Atomistry » Calcium » PDB 1rc8-1rpk » 1re4
Atomistry »
  Calcium »
    PDB 1rc8-1rpk »
      1re4 »

Calcium in PDB 1re4: Crystal Structure of Fragment D of BBETAD398A Fibrinogen

Protein crystallography data

The structure of Crystal Structure of Fragment D of BBETAD398A Fibrinogen, PDB code: 1re4 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) 17.99 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.538, 94.487, 227.088, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fragment D of BBETAD398A Fibrinogen (pdb code 1re4). 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 BBETAD398A Fibrinogen, PDB code: 1re4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1re4

Go back to Calcium Binding Sites List in 1re4
Calcium binding site 1 out of 6 in the Crystal Structure of Fragment D of BBETAD398A 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 BBETAD398A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:46.4
occ:1.00
 OD2 B:ASP381 2.2 41.6 1.0
O B:TRP385 2.3 66.4 1.0
O B:HOH545 2.5 26.8 1.0
OD1 B:ASP383 2.7 41.8 1.0
OD1 B:ASP381 2.8 40.9 1.0
CG B:ASP381 2.8 39.2 1.0
C B:TRP385 3.5 67.0 1.0
CG B:ASP383 3.6 40.3 1.0
OD2 B:ASP383 3.9 41.6 1.0
CB B:TRP385 4.1 68.3 1.0
CB B:ASP381 4.2 36.8 1.0
CA B:TRP385 4.2 65.2 1.0
O B:ASP383 4.5 42.8 1.0
N B:TRP385 4.5 60.2 1.0
N B:LEU386 4.6 70.2 1.0
N B:ASP383 4.8 38.0 1.0
O B:THR387 4.8 78.8 1.0
CA B:LEU386 4.8 72.5 1.0
C B:ASP383 4.9 43.8 1.0
N B:THR387 4.9 75.4 1.0
CB B:ASP383 4.9 39.8 1.0

Calcium binding site 2 out of 6 in 1re4

Go back to Calcium Binding Sites List in 1re4
Calcium binding site 2 out of 6 in the Crystal Structure of Fragment D of BBETAD398A 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 BBETAD398A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:50.2
occ:0.50
 OE2 C:GLU132 2.5 41.9 1.0
O B:GLY263 2.6 27.8 1.0
OD2 B:ASP261 3.1 19.6 1.0
O B:HOH546 3.3 33.6 1.0
NE2 C:GLN136 3.5 38.1 1.0
C B:GLY263 3.6 27.4 1.0
CD C:GLU132 3.7 39.0 1.0
OH B:TYR378 3.9 38.2 1.0
CG B:ASP261 4.0 20.5 1.0
OE1 C:GLN136 4.0 40.3 1.0
CD C:GLN136 4.1 38.1 1.0
CA B:ARG264 4.1 30.1 1.0
OD1 B:ASP261 4.2 23.1 1.0
N B:ARG264 4.3 29.1 1.0
OE1 C:GLU132 4.5 38.7 1.0
CG B:ARG264 4.6 32.0 1.0
CG C:GLU132 4.6 37.6 1.0
CE2 B:TYR378 4.6 36.1 1.0
CA B:GLY263 4.6 25.8 1.0
CZ B:TYR378 4.7 36.8 1.0
CB B:ARG264 4.8 31.4 1.0

Calcium binding site 3 out of 6 in 1re4

Go back to Calcium Binding Sites List in 1re4
Calcium binding site 3 out of 6 in the Crystal Structure of Fragment D of BBETAD398A 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 BBETAD398A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca407

b:39.8
occ:1.00
 O C:PHE322 2.1 54.2 1.0
O C:GLY324 2.2 45.8 1.0
O C:HOH429 2.3 39.2 1.0
OD1 C:ASP320 2.3 34.4 1.0
OD1 C:ASP318 2.4 46.9 1.0
OD2 C:ASP318 2.7 45.0 1.0
CG C:ASP318 2.8 45.5 1.0
CG C:ASP320 3.3 38.0 1.0
C C:PHE322 3.4 52.5 1.0
C C:GLY324 3.4 46.9 1.0
OD2 C:ASP320 3.6 39.5 1.0
N C:GLY324 3.9 50.2 1.0
C C:GLU323 3.9 52.0 1.0
CA C:GLY324 4.2 48.2 1.0
O C:GLU323 4.2 52.1 1.0
O C:ASP320 4.2 42.9 1.0
CB C:ASP318 4.2 45.5 1.0
N C:GLU323 4.3 52.8 1.0
N C:PHE322 4.3 50.5 1.0
CA C:PHE322 4.3 51.5 1.0
CA C:GLU323 4.3 52.8 1.0
N C:ASN325 4.4 45.1 1.0
CA C:ASN325 4.6 44.4 1.0
C C:ASP320 4.7 43.3 1.0
CB C:ASP320 4.7 39.2 1.0
CB C:PHE322 4.7 51.3 1.0
N C:ASP320 4.8 42.2 1.0
CA C:ASP320 5.0 42.2 1.0

