 L:ASP318 2.8 64.8 1.0
O L:PHE322 2.9 91.6 1.0
CG L:ASP318 3.3 73.6 1.0
OD2 L:ASP318 3.5 79.5 1.0
O L:GLY324 3.6 71.6 1.0
CG L:ASP320 3.8 63.3 1.0
C L:PHE322 3.8 88.8 1.0
CA L:GLU323 4.0 77.5 1.0
C L:GLU323 4.0 76.1 1.0
OD2 L:ASP320 4.2 56.5 1.0
O L:GLU323 4.3 71.3 1.0
O L:ASP320 4.3 63.1 1.0
N L:GLU323 4.3 83.5 1.0
CB L:ASP318 4.4 71.1 1.0
N L:GLY324 4.5 74.2 1.0
C L:GLY324 4.5 73.2 1.0
N L:PHE322 4.6 89.0 1.0
C L:ASP320 4.7 67.1 1.0
N L:ASP320 4.8 64.5 1.0
CA L:PHE322 4.9 90.1 1.0
CB L:ASP320 5.0 63.6 1.0

Calcium binding site 9 out of 10 in 2hod

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Calcium binding site 9 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Hydroxypro-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-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca3

b:88.4
occ:1.00
 OE2 F:GLU132 2.9 76.4 1.0
O E:GLY263 3.1 38.0 1.0
CD F:GLU132 3.1 70.5 1.0
OD2 E:ASP261 3.4 65.0 1.0
OH E:TYR378 3.5 69.1 1.0
OE1 F:GLU132 3.5 75.5 1.0
CG F:GLU132 3.8 56.0 1.0
C E:GLY263 4.3 32.4 1.0
CZ E:TYR378 4.3 62.8 1.0
CE2 E:TYR378 4.3 56.3 1.0
CG E:ASP261 4.4 58.7 1.0
OE1 F:GLN136 4.6 37.8 1.0
OD1 E:ASP261 4.7 59.6 1.0
CA E:ARG264 4.8 38.7 1.0

Calcium binding site 10 out of 10 in 2hod

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Calcium binding site 10 out of 10 in the Crystal Structure of Fragment D From Human Fibrinogen Complexed with Gly-Hydroxypro-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-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca3

b:94.3
occ:1.00
 O K:GLY263 3.0 38.1 1.0
OE2 L:GLU132 3.0 69.8 1.0
OD2 K:ASP261 3.1 66.2 1.0
CD L:GLU132 3.1 66.9 1.0
CG L:GLU132 3.6 63.8 1.0
OH K:TYR378 3.6 62.7 1.0
OE1 L:GLU132 3.7 62.0 1.0
C K:GLY263 4.1 32.4 1.0
CG K:ASP261 4.1 60.9 1.0
CE2 K:TYR378 4.3 56.2 1.0
CZ K:TYR378 4.4 59.7 1.0
OD1 K:ASP261 4.4 68.6 1.0
OE1 L:GLN136 4.5 40.2 1.0
CA K:ARG264 4.7 34.2 1.0
NE2 L:GLN136 4.8 44.3 1.0
N K:ARG264 4.9 24.1 1.0
CD L:GLN136 5.0 43.7 1.0

Reference:

R.F.Doolittle, J.M.Kollman, A.Chen, L.Pandi. N/A N/A.
Page generated: Tue Jul 8 06:00:22 2025

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