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

Protein crystallography data

The structure of Crystal Structure of Fragment D-Dimer From Human Fibrin Complexed with Gly-Hydroxypro-Arg-Pro-Amide, PDB code: 2hlo 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 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.690, 149.480, 232.930, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fragment D-Dimer From Human Fibrin Complexed with Gly-Hydroxypro-Arg-Pro-Amide (pdb code 2hlo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Fragment D-Dimer From Human Fibrin Complexed with Gly-Hydroxypro-Arg-Pro-Amide, PDB code: 2hlo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2hlo

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Calcium binding site 1 out of 7 in the Crystal Structure of Fragment D-Dimer From Human Fibrin 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 1 of Crystal Structure of Fragment D-Dimer From Human Fibrin Complexed with Gly-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:56.6
occ:1.00
 OD1 B:ASP381 2.8 49.5 1.0
O B:TRP385 2.8 68.8 1.0
OD1 B:ASP383 2.9 50.8 1.0
OD2 B:ASP381 2.9 65.4 1.0
O B:HOH520 2.9 34.1 1.0
CG B:ASP381 3.1 54.4 1.0
CG B:ASP383 3.5 47.0 1.0
OD2 B:ASP383 3.5 46.0 1.0
C B:TRP385 3.7 65.7 1.0
CB B:TRP385 4.4 64.6 1.0
CA B:TRP385 4.5 62.3 1.0
O B:LYS392 4.5 90.8 1.0
CB B:ASP381 4.5 46.0 1.0
N B:LEU386 4.6 73.9 1.0
O B:ASP383 4.6 38.2 1.0
N B:TRP385 4.6 57.4 1.0
CA B:LEU386 4.7 79.9 1.0
N B:THR387 4.7 97.0 1.0
CB B:ASP383 4.8 36.6 1.0
N B:ASP383 4.8 28.8 1.0
CG2 B:THR387 4.9 0.0 1.0
O B:THR387 4.9 0.8 1.0
C B:ASP383 5.0 38.8 1.0

Calcium binding site 2 out of 7 in 2hlo

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Calcium binding site 2 out of 7 in the Crystal Structure of Fragment D-Dimer From Human Fibrin 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 2 of Crystal Structure of Fragment D-Dimer From Human Fibrin Complexed with Gly-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:53.1
occ:1.00
 OD1 B:ASP398 2.7 48.9 1.0
O B:GLY263 2.7 37.9 1.0
OE2 C:GLU132 2.8 64.0 1.0
OD2 B:ASP261 2.8 57.7 1.0
O C:HOH439 2.8 50.8 1.0
OD1 B:ASP261 3.1 50.6 1.0
CD C:GLU132 3.3 68.6 1.0
CG B:ASP261 3.3 47.7 1.0
C B:GLY263 3.6 28.2 1.0
OE1 C:GLU132 3.7 71.9 1.0
CG B:ASP398 3.7 75.8 1.0
CA B:GLY263 3.9 25.2 1.0
CG C:GLU132 4.2 71.5 1.0
N B:GLY263 4.3 27.4 1.0
CA B:ASP398 4.3 64.9 1.0
CB B:ASP398 4.4 69.6 1.0
OD2 B:ASP398 4.6 85.1 1.0
N B:ARG264 4.8 32.5 1.0
CB B:ASP261 4.8 38.0 1.0
OE1 C:GLN136 4.9 37.1 1.0
OH B:TYR378 5.0 45.1 1.0

Calcium binding site 3 out of 7 in 2hlo

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Calcium binding site 3 out of 7 in the Crystal Structure of Fragment D-Dimer From Human Fibrin 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-Dimer From Human Fibrin Complexed with Gly-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:61.2
occ:1.00
 O C:GLY324 2.7 47.1 1.0
O C:PHE322 2.7 54.3 1.0
OD2 C:ASP320 2.8 54.7 1.0
OD1 C:ASP318 2.9 59.3 1.0
OD2 C:ASP318 2.9 68.5 1.0
CG C:ASP318 3.1 62.4 1.0
CG C:ASP320 3.6 43.4 1.0
C C:PHE322 3.6 47.7 1.0
OD1 C:ASP320 3.9 49.0 1.0
C C:GLY324 3.9 53.9 1.0
C C:GLU323 4.0 47.7 1.0
O C:GLU323 4.1 47.3 1.0
N C:GLY324 4.3 51.7 1.0
CA C:GLU323 4.3 44.9 1.0
O C:ASP320 4.4 48.2 1.0
CB C:ASP318 4.4 59.0 1.0
N C:GLU323 4.4 46.4 1.0
N C:PHE322 4.4 48.9 1.0
CA C:PHE322 4.5 47.8 1.0
CA C:GLY324 4.6 46.9 1.0
C C:ASP320 4.7 46.0 1.0
CB C:PHE322 4.8 44.1 1.0
N C:ASP320 4.8 43.2 1.0
N C:ASN325 4.8 52.4 1.0
CA C:ASN325 4.9 45.7 1.0
CB C:ASP320 4.9 35.9 1.0

