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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

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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

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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

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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

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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: Thu Jul 11 22:09:38 2024

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