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Calcium in PDB 1lt9: Crystal Structure of Recombinant Human Fibrinogen Fragment D

Protein crystallography data

The structure of Crystal Structure of Recombinant Human Fibrinogen Fragment D, PDB code: 1lt9 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 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.727, 94.511, 227.111, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 27.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Recombinant Human Fibrinogen Fragment D (pdb code 1lt9). 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 Recombinant Human Fibrinogen Fragment D, PDB code: 1lt9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1lt9

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


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 Recombinant Human Fibrinogen Fragment D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:54.6
occ:1.00
 O B:TRP385 2.2 72.6 1.0
OD2 B:ASP381 2.3 43.8 1.0
OD1 B:ASP383 2.3 50.4 1.0
O B:HOH125 2.7 39.4 1.0
OD1 B:ASP381 2.9 43.3 1.0
CG B:ASP381 2.9 42.6 1.0
CG B:ASP383 3.3 49.8 1.0
C B:TRP385 3.4 72.2 1.0
OD2 B:ASP383 3.5 49.9 1.0
CB B:TRP385 3.9 74.0 1.0
CA B:TRP385 4.1 71.2 1.0
N B:TRP385 4.3 67.6 1.0
CB B:ASP381 4.4 39.7 1.0
O B:ASP383 4.4 51.4 1.0
N B:LEU386 4.4 73.7 1.0
CB B:ASP383 4.6 48.6 1.0
CA B:LEU386 4.7 75.5 1.0
N B:ASP383 4.8 45.1 1.0
C B:ASP383 4.8 51.4 1.0
CA B:ASP383 5.0 48.8 1.0

Calcium binding site 2 out of 6 in 1lt9

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


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 Recombinant Human Fibrinogen Fragment D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:36.0
occ:1.00
 OE2 C:GLU132 2.2 41.4 1.0
OD1 B:ASP398 2.3 47.0 1.0
O B:GLY263 2.3 36.9 1.0
OD2 B:ASP261 2.4 20.2 1.0
OD1 B:ASP261 3.0 25.1 1.0
CG B:ASP261 3.1 22.2 1.0
C B:GLY263 3.4 35.0 1.0
CG B:ASP398 3.4 46.7 1.0
CD C:GLU132 3.4 41.0 1.0
CA B:GLY263 3.8 34.0 1.0
CA B:ASP398 4.0 41.1 1.0
O B:HOH126 4.0 20.0 1.0
OD2 B:ASP398 4.1 49.3 1.0
OE1 C:GLU132 4.1 37.8 1.0
OE1 C:GLN136 4.2 38.4 1.0
N B:GLY263 4.3 32.9 1.0
CB B:ASP398 4.3 44.2 1.0
CG C:GLU132 4.5 42.1 1.0
N B:ARG264 4.5 34.2 1.0
CB B:ASP261 4.6 22.6 1.0
OH B:TYR378 4.6 36.2 1.0
O B:HOH68 4.7 39.3 1.0
N B:ASP398 4.8 41.2 1.0
NE2 C:GLN136 4.9 39.2 1.0
CA B:ARG264 4.9 34.6 1.0
C B:ASP398 4.9 40.0 1.0
CD C:GLN136 4.9 37.7 1.0
CE2 B:TYR378 5.0 36.3 1.0

Calcium binding site 3 out of 6 in 1lt9

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


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 Recombinant Human Fibrinogen Fragment D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:46.2
occ:1.00
 OD1 C:ASP320 2.3 43.2 1.0
O C:PHE322 2.3 58.0 1.0
O C:GLY324 2.3 49.4 1.0
O C:HOH411 2.4 16.8 1.0
OD2 C:ASP318 2.5 50.8 1.0
OD1 C:ASP318 2.6 52.1 1.0
CG C:ASP318 2.8 51.5 1.0
CG C:ASP320 3.2 45.1 1.0
OD2 C:ASP320 3.4 46.4 1.0
C C:PHE322 3.4 57.3 1.0
C C:GLY324 3.5 50.3 1.0
C C:GLU323 4.0 56.6 1.0
O C:GLU323 4.0 55.5 1.0
N C:GLY324 4.1 55.1 1.0
N C:PHE322 4.2 55.9 1.0
CB C:ASP318 4.3 51.6 1.0
CA C:PHE322 4.3 56.5 1.0
CA C:GLY324 4.4 51.9 1.0
N C:GLU323 4.4 58.3 1.0
N C:ASN325 4.5 48.4 1.0
O C:ASP320 4.5 50.3 1.0
CA C:GLU323 4.5 58.8 1.0
CA C:ASN325 4.5 47.0 1.0
CB C:ASP320 4.6 47.1 1.0
CB C:PHE322 4.6 56.1 1.0
C C:ASP320 4.7 50.1 1.0
N C:ASP320 4.7 50.0 1.0
CA C:ASP320 4.9 49.6 1.0

Calcium binding site 4 out of 6 in 1lt9

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


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 Recombinant Human Fibrinogen Fragment D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2

b:41.4
occ:1.00
 O E:TRP385 2.2 62.5 1.0
OD1 E:ASP383 2.4 41.8 1.0
OD1 E:ASP381 2.5 29.2 1.0
O E:HOH510 2.8 31.5 1.0
OD2 E:ASP381 2.9 33.3 1.0
CG E:ASP381 3.0 31.8 1.0
C E:TRP385 3.3 61.9 1.0
CG E:ASP383 3.4 40.0 1.0
OD2 E:ASP383 3.8 39.8 1.0
CA E:TRP385 4.2 59.6 1.0
CB E:TRP385 4.2 60.0 1.0
N E:LEU386 4.3 65.2 1.0
N E:TRP385 4.3 55.5 1.0
CB E:ASP381 4.4 31.9 1.0
CA E:LEU386 4.5 68.0 1.0
O E:ASP383 4.5 43.5 1.0
N E:ASP383 4.6 37.9 1.0
CB E:ASP383 4.7 40.8 1.0
C E:ASP383 4.7 43.3 1.0
O E:THR387 4.8 73.6 1.0
C E:LEU386 4.8 69.1 1.0
CA E:ASP383 4.9 40.8 1.0

Calcium binding site 5 out of 6 in 1lt9

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


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 Recombinant Human Fibrinogen Fragment D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1

b:32.1
occ:1.00
 OD1 E:ASP398 2.2 39.6 1.0
O E:GLY263 2.4 33.6 1.0
OD2 E:ASP261 2.5 23.9 1.0
OE2 F:GLU132 2.6 45.1 1.0
OD1 E:ASP261 3.0 28.0 1.0
CG E:ASP261 3.1 25.0 1.0
C E:GLY263 3.4 31.3 1.0
CG E:ASP398 3.5 43.2 1.0
CD F:GLU132 3.7 44.6 1.0
CA E:GLY263 3.9 30.9 1.0
OE1 F:GLN136 4.2 33.1 1.0
CG F:GLU132 4.3 43.5 1.0
N E:GLY263 4.3 30.0 1.0
OD2 E:ASP398 4.3 46.6 1.0
CB E:ASP398 4.3 42.3 1.0
CA E:ASP398 4.3 40.9 1.0
OE1 F:GLU132 4.5 47.6 1.0
N E:ARG264 4.6 30.1 1.0
CB E:ASP261 4.6 26.7 1.0
NE2 F:GLN136 4.6 32.0 1.0
OH E:TYR378 4.7 40.7 1.0
CD F:GLN136 4.8 30.5 1.0
CA E:ARG264 5.0 27.9 1.0

Calcium binding site 6 out of 6 in 1lt9

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


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 Recombinant Human Fibrinogen Fragment D within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1

b:53.9
occ:1.00
 O F:HOH438 2.1 31.9 1.0
O F:GLY324 2.2 48.8 1.0
OD2 F:ASP318 2.4 49.2 1.0
OD1 F:ASP318 2.5 47.9 1.0
OD1 F:ASP320 2.5 48.5 1.0
O F:PHE322 2.6 57.8 1.0
CG F:ASP318 2.7 47.2 1.0
C F:GLY324 3.3 50.1 1.0
CG F:ASP320 3.4 47.6 1.0
OD2 F:ASP320 3.6 46.4 1.0
C F:PHE322 3.7 57.1 1.0
O F:GLU323 3.9 55.6 1.0
C F:GLU323 3.9 56.0 1.0
N F:GLY324 4.0 54.0 1.0
CA F:GLY324 4.1 51.7 1.0
CB F:ASP318 4.1 43.8 1.0
N F:ASN325 4.2 48.5 1.0
CA F:ASN325 4.4 46.3 1.0
N F:PHE322 4.5 53.6 1.0
CA F:PHE322 4.5 55.7 1.0
N F:GLU323 4.6 58.2 1.0
CA F:GLU323 4.6 58.3 1.0
CB F:PHE322 4.7 54.7 1.0
CB F:ASP320 4.8 46.3 1.0
N F:ASP320 4.9 43.3 1.0
O F:ASP320 4.9 44.6 1.0

Reference:

M.S.Kostelansky, L.Betts, O.V.Gorkun, S.T.Lord. 2.8 A Crystal Structures of Recombinant Fibrinogen Fragment D with and Without Two Peptide Ligands: Ghrp Binding to the "B" Site Disrupts Its Nearby Calcium-Binding Site. Biochemistry V. 41 12124 2002.
ISSN: ISSN 0006-2960
PubMed: 12356313
DOI: 10.1021/BI0261894
Page generated: Thu Jul 11 12:03:36 2024

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