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Calcium in PDB 2z4e: Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide

Protein crystallography data

The structure of Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide, PDB code: 2z4e was solved by R.F.Doolittle, L.Pandi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.630, 148.690, 232.680, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 27.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide (pdb code 2z4e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide, PDB code: 2z4e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2z4e

Go back to Calcium Binding Sites List in 2z4e
Calcium binding site 1 out of 8 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:34.9
occ:1.00
 OD2 C:ASP320 2.5 30.3 1.0
O C:PHE322 2.6 35.9 1.0
O C:GLY324 2.7 37.4 1.0
OD2 C:ASP318 2.8 38.0 1.0
OD1 C:ASP318 3.0 38.0 1.0
CG C:ASP318 3.1 38.0 1.0
C C:PHE322 3.5 35.9 1.0
CG C:ASP320 3.6 30.3 1.0
C C:GLY324 3.8 37.4 1.0
OD1 C:ASP320 4.0 30.3 1.0
C C:GLU323 4.0 32.9 1.0
O C:GLU323 4.2 32.9 1.0
N C:GLY324 4.2 37.4 1.0
N C:PHE322 4.3 35.9 1.0
N C:GLU323 4.3 32.9 1.0
CA C:PHE322 4.3 35.9 1.0
O C:ASP320 4.4 29.4 1.0
CB C:ASP318 4.4 38.0 1.0
CA C:GLU323 4.4 32.9 1.0
CB C:PHE322 4.4 33.7 1.0
CA C:GLY324 4.6 37.4 1.0
C C:ASP320 4.7 29.4 1.0
N C:ASN325 4.7 29.8 1.0
N C:ASP320 4.7 29.4 1.0
CA C:ASN325 4.8 29.8 1.0
CB C:ASP320 4.9 30.3 1.0

Calcium binding site 2 out of 8 in 2z4e

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Calcium binding site 2 out of 8 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:34.9
occ:1.00
 OD2 B:ASP381 2.7 40.6 1.0
OD1 B:ASP383 2.7 32.7 1.0
OD1 B:ASP381 2.8 40.6 1.0
O B:TRP385 2.8 42.8 1.0
CG B:ASP381 3.1 40.6 1.0
C B:TRP385 3.6 42.8 1.0
CG B:ASP383 3.7 32.7 1.0
OD2 B:ASP383 4.0 32.7 1.0
CB B:TRP385 4.3 34.4 1.0
CA B:TRP385 4.4 42.8 1.0
O B:LYS392 4.4 43.9 1.0
N B:THR387 4.4 41.2 1.0
O B:THR387 4.4 41.2 1.0
N B:LEU386 4.4 37.6 1.0
O B:ASP383 4.4 31.0 1.0
N B:TRP385 4.4 42.8 1.0
CG2 B:THR387 4.5 51.9 1.0
CB B:ASP381 4.5 40.6 1.0
CA B:LEU386 4.6 37.6 1.0
CG B:GLN393 4.7 36.5 1.0
N B:ASP383 4.9 31.0 1.0
C B:ASP383 4.9 31.0 1.0
CA B:GLN393 4.9 32.5 1.0
NE2 B:GLN393 5.0 36.5 1.0
C B:LEU386 5.0 37.6 1.0
CB B:ASP383 5.0 32.7 1.0

Calcium binding site 3 out of 8 in 2z4e

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Calcium binding site 3 out of 8 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:34.9
occ:1.00
 O B:GLY263 2.9 32.7 1.0
OD2 B:ASP261 3.1 28.3 1.0
OE2 C:GLU132 3.2 66.6 1.0
CD C:GLU132 3.3 66.6 1.0
OE1 C:GLN136 3.6 29.6 1.0
CG C:GLU132 3.7 66.6 1.0
OE1 C:GLU132 3.8 66.6 1.0
C B:GLY263 4.0 32.7 1.0
CG B:ASP261 4.1 28.3 1.0
OD1 B:ASP261 4.3 28.3 1.0
CD C:GLN136 4.4 29.6 1.0
NE2 C:GLN136 4.7 29.6 1.0
CA B:GLY263 4.8 32.7 1.0
OH B:TYR378 4.9 43.2 1.0
CE2 B:TYR378 4.9 43.2 1.0

