Atomistry » Calcium » PDB 3dsx-3ead » 3e1i
Atomistry »
  Calcium »
    PDB 3dsx-3ead »
      3e1i »

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

Go back to Calcium Binding Sites List in 3e1i
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

Go back to Calcium Binding Sites List in 3e1i
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

Go back to Calcium Binding Sites List in 3e1i
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

Go back to Calcium Binding Sites List in 3e1i
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

Go back to Calcium Binding Sites List in 3e1i
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

Go back to Calcium Binding Sites List in 3e1i
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 Dec 12 04:09:36 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy