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Calcium in PDB 1re3: Crystal Structure of Fragment D of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide

Protein crystallography data

The structure of Crystal Structure of Fragment D of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 1re3 was solved by M.S.Kostelansky, L.Betts, O.V.Gorkun, S.T.Lord, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.98 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.514, 147.665, 229.716, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 26.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fragment D of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide (pdb code 1re3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Fragment D of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 1re3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 1re3

Go back to Calcium Binding Sites List in 1re3
Calcium binding site 1 out of 5 in the Crystal Structure of Fragment D of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-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 of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca472

b:44.8
occ:1.00
 OD1 B:ASP383 2.3 42.1 1.0
O B:HOH523 2.4 41.2 1.0
OD2 B:ASP381 2.5 44.1 1.0
OD1 B:ASP381 2.6 45.2 1.0
O B:TRP385 2.7 68.0 1.0
CG B:ASP381 2.9 43.2 1.0
CG B:ASP383 3.3 40.8 1.0
OD2 B:ASP383 3.6 38.5 1.0
C B:TRP385 3.6 68.3 1.0
O B:ASP383 4.2 43.5 1.0
N B:ASP383 4.4 39.0 1.0
CB B:ASP381 4.4 41.6 1.0
N B:LEU386 4.4 71.5 1.0
CA B:LEU386 4.5 74.5 1.0
CA B:TRP385 4.5 66.5 1.0
N B:TRP385 4.5 62.3 1.0
CB B:ASP383 4.6 41.2 1.0
C B:ASP383 4.6 43.6 1.0
CB B:TRP385 4.7 68.7 1.0
CA B:ASP383 4.7 41.4 1.0
O B:ASP381 4.9 38.7 1.0
C B:ASP381 5.0 38.6 1.0

Calcium binding site 2 out of 5 in 1re3

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Calcium binding site 2 out of 5 in the Crystal Structure of Fragment D of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-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 of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca407

b:32.6
occ:1.00
 O C:GLY324 2.3 29.8 1.0
O C:HOH448 2.3 23.6 1.0
O C:PHE322 2.4 34.2 1.0
OD2 C:ASP318 2.5 33.0 1.0
OD1 C:ASP320 2.5 31.4 1.0
OD1 C:ASP318 2.5 32.1 1.0
CG C:ASP318 2.8 32.9 1.0
CG C:ASP320 3.2 33.2 1.0
OD2 C:ASP320 3.3 31.1 1.0
C C:GLY324 3.5 31.8 1.0
C C:PHE322 3.5 33.7 1.0
N C:GLY324 4.1 33.7 1.0
C C:GLU323 4.1 35.0 1.0
N C:PHE322 4.2 32.2 1.0
CB C:ASP318 4.2 31.4 1.0
CA C:PHE322 4.3 32.3 1.0
O C:HOH430 4.4 24.2 1.0
O C:ASP320 4.4 32.7 1.0
N C:ASN325 4.4 30.8 1.0
CA C:GLY324 4.4 31.4 1.0
CA C:ASN325 4.4 30.7 1.0
O C:GLU323 4.4 34.3 1.0
CB C:PHE322 4.4 29.7 1.0
N C:GLU323 4.4 35.2 1.0
CB C:ASP320 4.5 31.8 1.0
N C:ASP320 4.5 28.7 1.0
CA C:GLU323 4.6 37.3 1.0
C C:ASP320 4.6 32.3 1.0
O C:HOH445 4.6 38.2 1.0
CA C:ASP320 4.8 30.4 1.0

Calcium binding site 3 out of 5 in 1re3

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Calcium binding site 3 out of 5 in the Crystal Structure of Fragment D of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-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 of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca408