Calcium binding site 4 out of 6 in 1re4

Go back to Calcium Binding Sites List in 1re4
Calcium binding site 4 out of 6 in the Crystal Structure of Fragment D of BBETAD398A 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 BBETAD398A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca501

b:37.8
occ:1.00
 O E:TRP385 2.2 47.8 1.0
OD1 E:ASP381 2.4 36.9 1.0
O E:HOH540 2.4 14.3 1.0
OD1 E:ASP383 2.4 31.9 1.0
OD2 E:ASP381 2.6 37.8 1.0
CG E:ASP381 2.8 35.0 1.0
CG E:ASP383 3.3 32.2 1.0
C E:TRP385 3.4 48.4 1.0
OD2 E:ASP383 3.5 29.9 1.0
CB E:TRP385 3.9 46.7 1.0
CA E:TRP385 4.0 46.0 1.0
N E:TRP385 4.3 43.1 1.0
CB E:ASP381 4.3 32.0 1.0
N E:LEU386 4.5 52.2 1.0
O E:ASP383 4.5 38.1 1.0
N E:ASP383 4.7 32.0 1.0
CB E:ASP383 4.7 32.4 1.0
C E:ASP383 4.8 36.6 1.0
O E:THR387 4.8 64.0 1.0
CA E:LEU386 4.9 55.1 1.0

Calcium binding site 5 out of 6 in 1re4

Go back to Calcium Binding Sites List in 1re4
Calcium binding site 5 out of 6 in the Crystal Structure of Fragment D of BBETAD398A 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 BBETAD398A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:50.4
occ:0.50
 O E:GLY263 2.7 27.2 1.0
O F:HOH438 3.2 27.9 1.0
OD2 E:ASP261 3.5 25.3 1.0
NE2 F:GLN136 3.5 35.3 1.0
OE1 F:GLN136 3.7 37.8 1.0
OE1 F:GLU132 3.8 47.4 1.0
C E:GLY263 3.9 25.6 1.0
CD F:GLN136 3.9 35.8 1.0
OH E:TYR378 3.9 37.6 1.0
CD F:GLU132 4.0 46.5 1.0
OE2 F:GLU132 4.3 48.4 1.0
CG E:ASP261 4.3 22.7 1.0
CA E:ARG264 4.4 27.1 1.0
CG F:GLU132 4.5 43.8 1.0
OD1 E:ASP261 4.5 26.6 1.0
CE2 E:TYR378 4.7 36.6 1.0
N E:ARG264 4.7 26.7 1.0
CZ E:TYR378 4.8 37.3 1.0
CG E:ARG264 4.8 30.5 1.0
CA E:GLY263 5.0 24.0 1.0

Calcium binding site 6 out of 6 in 1re4

Go back to Calcium Binding Sites List in 1re4
Calcium binding site 6 out of 6 in the Crystal Structure of Fragment D of BBETAD398A 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 BBETAD398A Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca407

b:46.8
occ:1.00
 OD1 F:ASP318 2.2 44.2 1.0
OD1 F:ASP320 2.3 51.7 1.0
O F:PHE322 2.4 57.0 1.0
O F:HOH434 2.6 33.6 1.0
CG F:ASP318 2.7 44.0 1.0
O F:GLY324 2.7 45.0 1.0
OD2 F:ASP318 2.8 44.8 1.0
CG F:ASP320 3.1 49.9 1.0
O F:ASP320 3.3 47.5 1.0
OD2 F:ASP320 3.5 49.6 1.0
C F:PHE322 3.5 55.4 1.0
N F:PHE322 3.9 53.1 1.0
C F:GLY324 4.0 48.7 1.0
CB F:ASP318 4.0 42.2 1.0
C F:ASP320 4.0 48.5 1.0
N F:ASP320 4.2 44.6 1.0
CA F:PHE322 4.2 54.2 1.0
CB F:ASP320 4.3 47.7 1.0
CA F:ASP320 4.4 46.8 1.0
C F:GLU323 4.5 54.8 1.0
CB F:PHE322 4.5 53.3 1.0
N F:GLY324 4.6 52.1 1.0
N F:GLU323 4.6 56.4 1.0
O F:GLU323 4.6 54.3 1.0
C F:ASP318 4.8 41.3 1.0
CA F:GLY324 4.9 49.6 1.0
N F:ASN319 4.9 42.1 1.0
CA F:GLU323 4.9 57.0 1.0
N F:ASN325 4.9 48.5 1.0
CA F:ASN325 4.9 48.0 1.0
CA F:ASP318 5.0 41.3 1.0
C F:ASN319 5.0 44.3 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: Tue Jul 8 01:36:04 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy