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Calcium in PDB 2q9i: Crystal Structure of D-Dimer From Human Fibrin Complexed with Met-His- Arg-Pro-Tyr-Amide.

Protein crystallography data

The structure of Crystal Structure of D-Dimer From Human Fibrin Complexed with Met-His- Arg-Pro-Tyr-Amide., PDB code: 2q9i 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 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.380, 147.230, 231.480, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 27.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Met-His- Arg-Pro-Tyr-Amide. (pdb code 2q9i). 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 Met-His- Arg-Pro-Tyr-Amide., PDB code: 2q9i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2q9i

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Calcium binding site 1 out of 8 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Met-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 Met-His- Arg-Pro-Tyr-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:58.6
occ:1.00
 O C:PHE322 2.5 68.0 1.0
OD2 C:ASP320 2.7 51.2 1.0
O C:GLY324 2.7 63.3 1.0
OD2 C:ASP318 2.8 67.4 1.0
OD1 C:ASP318 2.9 67.4 1.0
CG C:ASP318 3.0 67.4 1.0
C C:PHE322 3.7 68.0 1.0
C C:GLY324 3.8 63.3 1.0
CG C:ASP320 3.8 51.2 1.0
C C:GLU323 3.9 78.4 1.0
O C:GLU323 4.0 78.4 1.0
O C:ASP320 4.1 46.8 1.0
N C:GLY324 4.1 63.3 1.0
OD1 C:ASP320 4.3 51.2 1.0
CA C:GLU323 4.3 78.4 1.0
CB C:ASP318 4.3 67.4 1.0
CA C:GLY324 4.4 63.3 1.0
N C:GLU323 4.5 78.4 1.0
N C:PHE322 4.6 68.0 1.0
C C:ASP320 4.7 46.8 1.0
CA C:PHE322 4.7 68.0 1.0
N C:ASN325 4.8 49.4 1.0
N C:ASP320 4.8 46.8 1.0
CA C:ASN325 4.9 49.4 1.0

Calcium binding site 2 out of 8 in 2q9i

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

b:58.6
occ:1.00
 OD2 B:ASP381 2.6 61.6 1.0
O B:TRP385 2.7 63.9 1.0
OD1 B:ASP383 2.8 57.8 1.0
OD1 B:ASP381 2.9 61.6 1.0
CG B:ASP381 3.1 61.6 1.0
C B:TRP385 3.4 63.9 1.0
O B:ASP383 3.7 66.6 1.0
CG B:ASP383 3.7 57.8 1.0
OD2 B:ASP383 4.1 57.8 1.0
CB B:TRP385 4.1 53.1 1.0
CA B:TRP385 4.1 63.9 1.0
N B:TRP385 4.1 63.9 1.0
N B:LEU386 4.2 76.2 1.0
N B:THR387 4.4 84.5 1.0
O B:LYS392 4.4 67.5 1.0
CG2 B:THR387 4.4 71.0 1.0
CA B:LEU386 4.4 76.2 1.0
C B:ASP383 4.5 66.6 1.0
O B:THR387 4.6 84.5 1.0
CB B:ASP381 4.6 61.6 1.0
N B:ASP383 4.8 66.6 1.0
CB B:ASP383 4.9 57.8 1.0
C B:LEU386 4.9 76.2 1.0
CA B:GLN393 4.9 82.2 1.0
CG B:TRP385 4.9 53.1 1.0
CA B:ASP383 5.0 66.6 1.0

Calcium binding site 3 out of 8 in 2q9i

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

b:58.6
occ:1.00
 O B:GLY263 2.9 62.6 1.0
OD2 B:ASP261 3.3 58.5 1.0
CD C:GLU132 3.4 82.0 1.0
OE2 C:GLU132 3.5 82.0 1.0
OE1 C:GLU132 3.5 82.0 1.0
OD1 B:ASP261 3.9 58.5 1.0
CG C:GLU132 3.9 82.0 1.0
CG B:ASP261 4.0 58.5 1.0
C B:GLY263 4.0 62.6 1.0
CA B:GLY263 4.6 62.6 1.0
OE1 C:GLN136 4.7 57.8 1.0
CE2 B:TYR378 4.8 85.8 1.0

Calcium binding site 4 out of 8 in 2q9i

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

b:58.6
occ:1.00
 OD2 C:ASP294 2.5 71.8 1.0
OD2 C:ASP301 2.7 73.0 1.0
O C:ASP298 2.8 87.8 1.0
CG C:ASP301 3.4 73.0 1.0
CG C:ASP294 3.4 71.8 1.0
CB C:ASP301 3.4 73.0 1.0
N C:GLY296 3.7 71.1 1.0
C C:ASP298 3.7 87.8 1.0
CA C:PRO299 3.8 50.5 1.0
OD1 C:ASP294 3.9 71.8 1.0
C C:GLY296 3.9 71.1 1.0
CA C:GLY296 4.0 71.1 1.0
O C:ASP297 4.0 98.5 1.0
O C:GLY296 4.2 71.1 1.0
N C:PRO299 4.2 50.5 1.0
N C:ASP301 4.2 57.3 1.0
C C:PRO299 4.3 50.5 1.0
N C:ASP297 4.3 98.5 1.0
C C:ASP297 4.3 98.5 1.0
N C:PHE295 4.4 63.1 1.0
CA C:ASP294 4.4 58.7 1.0
CB C:ASP294 4.4 71.8 1.0
OD1 C:ASP301 4.5 73.0 1.0
CA C:ASP301 4.5 57.3 1.0
C C:ASP294 4.6 58.7 1.0
N C:ASP298 4.7 87.8 1.0
N C:SER300 4.7 58.8 1.0
O C:PRO299 4.8 50.5 1.0
C C:PHE295 4.8 63.1 1.0
CA C:ASP298 4.9 87.8 1.0
N C:LYS302 5.0 64.4 1.0
CA C:ASP297 5.0 98.5 1.0