b:31.2
occ:1.00
 O C:ASP298 2.2 33.9 1.0
OD1 C:ASP294 2.3 31.2 1.0
O C:GLY296 2.5 33.8 1.0
O C:HOH456 2.6 28.1 1.0
OD2 C:ASP301 2.9 46.5 1.0
CB C:ASP301 3.1 39.0 1.0
C C:ASP298 3.3 34.7 1.0
CG C:ASP294 3.4 31.3 1.0
CG C:ASP301 3.4 44.4 1.0
C C:GLY296 3.7 35.4 1.0
O C:ASP297 3.9 35.9 1.0
CA C:PRO299 3.9 34.2 1.0
OD2 C:ASP294 3.9 29.5 1.0
N C:PRO299 4.0 34.6 1.0
C C:ASP297 4.0 36.9 1.0
N C:ASP298 4.2 36.8 1.0
CA C:ASP301 4.3 37.3 1.0
CA C:ASP298 4.3 35.1 1.0
N C:ASP301 4.4 35.9 1.0
C C:PRO299 4.4 34.8 1.0
N C:GLY296 4.4 34.0 1.0
CB C:ASP294 4.4 31.1 1.0
CA C:ASP294 4.4 30.9 1.0
N C:ASP297 4.6 37.1 1.0
CA C:GLY296 4.6 33.8 1.0
OD1 C:ASP301 4.7 50.0 1.0
O C:PRO299 4.7 35.5 1.0
CA C:ASP297 4.7 37.4 1.0
C C:ASP294 4.7 30.8 1.0
N C:SER300 5.0 33.2 1.0

Calcium binding site 4 out of 5 in 1re3

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Calcium binding site 4 out of 5 in the Crystal Structure of Fragment D of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-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 of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca472

b:46.1
occ:1.00
 OD1 E:ASP383 2.2 44.1 1.0
OD2 E:ASP381 2.3 39.5 1.0
O E:TRP385 2.5 60.3 1.0
O E:HOH535 2.5 42.8 1.0
OD1 E:ASP381 2.6 36.8 1.0
CG E:ASP381 2.8 37.9 1.0
CG E:ASP383 3.1 43.3 1.0
OD2 E:ASP383 3.4 44.2 1.0
C E:TRP385 3.6 60.6 1.0
O E:ASP383 4.1 45.5 1.0
N E:TRP385 4.2 53.6 1.0
CA E:TRP385 4.2 58.5 1.0
CB E:TRP385 4.2 59.2 1.0
N E:ASP383 4.2 39.9 1.0
CB E:ASP381 4.2 36.6 1.0
CB E:ASP383 4.3 42.4 1.0
C E:ASP383 4.4 44.4 1.0
CA E:ASP383 4.5 42.3 1.0
N E:LEU386 4.6 64.2 1.0
C E:ASP381 4.8 37.1 1.0
O E:ASP381 4.9 37.4 1.0
O E:THR387 4.9 76.6 1.0
CA E:LEU386 4.9 68.4 1.0

Calcium binding site 5 out of 5 in 1re3

Go back to Calcium Binding Sites List in 1re3
Calcium binding site 5 out of 5 in the Crystal Structure of Fragment D of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-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 of BBETAD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca407

b:27.6
occ:1.00
 O F:PHE322 2.2 30.6 1.0
OD1 F:ASP320 2.3 28.9 1.0
O F:GLY324 2.3 24.3 1.0
O F:HOH457 2.3 25.4 1.0
OD1 F:ASP318 2.5 24.0 1.0
OD2 F:ASP318 2.5 25.9 1.0
CG F:ASP318 2.8 24.2 1.0
CG F:ASP320 3.1 28.9 1.0
OD2 F:ASP320 3.3 24.4 1.0
C F:PHE322 3.4 31.5 1.0
C F:GLY324 3.5 26.5 1.0
N F:PHE322 4.1 33.0 1.0
C F:GLU323 4.1 31.2 1.0
CA F:PHE322 4.1 31.6 1.0
O F:GLU323 4.2 30.7 1.0
N F:GLY324 4.2 29.9 1.0
CB F:ASP318 4.3 24.7 1.0
CA F:ASN325 4.3 26.6 1.0
CB F:PHE322 4.3 30.0 1.0
N F:ASN325 4.3 26.4 1.0
O F:ASP320 4.4 29.8 1.0
N F:GLU323 4.4 31.8 1.0
CB F:ASP320 4.4 29.0 1.0
N F:ASP320 4.5 26.8 1.0
CA F:GLY324 4.5 27.3 1.0
C F:ASP320 4.5 30.5 1.0
CA F:GLU323 4.6 32.0 1.0
CA F:ASP320 4.7 28.4 1.0
O F:HOH411 4.7 23.5 1.0

Reference:

M.S.Kostelansky, B.Bolliger-Stucki, L.Betts, O.V.Gorkun, S.T.Lord. BBETAGLU397 and BBETAASP398 But Not BBETAASP432 Are Required For "B:B" Interactions. Biochemistry V. 43 2465 2004.
ISSN: ISSN 0006-2960
PubMed: 14992584
DOI: 10.1021/BI035996F
Page generated: Thu Jul 11 22:08:59 2024

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