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Calcium in PDB 1rf0: Crystal Structure of Fragment D of GAMMAE132A Fibrinogen

Protein crystallography data

The structure of Crystal Structure of Fragment D of GAMMAE132A Fibrinogen, PDB code: 1rf0 was solved by M.S.Kostelansky, 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) 17.97 / 2.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.408, 94.948, 227.614, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 28.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fragment D of GAMMAE132A Fibrinogen (pdb code 1rf0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Fragment D of GAMMAE132A Fibrinogen, PDB code: 1rf0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1rf0

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Calcium binding site 1 out of 6 in the Crystal Structure of Fragment D of GAMMAE132A Fibrinogen


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 GAMMAE132A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:49.0
occ:1.00
 OD1 B:ASP383 2.1 44.5 1.0
O B:TRP385 2.2 63.3 1.0
OD2 B:ASP381 2.3 42.6 1.0
OD1 B:ASP381 2.8 42.5 1.0
CG B:ASP381 2.9 40.1 1.0
CG B:ASP383 3.0 43.8 1.0
O B:HOH37 3.1 23.1 1.0
OD2 B:ASP383 3.3 43.6 1.0
C B:TRP385 3.3 64.0 1.0
CB B:TRP385 3.9 65.9 1.0
CA B:TRP385 4.0 62.9 1.0
N B:TRP385 4.1 59.1 1.0
O B:ASP383 4.3 46.6 1.0
CB B:ASP381 4.4 36.6 1.0
CB B:ASP383 4.4 43.1 1.0
N B:LEU386 4.5 66.4 1.0
C B:ASP383 4.6 45.8 1.0
N B:ASP383 4.6 40.5 1.0
CA B:ASP383 4.8 43.3 1.0
CA B:LEU386 4.8 68.3 1.0

Calcium binding site 2 out of 6 in 1rf0

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Calcium binding site 2 out of 6 in the Crystal Structure of Fragment D of GAMMAE132A Fibrinogen


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 GAMMAE132A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:40.4
occ:1.00
 O B:GLY263 2.4 28.8 1.0
OD2 B:ASP261 2.6 18.8 1.0
OD1 B:ASP398 3.2 39.6 1.0
CG B:ASP261 3.4 20.8 1.0
OD1 B:ASP261 3.4 23.4 1.0
C B:GLY263 3.6 28.4 1.0
CG B:ASP398 4.2 38.0 1.0
CA B:GLY263 4.3 28.9 1.0
OE1 C:GLN136 4.4 33.8 1.0
NE2 C:GLN136 4.5 33.6 1.0
CA B:ASP398 4.5 34.0 1.0
N B:ARG264 4.6 28.6 1.0
OH B:TYR378 4.6 36.2 1.0
N B:GLY263 4.7 29.3 1.0
CA B:ARG264 4.7 28.8 1.0
CE2 B:TYR378 4.8 34.2 1.0
CD C:GLN136 4.8 33.3 1.0
CB B:ASP261 4.8 22.1 1.0
OD2 B:ASP398 5.0 38.5 1.0
CB B:ASP398 5.0 36.0 1.0
CG B:ARG264 5.0 27.8 1.0

Calcium binding site 3 out of 6 in 1rf0

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Calcium binding site 3 out of 6 in the Crystal Structure of Fragment D of GAMMAE132A Fibrinogen


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 GAMMAE132A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca407

b:50.1
occ:1.00
 OD1 C:ASP320 2.2 40.5 1.0
OD1 C:ASP318 2.4 49.1 1.0
O C:GLY324 2.6 46.0 1.0
O C:PHE322 2.6 54.4 1.0
OD2 C:ASP318 2.8 47.4 1.0
CG C:ASP318 2.9 47.2 1.0
CG C:ASP320 3.2 41.7 1.0
OD2 C:ASP320 3.5 41.9 1.0
C C:PHE322 3.7 53.8 1.0
C C:GLY324 3.8 47.5 1.0
O C:GLU323 4.2 53.6 1.0
C C:GLU323 4.3 53.6 1.0
N C:PHE322 4.3 52.4 1.0
CB C:ASP318 4.3 46.0 1.0
N C:GLY324 4.4 51.4 1.0
CA C:PHE322 4.5 52.6 1.0
CB C:ASP320 4.5 43.0 1.0
CA C:GLY324 4.6 49.1 1.0
N C:ASP320 4.6 43.6 1.0
O C:ASP320 4.7 45.5 1.0
N C:GLU323 4.7 54.6 1.0
C C:ASP320 4.7 45.2 1.0
N C:ASN325 4.7 46.0 1.0
CB C:PHE322 4.8 52.0 1.0
CA C:ASN325 4.8 44.1 1.0
CA C:GLU323 4.8 55.1 1.0
CA C:ASP320 4.8 44.3 1.0

