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Calcium in PDB 3ghg: Crystal Structure of Human Fibrinogen

Protein crystallography data

The structure of Crystal Structure of Human Fibrinogen, PDB code: 3ghg was solved by R.F.Doolittle, J.M.Kollman, M.R.Sawaya, L.Pandi, M.Riley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.238, 94.866, 300.812, 90.00, 94.81, 90.00
R / Rfree (%) 25.2 / 30.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Fibrinogen (pdb code 3ghg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Human Fibrinogen, PDB code: 3ghg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3ghg

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Calcium binding site 1 out of 8 in the Crystal Structure of Human 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 Human Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:77.3
occ:1.00
 O B:TRP385 2.4 53.8 1.0
OD1 B:ASP381 2.5 45.0 1.0
OD1 B:ASP383 2.5 54.8 1.0
OD2 B:ASP381 3.0 49.8 1.0
CG B:ASP381 3.1 47.5 1.0
C B:TRP385 3.4 53.4 1.0
CG B:ASP383 3.4 58.1 1.0
OD2 B:ASP383 3.5 58.8 1.0
CA B:LEU386 3.7 58.2 1.0
N B:LEU386 4.0 55.8 1.0
N B:THR387 4.1 65.4 1.0
CD2 B:LEU386 4.2 64.8 1.0
N B:TRP385 4.4 47.4 1.0
C B:LEU386 4.4 63.3 1.0
CA B:TRP385 4.5 49.8 1.0
CB B:ASP381 4.6 48.9 1.0
O B:ASP383 4.7 48.5 1.0
CB B:ASP383 4.8 50.5 1.0
CB B:LEU386 4.8 58.4 1.0
CB B:TRP385 4.8 52.8 1.0
O B:THR387 4.9 73.6 1.0
C B:ASP383 5.0 49.9 1.0

Calcium binding site 2 out of 8 in 3ghg

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Calcium binding site 2 out of 8 in the Crystal Structure of Human 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 Human Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca601

b:49.0
occ:1.00
 OD2 F:ASP318 2.1 69.6 1.0
OD2 F:ASP320 2.3 89.6 1.0
O F:GLY324 2.8 0.5 1.0
CG F:ASP318 2.9 69.3 1.0
OD1 F:ASP318 3.1 70.4 1.0
O F:GLU323 3.3 93.5 1.0
CG F:ASP320 3.3 86.6 1.0
C F:GLY324 3.4 0.5 1.0
C F:GLU323 3.4 96.1 1.0
C F:PHE322 3.5 93.0 1.0
O F:ASP320 3.6 88.7 1.0
O F:PHE322 3.6 92.5 1.0
CB F:PHE322 3.6 93.5 1.0
N F:GLU323 3.7 96.0 1.0
OD1 F:ASP320 3.8 86.0 1.0
CA F:PHE322 3.9 91.0 1.0
N F:PHE322 3.9 88.7 1.0
N F:GLY324 3.9 0.0 1.0
CA F:GLU323 3.9 97.7 1.0
N F:ASN325 4.0 96.9 1.0
CA F:ASN325 4.2 93.0 1.0
CA F:GLY324 4.2 99.5 1.0
C F:ASP320 4.3 89.5 1.0
CB F:ASP318 4.4 72.3 1.0
CB F:ASP320 4.6 85.5 1.0
CG F:PHE322 4.7 97.7 1.0
CD1 F:PHE322 4.8 99.7 1.0
N F:ASP320 4.8 84.9 1.0
CA F:ASP320 4.8 86.5 1.0
C F:LYS321 4.9 85.2 1.0

Calcium binding site 3 out of 8 in 3ghg

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Calcium binding site 3 out of 8 in the Crystal Structure of Human 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 Human Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:31.8
occ:1.00
 OD1 C:ASP318 2.0 32.4 1.0
OD1 C:ASP320 2.3 46.5 1.0
O C:PHE322 2.7 40.0 1.0
CG C:ASP318 3.0 39.5 1.0
O C:GLY324 3.1 25.6 1.0
CB C:ASP318 3.2 42.6 1.0
CG C:ASP320 3.5 44.7 1.0
O C:ASP320 3.6 40.6 1.0
C C:PHE322 3.8 43.1 1.0
O C:ASP318 3.8 46.7 1.0
C C:ASP318 4.0 40.8 1.0
CA C:ASP318 4.1 39.7 1.0
OD2 C:ASP320 4.1 36.4 1.0
OD2 C:ASP318 4.2 44.8 1.0
C C:GLY324 4.2 27.8 1.0
N C:ASP320 4.2 36.6 1.0
C C:ASP320 4.3 39.6 1.0
N C:PHE322 4.3 43.3 1.0
O C:GLU323 4.4 35.0 1.0
CA C:PHE322 4.5 41.9 1.0
CB C:PHE322 4.6 39.4 1.0
CB C:ASP320 4.6 41.0 1.0
CA C:ASP320 4.6 38.5 1.0
C C:GLU323 4.6 37.7 1.0
N C:ASN319 4.8 38.4 1.0
N C:GLU323 4.9 46.3 1.0
N C:GLY324 5.0 35.6 1.0