Calcium binding site 4 out of 7 in 2hlo

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Calcium binding site 4 out of 7 in the Crystal Structure of Fragment D-Dimer From Human Fibrin 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-Dimer From Human Fibrin Complexed with Gly-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4

b:55.6
occ:1.00
 OD2 C:ASP294 2.7 67.7 1.0
O C:ASP298 2.7 40.8 1.0
OD2 C:ASP301 2.7 60.7 1.0
O C:GLY296 2.7 38.3 1.0
CG C:ASP294 3.0 62.5 1.0
OD1 C:ASP294 3.2 53.9 1.0
O C:HOH446 3.6 77.1 1.0
CG C:ASP301 3.7 58.0 1.0
C C:ASP298 3.8 57.9 1.0
C C:GLY296 3.9 42.4 1.0
CB C:ASP294 4.1 52.2 1.0
CB C:ASP301 4.1 52.4 1.0
CA C:ASP294 4.4 46.7 1.0
CA C:PRO299 4.4 52.7 1.0
O C:ASP297 4.4 48.9 1.0
N C:GLY296 4.5 42.4 1.0
C C:ASP297 4.5 52.0 1.0
N C:PRO299 4.5 55.4 1.0
N C:ASP301 4.6 57.0 1.0
N C:ASP298 4.6 51.1 1.0
C C:PRO299 4.6 53.7 1.0
CA C:GLY296 4.7 36.3 1.0
C C:ASP294 4.7 33.5 1.0
OD1 C:ASP301 4.8 76.8 1.0
CA C:ASP298 4.8 58.0 1.0
N C:ASP297 4.9 45.4 1.0
N C:SER300 4.9 51.3 1.0
N C:PHE295 5.0 30.2 1.0
CA C:ASP301 5.0 54.6 1.0

Calcium binding site 5 out of 7 in 2hlo

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Calcium binding site 5 out of 7 in the Crystal Structure of Fragment D-Dimer From Human Fibrin 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-Dimer From Human Fibrin Complexed with Gly-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2

b:58.5
occ:1.00
 OD1 E:ASP383 2.7 43.8 1.0
OD2 E:ASP381 2.8 62.7 1.0
O E:TRP385 2.8 83.4 1.0
OD1 E:ASP381 3.0 54.2 1.0
CG E:ASP381 3.2 54.0 1.0
CG E:ASP383 3.5 41.2 1.0
C E:TRP385 3.6 76.6 1.0
OD2 E:ASP383 3.6 61.3 1.0
CB E:TRP385 3.9 84.5 1.0
CA E:TRP385 4.2 73.0 1.0
CG2 E:THR387 4.2 95.0 1.0
O E:LYS392 4.2 0.6 1.0
N E:TRP385 4.3 64.7 1.0
N E:LEU386 4.4 85.4 1.0
N E:THR387 4.5 0.4 1.0
CB E:ASP381 4.6 40.1 1.0
CA E:LEU386 4.7 91.7 1.0
O E:ASP383 4.7 50.6 1.0
CB E:ASP383 4.8 30.8 1.0
N E:ASP383 4.9 40.5 1.0
CG E:TRP385 4.9 0.3 1.0
C E:ASP383 4.9 40.0 1.0

Calcium binding site 6 out of 7 in 2hlo

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Calcium binding site 6 out of 7 in the Crystal Structure of Fragment D-Dimer From Human Fibrin 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-Dimer From Human Fibrin Complexed with Gly-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca3

b:47.4
occ:1.00
 O E:GLY263 2.7 31.6 1.0
OD2 E:ASP261 2.7 37.9 1.0
OD2 E:ASP398 2.7 54.7 1.0
OE1 F:GLU132 2.8 72.9 1.0
OD1 E:ASP261 3.1 41.6 1.0
CG E:ASP261 3.2 27.2 1.0
C E:GLY263 3.6 35.9 1.0
CG E:ASP398 3.8 40.1 1.0
CD F:GLU132 3.9 74.6 1.0
CA E:GLY263 4.0 31.5 1.0
OE1 F:GLN136 4.1 44.1 1.0
N E:GLY263 4.4 35.7 1.0
CG F:GLU132 4.5 68.5 1.0
CA E:ASP398 4.5 44.7 1.0
OD1 E:ASP398 4.6 63.0 1.0
CB E:ASP261 4.7 30.9 1.0
OE2 F:GLU132 4.7 85.8 1.0
CB E:ASP398 4.7 40.5 1.0
N E:ARG264 4.8 38.2 1.0
CD F:GLN136 5.0 34.6 1.0

Calcium binding site 7 out of 7 in 2hlo

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Calcium binding site 7 out of 7 in the Crystal Structure of Fragment D-Dimer From Human Fibrin 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-Dimer From Human Fibrin Complexed with Gly-Hydroxypro-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1

b:44.5
occ:1.00
 O F:PHE322 2.5 32.8 1.0
OD2 F:ASP318 2.6 35.3 1.0
OD2 F:ASP320 2.6 45.1 1.0
O F:GLY324 2.6 30.4 1.0
OD1 F:ASP318 2.8 36.8 1.0
CG F:ASP318 3.0 35.6 1.0
CG F:ASP320 3.5 41.3 1.0
C F:PHE322 3.7 36.3 1.0
OD1 F:ASP320 3.8 30.6 1.0
C F:GLY324 3.8 37.0 1.0
O F:ASP320 3.9 45.7 1.0
O F:GLU323 4.2 42.3 1.0
N F:PHE322 4.2 35.4 1.0
C F:GLU323 4.2 44.9 1.0
CB F:ASP318 4.3 28.9 1.0
CA F:PHE322 4.4 35.2 1.0
C F:ASP320 4.4 40.7 1.0
N F:GLY324 4.5 43.1 1.0
N F:ASP320 4.6 28.2 1.0
N F:GLU323 4.6 40.3 1.0
CA F:ASN325 4.6 34.2 1.0
CB F:PHE322 4.6 23.9 1.0
CA F:GLU323 4.7 39.6 1.0
N F:ASN325 4.7 35.8 1.0
CB F:ASP320 4.7 28.5 1.0
CA F:GLY324 4.8 30.9 1.0
CA F:ASP320 4.8 32.2 1.0

Reference:

R.F.Doolittle, J.M.Kollman, A.Chen, L.Pandi. N/A N/A.
Page generated: Tue Jul 8 05:59:28 2025

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