Calcium binding site 5 out of 8 in 2q9i

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

b:58.6
occ:1.00
 O F:PHE322 2.4 55.9 1.0
OD2 F:ASP320 2.6 55.8 1.0
O F:GLY324 2.7 61.5 1.0
OD2 F:ASP318 2.7 50.9 1.0
OD1 F:ASP318 2.8 50.9 1.0
CG F:ASP318 3.0 50.9 1.0
C F:PHE322 3.6 55.9 1.0
CG F:ASP320 3.7 55.8 1.0
C F:GLY324 3.8 61.5 1.0
C F:GLU323 3.9 61.1 1.0
O F:ASP320 4.0 57.4 1.0
O F:GLU323 4.0 61.1 1.0
N F:GLY324 4.1 61.5 1.0
OD1 F:ASP320 4.1 55.8 1.0
CB F:ASP318 4.3 50.9 1.0
CA F:GLU323 4.3 61.1 1.0
N F:GLU323 4.4 61.1 1.0
N F:PHE322 4.5 55.9 1.0
CA F:GLY324 4.5 61.5 1.0
C F:ASP320 4.6 57.4 1.0
CA F:PHE322 4.6 55.9 1.0
N F:ASP320 4.7 57.4 1.0
N F:ASN325 4.8 52.7 1.0
CA F:ASN325 4.9 52.7 1.0
CB F:ASP320 4.9 55.8 1.0
CA F:ASP320 5.0 57.4 1.0

Calcium binding site 6 out of 8 in 2q9i

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

b:58.6
occ:1.00
 O E:TRP385 2.7 67.8 1.0
OD2 E:ASP381 2.8 53.6 1.0
OD1 E:ASP381 2.9 53.6 1.0
OD1 E:ASP383 2.9 78.8 1.0
CG E:ASP381 3.2 53.6 1.0
O E:ASP383 3.4 64.6 1.0
C E:TRP385 3.4 67.8 1.0
CG E:ASP383 3.9 78.8 1.0
N E:LEU386 4.0 71.0 1.0
N E:TRP385 4.1 67.8 1.0
CA E:LEU386 4.1 71.0 1.0
CA E:TRP385 4.2 67.8 1.0
N E:THR387 4.3 76.7 1.0
C E:ASP383 4.3 64.6 1.0
OD2 E:ASP383 4.3 78.8 1.0
CB E:TRP385 4.5 78.7 1.0
CB E:ASP381 4.6 53.6 1.0
O E:THR387 4.7 76.7 1.0
N E:ASP383 4.7 64.6 1.0
C E:LEU386 4.7 71.0 1.0
CD2 E:LEU386 4.8 82.7 1.0
CG2 E:THR387 4.8 79.0 1.0
CA E:ASP383 4.9 64.6 1.0
CB E:ASP383 5.0 78.8 1.0

Calcium binding site 7 out of 8 in 2q9i

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

b:58.6
occ:1.00
 OE1 F:GLU132 2.8 71.4 1.0
O E:GLY263 3.1 56.3 1.0
OD2 E:ASP261 3.3 62.8 1.0
OD1 E:ASP261 3.6 62.8 1.0
CG E:ASP261 3.9 62.8 1.0
CD F:GLU132 4.0 71.4 1.0
C E:GLY263 4.1 56.3 1.0
CA E:GLY263 4.4 56.3 1.0
CG F:GLU132 4.6 71.4 1.0
N E:GLY263 4.9 56.3 1.0
OE2 F:GLU132 4.9 71.4 1.0

Calcium binding site 8 out of 8 in 2q9i

Go back to Calcium Binding Sites List in 2q9i
Calcium binding site 8 out of 8 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Met-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 Met-His- Arg-Pro-Tyr-Amide. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca4

b:58.6
occ:1.00
 OD2 F:ASP294 3.1 87.6 1.0
O F:ASP298 3.5 58.5 1.0
CA F:PRO299 3.6 66.4 1.0
O F:ASP297 3.6 99.1 1.0
CG F:ASP294 3.9 87.6 1.0
OD1 F:ASP294 3.9 87.6 1.0
C F:ASP298 3.9 58.5 1.0
O F:GLY296 4.0 77.3 1.0
N F:PRO299 4.0 66.4 1.0
C F:GLY296 4.1 77.3 1.0
OD2 F:ASP301 4.1 75.9 1.0
CA F:GLY296 4.3 77.3 1.0
C F:ASP297 4.4 99.1 1.0
N F:GLY296 4.4 77.3 1.0
CB F:PRO299 4.5 62.1 1.0
C F:PRO299 4.5 66.4 1.0
N F:ASP297 4.6 99.1 1.0
CG F:ASP301 4.9 75.9 1.0
O F:PRO299 5.0 66.4 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: Tue Jul 8 07:52:57 2025

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