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Calcium in PDB 3e1i: Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide

Protein crystallography data

The structure of Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 3e1i was solved by S.R.Bowley, S.T.Lord, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.21 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.476, 146.596, 228.960, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 24.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide (pdb code 3e1i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 3e1i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3e1i

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Calcium binding site 1 out of 7 in the Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D 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 BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:60.1
occ:1.00
 O B:TRP385 2.2 52.3 1.0
OD1 B:ASP383 2.4 39.5 1.0
OD2 B:ASP381 2.5 35.7 1.0
OD1 B:ASP381 2.9 34.8 1.0
CG B:ASP381 3.0 34.9 1.0
C B:TRP385 3.4 52.2 1.0
CG B:ASP383 3.4 39.7 1.0
OD2 B:ASP383 3.7 38.6 1.0
CB B:TRP385 4.0 51.5 1.0
CA B:TRP385 4.0 51.2 1.0
N B:TRP385 4.2 49.3 1.0
O B:LYS392 4.2 55.3 1.0
N B:LEU386 4.5 53.5 1.0
CB B:ASP381 4.5 34.9 1.0
N B:ASP383 4.6 38.7 1.0
O B:ASP383 4.6 41.7 1.0
CB B:ASP383 4.7 39.8 1.0
CA B:LEU386 4.7 54.9 1.0
C B:ASP383 4.8 41.6 1.0
O B:THR387 4.8 58.5 1.0
CA B:ASP383 4.9 40.2 1.0

Calcium binding site 2 out of 7 in 3e1i

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Calcium binding site 2 out of 7 in the Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D 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 BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:43.5
occ:1.00
 OD1 B:ASP398 2.4 39.8 1.0
OD2 B:ASP261 2.4 25.3 1.0
O B:GLY263 2.4 26.3 1.0
OE2 C:GLU132 2.5 40.5 1.0
OD1 B:ASP261 3.0 25.2 1.0
CG B:ASP261 3.1 26.2 1.0
C B:GLY263 3.4 26.9 1.0
CG B:ASP398 3.5 39.5 1.0
CD C:GLU132 3.5 39.8 1.0
CA B:GLY263 3.9 26.8 1.0
CG C:GLU132 4.1 39.8 1.0
CA B:ASP398 4.3 38.6 1.0
OD2 B:ASP398 4.3 41.0 1.0
CB B:ASP398 4.3 38.8 1.0
OE1 C:GLN136 4.4 29.4 1.0
OE1 C:GLU132 4.4 40.9 1.0
N B:GLY263 4.4 26.9 1.0
CB B:ASP261 4.5 26.4 1.0
N B:ARG264 4.6 27.2 1.0
OH B:TYR378 4.8 31.6 1.0
NE2 C:GLN136 4.8 29.4 1.0
CA B:ARG264 5.0 27.3 1.0

Calcium binding site 3 out of 7 in 3e1i

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Calcium binding site 3 out of 7 in the Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D 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 BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:30.4
occ:1.00
 OD1 C:ASP320 2.4 18.8 1.0
O C:GLY324 2.4 19.5 1.0
O C:PHE322 2.4 21.5 1.0
O C:HOH637 2.4 29.1 1.0
OD2 C:ASP318 2.5 21.1 1.0
OD1 C:ASP318 2.7 21.3 1.0
CG C:ASP318 2.9 20.0 1.0
CG C:ASP320 3.2 19.8 1.0
OD2 C:ASP320 3.4 20.6 1.0
C C:PHE322 3.5 21.7 1.0
C C:GLY324 3.6 20.7 1.0
N C:PHE322 4.1 20.9 1.0
CA C:PHE322 4.2 20.8 1.0
C C:GLU323 4.2 22.4 1.0
O C:GLU323 4.2 22.3 1.0
O C:ASP320 4.3 20.2 1.0
CB C:PHE322 4.3 20.4 1.0
CB C:ASP318 4.4 19.1 1.0
N C:GLY324 4.4 21.6 1.0
N C:ASN325 4.5 20.2 1.0
C C:ASP320 4.5 19.9 1.0
CA C:ASN325 4.5 20.0 1.0
CB C:ASP320 4.5 19.2 1.0
N C:GLU323 4.5 22.2 1.0
N C:ASP320 4.5 19.5 1.0
CA C:GLY324 4.6 20.7 1.0
O C:HOH656 4.6 35.2 1.0
CA C:GLU323 4.7 23.5 1.0
CA C:ASP320 4.7 19.5 1.0

Calcium binding site 4 out of 7 in 3e1i

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Calcium binding site 4 out of 7 in the Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D 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 BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:31.0
occ:1.00
 OD2 C:ASP294 2.3 16.9 1.0
O C:ASP298 2.3 22.1 1.0
O C:GLY296 2.5 23.6 1.0
OD1 C:ASP301 2.5 21.0 1.0
OD2 C:ASP301 2.8 21.8 1.0
CG C:ASP301 3.0 21.4 1.0
CG C:ASP294 3.4 18.0 1.0
C C:ASP298 3.5 22.8 1.0
C C:GLY296 3.6 23.1 1.0
O C:HOH677 4.1 44.8 1.0
OD1 C:ASP294 4.1 18.2 1.0
N C:GLY296 4.1 21.3 1.0
C C:ASP297 4.1 23.8 1.0
N C:ASP298 4.2 23.6 1.0
CA C:PRO299 4.3 23.0 1.0
N C:PRO299 4.3 23.0 1.0
CA C:ASP294 4.3 18.4 1.0
O F:HOH645 4.3 30.4 1.0
CB C:ASP294 4.4 18.2 1.0
CB C:ASP301 4.4 21.9 1.0
O C:ASP297 4.4 23.9 1.0
CA C:ASP298 4.4 22.9 1.0
CA C:GLY296 4.4 22.3 1.0
N C:ASP297 4.4 23.7 1.0
C C:ASP294 4.5 18.8 1.0
N C:PHE295 4.6 19.5 1.0
C C:PRO299 4.6 23.0 1.0
N C:ASP301 4.6 22.1 1.0
CA C:ASP297 4.6 24.4 1.0
O C:HOH641 4.8 37.1 1.0
O C:PRO299 4.9 23.5 1.0
O C:ASP294 5.0 19.0 1.0
CB C:ASP298 5.0 23.2 1.0

Calcium binding site 5 out of 7 in 3e1i

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Calcium binding site 5 out of 7 in the Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D 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 BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:70.9
occ:1.00
 OD1 E:ASP383 2.3 40.7 1.0
O E:TRP385 2.3 50.1 1.0
OD2 E:ASP381 2.3 37.6 1.0
OD1 E:ASP381 2.9 39.1 1.0
CG E:ASP381 3.0 38.5 1.0
CG E:ASP383 3.3 41.5 1.0
C E:TRP385 3.4 50.1 1.0
OD2 E:ASP383 3.7 41.0 1.0
CB E:TRP385 3.9 48.8 1.0
CA E:TRP385 4.0 49.0 1.0
N E:TRP385 4.1 47.7 1.0
O E:ASP383 4.2 42.7 1.0
CB E:ASP381 4.5 37.8 1.0
N E:ASP383 4.5 40.5 1.0
C E:ASP383 4.5 42.6 1.0
CB E:ASP383 4.6 41.5 1.0
N E:LEU386 4.6 51.5 1.0
CA E:ASP383 4.7 41.6 1.0
O E:THR387 4.8 56.7 1.0
CA E:LEU386 5.0 53.1 1.0

Calcium binding site 6 out of 7 in 3e1i

Go back to Calcium Binding Sites List in 3e1i
Calcium binding site 6 out of 7 in the Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D 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 6 of Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca503

b:42.7
occ:1.00
 O E:GLY263 2.4 27.4 1.0
OD1 E:ASP398 2.4 39.6 1.0
OD2 E:ASP261 2.6 26.8 1.0
OE2 F:GLU132 2.8 42.9 1.0
OD1 E:ASP261 3.0 27.5 1.0
CG E:ASP261 3.1 26.7 1.0
CG E:ASP398 3.4 38.9 1.0
C E:GLY263 3.4 27.2 1.0
CD F:GLU132 3.7 42.9 1.0
CA E:GLY263 3.8 26.8 1.0
OD2 E:ASP398 4.0 39.8 1.0
N E:GLY263 4.3 26.2 1.0
CG F:GLU132 4.3 43.1 1.0
CA E:ASP398 4.4 38.0 1.0
CB E:ASP398 4.4 38.1 1.0
NE2 F:GLN136 4.5 32.7 1.0
OE1 F:GLU132 4.5 44.6 1.0
OE1 F:GLN136 4.6 33.6 1.0
N E:ARG264 4.6 27.9 1.0
CB E:ASP261 4.6 26.3 1.0
OH E:TYR378 4.7 32.1 1.0
CD F:GLN136 5.0 33.3 1.0
CA E:ARG264 5.0 28.4 1.0

Calcium binding site 7 out of 7 in 3e1i

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Calcium binding site 7 out of 7 in the Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D 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 7 of Crystal Structure of BBETAD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca501

b:26.6
occ:1.00
 O F:PHE322 2.3 18.0 1.0
O F:GLY324 2.3 15.7 1.0
OD1 F:ASP320 2.3 13.7 1.0
OD2 F:ASP318 2.5 19.2 1.0
OD1 F:ASP318 2.5 20.7 1.0
CG F:ASP318 2.9 19.1 1.0
CG F:ASP320 3.1 16.0 1.0
OD2 F:ASP320 3.3 15.3 1.0
C F:PHE322 3.4 18.7 1.0
C F:GLY324 3.5 16.3 1.0
N F:PHE322 4.0 18.3 1.0
CA F:PHE322 4.1 18.1 1.0
O F:ASP320 4.3 16.8 1.0
CB F:PHE322 4.3 17.3 1.0
C F:GLU323 4.3 18.8 1.0
CA F:ASN325 4.3 15.7 1.0
N F:ASN325 4.4 15.9 1.0
O F:GLU323 4.4 19.0 1.0
CB F:ASP318 4.4 18.1 1.0
N F:GLY324 4.4 17.7 1.0
N F:ASP320 4.4 17.5 1.0
O F:HOH638 4.5 26.3 1.0
CB F:ASP320 4.5 16.8 1.0
N F:GLU323 4.5 19.1 1.0
C F:ASP320 4.5 17.3 1.0
CA F:GLY324 4.5 16.6 1.0
O F:HOH661 4.5 32.7 1.0
CA F:ASP320 4.7 17.3 1.0
CA F:GLU323 4.7 19.8 1.0

Reference:

S.R.Bowley, S.T.Lord. Fibrinogen Variant BBETAD432A Has Normal Polymerization But Does Not Bind Knob "B". Blood V. 113 4425 2009.
ISSN: ISSN 0006-4971
PubMed: 19075185
DOI: 10.1182/BLOOD-2008-09-178178
Page generated: Sat Jul 13 09:15:02 2024

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