Calcium binding site 4 out of 8 in 3ghg

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Calcium binding site 4 out of 8 in the Crystal Structure of Human 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 Human Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca501

b:47.7
occ:1.00
 OD1 E:ASP383 2.0 49.9 1.0
O E:TRP385 2.6 66.4 1.0
OD1 E:ASP381 2.9 58.4 1.0
C E:TRP385 3.0 61.9 1.0
OD2 E:ASP381 3.0 59.7 1.0
CG E:ASP383 3.0 48.9 1.0
OD2 E:ASP383 3.3 51.2 1.0
CG E:ASP381 3.3 57.0 1.0
N E:LEU386 3.6 63.7 1.0
N E:TRP385 3.6 56.7 1.0
CA E:TRP385 3.7 59.3 1.0
CA E:LEU386 3.7 65.3 1.0
CB E:TRP385 3.8 59.8 1.0
O E:ASP383 3.8 56.5 1.0
N E:THR387 4.0 70.8 1.0
CD2 E:LEU386 4.0 72.4 1.0
CB E:ASP383 4.3 55.9 1.0
C E:ASP383 4.3 59.0 1.0
C E:LEU386 4.4 70.5 1.0
O E:LYS392 4.4 68.4 1.0
O E:THR387 4.5 66.7 1.0
CA E:ASP383 4.8 60.0 1.0
C E:GLY384 4.8 56.5 1.0
N E:ASP383 4.8 62.4 1.0
CB E:LEU386 4.8 66.7 1.0
CB E:ASP381 4.8 58.0 1.0
CG E:TRP385 4.9 59.2 1.0

Calcium binding site 5 out of 8 in 3ghg

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Calcium binding site 5 out of 8 in the Crystal Structure of Human 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 Human Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca501

b:51.0
occ:1.00
 O H:TRP385 2.1 57.0 1.0
OD1 H:ASP383 2.1 53.2 1.0
OD1 H:ASP381 2.6 51.5 1.0
OD2 H:ASP381 2.6 51.6 1.0
CG H:ASP381 3.0 53.3 1.0
CG H:ASP383 3.1 53.1 1.0
C H:TRP385 3.2 57.8 1.0
OD2 H:ASP383 3.5 56.1 1.0
CA H:TRP385 4.0 56.0 1.0
CB H:TRP385 4.1 56.1 1.0
N H:TRP385 4.1 55.5 1.0
N H:LEU386 4.2 58.9 1.0
O H:ASP383 4.2 57.3 1.0
CA H:LEU386 4.3 62.4 1.0
O H:LYS392 4.4 65.5 1.0
CB H:ASP383 4.5 52.2 1.0
N H:ASP383 4.5 52.5 1.0
CB H:ASP381 4.5 55.0 1.0
C H:ASP383 4.5 59.5 1.0
CD2 H:LEU386 4.6 65.0 1.0
N H:THR387 4.7 63.3 1.0
CA H:ASP383 4.7 54.2 1.0
C H:GLY384 4.9 54.5 1.0

Calcium binding site 6 out of 8 in 3ghg

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Calcium binding site 6 out of 8 in the Crystal Structure of Human 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 Human Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca601