Calcium binding site 4 out of 8 in 2z4e

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Calcium binding site 4 out of 8 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4

b:34.9
occ:1.00
 OD2 C:ASP294 2.7 38.5 1.0
O C:ASP298 2.9 47.5 1.0
OD2 C:ASP301 3.0 39.4 1.0
CG C:ASP294 3.4 38.5 1.0
CB C:ASP301 3.4 39.4 1.0
CG C:ASP301 3.5 39.4 1.0
O C:GLY296 3.6 45.3 1.0
C C:GLY296 3.8 45.3 1.0
OD1 C:ASP294 3.8 38.5 1.0
C C:ASP298 3.8 47.5 1.0
N C:GLY296 3.8 45.3 1.0
CA C:PRO299 3.9 32.1 1.0
CA C:GLY296 3.9 45.3 1.0
N C:PRO299 4.2 32.1 1.0
C C:PRO299 4.3 32.1 1.0
CA C:ASP294 4.3 33.7 1.0
CB C:ASP294 4.4 38.5 1.0
N C:ASP301 4.4 44.1 1.0
O C:PRO299 4.5 32.1 1.0
CA C:ASP301 4.5 44.1 1.0
N C:ASP297 4.5 95.6 1.0
C C:ASP294 4.6 33.7 1.0
OD1 C:ASP301 4.6 39.4 1.0
N C:PHE295 4.7 35.3 1.0
N C:ASP298 4.7 47.5 1.0
C C:ASP297 4.7 95.6 1.0
CA C:ASP298 4.9 47.5 1.0
O C:ASP297 4.9 95.6 1.0
N C:LYS302 5.0 29.4 1.0

Calcium binding site 5 out of 8 in 2z4e

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Calcium binding site 5 out of 8 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1

b:34.9
occ:1.00
 O F:PHE322 2.3 32.2 1.0
OD2 F:ASP320 2.5 37.4 1.0
O F:GLY324 2.7 26.4 1.0
OD2 F:ASP318 2.7 35.6 1.0
OD1 F:ASP318 2.8 35.6 1.0
CG F:ASP318 3.0 35.6 1.0
C F:PHE322 3.5 32.2 1.0
CG F:ASP320 3.6 37.4 1.0
C F:GLY324 3.8 26.4 1.0
OD1 F:ASP320 4.0 37.4 1.0
C F:GLU323 4.0 34.4 1.0
O F:GLU323 4.1 34.4 1.0
N F:PHE322 4.3 32.2 1.0
N F:GLY324 4.3 26.4 1.0
CB F:ASP318 4.3 35.6 1.0
CA F:PHE322 4.4 32.2 1.0
O F:ASP320 4.4 33.1 1.0
N F:GLU323 4.4 34.4 1.0
CA F:GLU323 4.4 34.4 1.0
CB F:PHE322 4.6 24.7 1.0
CA F:GLY324 4.6 26.4 1.0
N F:ASN325 4.7 29.8 1.0
N F:ASP320 4.7 33.1 1.0
C F:ASP320 4.7 33.1 1.0
CA F:ASN325 4.7 29.8 1.0
CB F:ASP320 4.9 37.4 1.0
CA F:ASP320 5.0 33.1 1.0