Calcium binding site 4 out of 6 in 1rf0

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Calcium binding site 4 out of 6 in the Crystal Structure of Fragment D of GAMMAE132A Fibrinogen


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 GAMMAE132A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca501

b:31.2
occ:1.00
 OD1 E:ASP381 2.4 26.8 1.0
O E:TRP385 2.4 45.9 1.0
O E:HOH61 2.4 28.5 1.0
OD2 E:ASP381 2.5 26.7 1.0
OD1 E:ASP383 2.5 31.3 1.0
CG E:ASP381 2.7 25.1 1.0
CG E:ASP383 3.1 30.6 1.0
OD2 E:ASP383 3.2 30.2 1.0
C E:TRP385 3.4 47.2 1.0
CB E:TRP385 4.0 43.2 1.0
CA E:TRP385 4.1 44.1 1.0
N E:TRP385 4.2 41.2 1.0
CB E:ASP381 4.2 24.5 1.0
O E:ASP383 4.3 32.2 1.0
N E:ASP383 4.5 28.9 1.0
CB E:ASP383 4.5 30.1 1.0
N E:LEU386 4.5 52.2 1.0
C E:ASP383 4.6 31.6 1.0
CA E:ASP383 4.7 29.7 1.0
O E:THR387 4.9 64.8 1.0
CA E:LEU386 4.9 56.8 1.0

Calcium binding site 5 out of 6 in 1rf0

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Calcium binding site 5 out of 6 in the Crystal Structure of Fragment D of GAMMAE132A Fibrinogen


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 GAMMAE132A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:38.0
occ:1.00
 O E:GLY263 2.4 29.5 1.0
OD2 E:ASP261 2.4 22.5 1.0
OD2 E:ASP398 2.6 34.2 1.0
CG E:ASP261 3.3 21.7 1.0
OD1 E:ASP261 3.3 24.5 1.0
C E:GLY263 3.5 27.3 1.0
CG E:ASP398 3.8 35.5 1.0
CA E:GLY263 4.1 26.1 1.0
OE1 F:GLN136 4.4 26.6 1.0
OD1 E:ASP398 4.5 37.0 1.0
N E:GLY263 4.5 25.9 1.0
CA E:ASP398 4.6 31.7 1.0
N E:ARG264 4.6 26.8 1.0
OH E:TYR378 4.6 32.3 1.0
NE2 F:GLN136 4.7 24.6 1.0
CB E:ASP261 4.7 21.9 1.0
CB E:ASP398 4.8 32.9 1.0
CD F:GLN136 4.9 27.0 1.0
CA E:ARG264 4.9 25.6 1.0
CE2 E:TYR378 5.0 29.3 1.0

Calcium binding site 6 out of 6 in 1rf0

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Calcium binding site 6 out of 6 in the Crystal Structure of Fragment D of GAMMAE132A Fibrinogen


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 of GAMMAE132A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca407

b:39.7
occ:1.00
 O F:GLY324 2.5 41.2 1.0
OD1 F:ASP318 2.6 37.8 1.0
OD2 F:ASP318 2.6 37.8 1.0
OD1 F:ASP320 2.6 41.2 1.0
O F:PHE322 2.6 51.5 1.0
CG F:ASP318 2.7 39.5 1.0
CG F:ASP320 3.6 38.3 1.0
C F:GLY324 3.8 43.7 1.0
C F:PHE322 3.8 49.5 1.0
OD2 F:ASP320 3.9 36.0 1.0
CB F:ASP318 4.0 39.0 1.0
O F:GLU323 4.2 47.6 1.0
C F:GLU323 4.3 48.4 1.0
N F:PHE322 4.3 46.1 1.0
CA F:PHE322 4.5 47.7 1.0
N F:GLY324 4.6 45.4 1.0
N F:ASP320 4.6 37.8 1.0
CA F:ASN325 4.6 43.1 1.0
N F:ASN325 4.6 43.7 1.0
O F:ASP320 4.7 39.8 1.0
CA F:GLY324 4.7 43.5 1.0
CB F:PHE322 4.8 46.5 1.0
N F:GLU323 4.8 50.2 1.0
C F:ASP320 4.8 39.9 1.0
CB F:ASP320 4.8 37.8 1.0
CA F:GLU323 4.9 50.7 1.0
CA F:ASP320 5.0 38.6 1.0

Reference:

M.S.Kostelansky, K.C.Lounes, L.F.Ping, S.K.Dickerson, O.V.Gorkun, S.T.Lord. Calcium-Binding Site BETA2, Adjacent to the "B" Polymerization Site, Modulates Lateral Aggregation of Protofibrils During Fibrin Polymerization. Biochemistry V. 43 2475 2004.
ISSN: ISSN 0006-2960
PubMed: 14992585
DOI: 10.1021/BI0359978
Page generated: Thu Jul 11 22:09:56 2024

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