b:56.9
occ:1.00
 OD2 I:ASP318 1.9 41.1 1.0
OD2 I:ASP320 2.0 41.6 1.0
O I:PHE322 2.5 52.4 1.0
CG I:ASP318 2.7 43.6 1.0
O I:GLY324 2.8 69.1 1.0
OD1 I:ASP318 2.9 43.6 1.0
CG I:ASP320 2.9 43.2 1.0
OD1 I:ASP320 3.3 47.5 1.0
O I:ASP320 3.5 44.8 1.0
O I:GLU323 3.7 53.7 1.0
C I:PHE322 3.7 49.8 1.0
C I:GLY324 3.9 69.3 1.0
C I:GLU323 3.9 55.7 1.0
CB I:ASP318 4.1 44.1 1.0
C I:ASP320 4.2 40.4 1.0
CB I:ASP320 4.2 39.0 1.0
N I:ASP320 4.2 42.8 1.0
CA I:GLU323 4.3 59.6 1.0
CA I:ASP320 4.4 40.4 1.0
N I:GLY324 4.5 64.4 1.0
N I:GLU323 4.5 53.7 1.0
N I:PHE322 4.6 52.0 1.0
CA I:ASN325 4.7 67.0 1.0
CA I:PHE322 4.7 49.0 1.0
N I:ASN325 4.7 70.3 1.0
CA I:GLY324 4.8 67.9 1.0
O I:ASP318 4.9 40.4 1.0
C I:ASP318 4.9 40.5 1.0

Calcium binding site 7 out of 8 in 3ghg

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Calcium binding site 7 out of 8 in the Crystal Structure of Human Fibrinogen


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 Human Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca501

b:68.6
occ:1.00
 OD1 K:ASP381 2.4 59.0 1.0
O K:TRP385 2.4 63.0 1.0
OD2 K:ASP381 2.5 62.0 1.0
CG K:ASP381 2.8 58.5 1.0
OD1 K:ASP383 2.9 58.1 1.0
C K:TRP385 3.4 62.6 1.0
CG K:ASP383 3.6 58.7 1.0
OD2 K:ASP383 3.8 65.4 1.0
CA K:LEU386 4.0 65.2 1.0
N K:LEU386 4.1 63.6 1.0
N K:THR387 4.3 70.0 1.0
O K:ASP383 4.3 61.2 1.0
CA K:TRP385 4.3 61.2 1.0
CB K:ASP381 4.3 56.7 1.0
N K:TRP385 4.4 61.7 1.0
CG K:GLN393 4.4 62.9 1.0
CD2 K:LEU386 4.6 74.9 1.0
CB K:TRP385 4.6 60.6 1.0
C K:LEU386 4.7 66.9 1.0
O K:LYS392 4.8 71.3 1.0
C K:ASP383 4.8 60.5 1.0
N K:ASP383 4.9 60.0 1.0
CB K:ASP383 4.9 60.4 1.0
OG1 K:THR387 5.0 68.6 1.0

Calcium binding site 8 out of 8 in 3ghg

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Calcium binding site 8 out of 8 in the Crystal Structure of Human Fibrinogen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human Fibrinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca601

b:51.4
occ:1.00
 OD2 L:ASP320 2.0 62.8 1.0
OD2 L:ASP318 2.1 66.4 1.0
CG L:ASP318 2.7 64.9 1.0
O L:PHE322 2.7 81.9 1.0
OD1 L:ASP318 2.9 66.8 1.0
O L:ASP320 3.0 66.5 1.0
CG L:ASP320 3.0 63.0 1.0
O L:GLY324 3.1 64.6 1.0
OD1 L:ASP320 3.6 65.3 1.0
N L:ASP320 3.8 68.0 1.0
C L:PHE322 3.8 82.7 1.0
C L:ASP320 3.8 68.8 1.0
CB L:ASP318 3.9 63.0 1.0
O L:ASP318 4.1 56.2 1.0
CA L:ASP320 4.1 66.2 1.0
N L:PHE322 4.1 80.7 1.0
CB L:ASP320 4.2 63.9 1.0
C L:ASP318 4.2 57.5 1.0
C L:GLY324 4.4 68.6 1.0
CA L:PHE322 4.4 79.8 1.0
O L:GLU323 4.5 91.4 1.0
CA L:ASP318 4.6 62.0 1.0
CB L:PHE322 4.6 78.4 1.0
N L:ASN319 4.7 55.9 1.0
C L:GLU323 4.8 88.7 1.0
C L:ASN319 4.8 65.2 1.0
N L:GLU323 4.9 84.9 1.0
N L:LYS321 4.9 71.5 1.0
CA L:ASN325 4.9 74.9 1.0
ND2 L:ASN325 4.9 65.6 1.0

Reference:

J.M.Kollman, L.Pandi, M.R.Sawaya, M.Riley, R.F.Doolittle. Crystal Structure of Human Fibrinogen. Biochemistry V. 48 3877 2009.
ISSN: ISSN 0006-2960
PubMed: 19296670
DOI: 10.1021/BI802205G
Page generated: Sat Jul 13 10:37:27 2024

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