Calcium binding site 6 out of 8 in 2z4e

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Calcium binding site 6 out of 8 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2

b:34.9
occ:1.00
 OD2 E:ASP381 2.7 42.5 1.0
OD1 E:ASP383 2.8 51.6 1.0
O E:TRP385 2.8 48.0 1.0
OD1 E:ASP381 2.9 42.5 1.0
CG E:ASP381 3.2 42.5 1.0
C E:TRP385 3.4 48.0 1.0
O E:ASP383 3.5 43.7 1.0
CG E:ASP383 3.8 51.6 1.0
N E:LEU386 3.9 58.7 1.0
CA E:LEU386 4.0 58.7 1.0
N E:TRP385 4.1 48.0 1.0
CA E:TRP385 4.2 48.0 1.0
OD2 E:ASP383 4.2 51.6 1.0
N E:THR387 4.3 76.6 1.0
C E:ASP383 4.4 43.7 1.0
CB E:TRP385 4.4 71.1 1.0
N E:ASP383 4.6 43.7 1.0
CB E:ASP381 4.7 42.5 1.0
C E:LEU386 4.7 58.7 1.0
O E:THR387 4.7 76.6 1.0
CD2 E:LEU386 4.8 80.0 1.0
CG2 E:THR387 4.8 83.4 1.0
CA E:ASP383 4.9 43.7 1.0
CB E:ASP383 4.9 51.6 1.0

Calcium binding site 7 out of 8 in 2z4e

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Calcium binding site 7 out of 8 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca3

b:34.9
occ:1.00
 O E:GLY263 2.7 31.4 1.0
OD2 E:ASP261 2.7 41.0 1.0
OE1 F:GLU132 3.0 48.1 1.0
OD1 E:ASP261 3.5 41.0 1.0
CG E:ASP261 3.5 41.0 1.0
C E:GLY263 3.7 31.4 1.0
CD F:GLU132 3.9 48.1 1.0
OE1 F:GLN136 4.2 28.0 1.0
CA E:GLY263 4.2 31.4 1.0
CG F:GLU132 4.3 48.1 1.0
N E:GLY263 4.6 31.4 1.0
OE2 F:GLU132 4.7 48.1 1.0
N E:ARG264 4.8 41.9 1.0
CB E:ASP261 4.9 41.0 1.0

Calcium binding site 8 out of 8 in 2z4e

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Calcium binding site 8 out of 8 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca4

b:34.9
occ:1.00
 OD2 F:ASP294 2.9 75.4 1.0
O F:ASP298 2.9 28.9 1.0
CA F:GLY296 3.4 39.1 1.0
N F:GLY296 3.4 39.1 1.0
CG F:ASP294 3.5 75.4 1.0
C F:ASP298 3.6 28.9 1.0
OD2 F:ASP301 3.7 43.7 1.0
OD1 F:ASP294 3.8 75.4 1.0
CA F:PRO299 3.8 49.1 1.0
C F:GLY296 3.8 39.1 1.0
N F:PRO299 4.0 49.1 1.0
CB F:ASP301 4.1 43.7 1.0
CG F:ASP301 4.2 43.7 1.0
N F:ASP297 4.2 54.9 1.0
N F:ASP298 4.3 28.9 1.0
C F:PRO299 4.3 49.1 1.0
O F:GLY296 4.4 39.1 1.0
O F:PRO299 4.4 49.1 1.0
CB F:ASP294 4.6 75.4 1.0
CA F:ASP294 4.6 40.0 1.0
C F:ASP294 4.6 40.0 1.0
CA F:ASP298 4.6 28.9 1.0
N F:PHE295 4.7 40.2 1.0
C F:PHE295 4.7 40.2 1.0
N F:ASP301 4.8 36.9 1.0
C F:ASP297 5.0 54.9 1.0

Reference:

R.F.Doolittle, L.Pandi. Probing the Beta-Chain Hole of Fibrinogen with Synthetic Peptides That Differ at Their Amino Termini Biochemistry V. 46 10033 2007.
ISSN: ISSN 0006-2960
PubMed: 17688324
DOI: 10.1021/BI7010916
Page generated: Fri Jul 12 19:44:05 2024

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