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Calcium in PDB 2h43: Crystal Structure of Human Fragment D Complexed with Ala-His-Arg-Pro- Amide

Protein crystallography data

The structure of Crystal Structure of Human Fragment D Complexed with Ala-His-Arg-Pro- Amide, PDB code: 2h43 was solved by R.F.Doolittle, L.Pandi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.000, 47.900, 171.400, 90.00, 105.41, 90.00
R / Rfree (%) 25.1 / 30.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Fragment D Complexed with Ala-His-Arg-Pro- Amide (pdb code 2h43). 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 Human Fragment D Complexed with Ala-His-Arg-Pro- Amide, PDB code: 2h43:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2h43

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Calcium binding site 1 out of 6 in the Crystal Structure of Human Fragment D Complexed with Ala-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 Human Fragment D Complexed with Ala-His-Arg-Pro- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:61.0
occ:1.00
 OD2 C:ASP320 2.5 58.0 1.0
O C:PHE322 2.5 73.8 1.0
OD1 C:ASP318 2.7 65.9 1.0
O C:GLY324 2.7 64.9 1.0
OD2 C:ASP318 2.8 55.4 1.0
CG C:ASP318 3.0 53.3 1.0
C C:PHE322 3.6 74.2 1.0
O C:GLU323 3.6 78.9 1.0
CG C:ASP320 3.7 64.7 1.0
O C:ASP320 3.9 64.2 1.0
C C:GLY324 3.9 68.3 1.0
C C:GLU323 4.0 79.6 1.0
N C:PHE322 4.1 66.5 1.0
OD1 C:ASP320 4.3 66.0 1.0
CA C:PHE322 4.4 71.3 1.0
C C:ASP320 4.4 60.4 1.0
N C:GLY324 4.5 80.6 1.0
CB C:ASP318 4.5 53.4 1.0
N C:GLU323 4.5 80.0 1.0
N C:ASP320 4.6 51.5 1.0
CA C:GLU323 4.6 80.0 1.0
CA C:GLY324 4.6 74.1 1.0
CB C:PHE322 4.7 73.6 1.0
CA C:ASP320 4.8 58.1 1.0
CB C:ASP320 4.9 58.1 1.0
N C:ASN325 4.9 66.6 1.0
CA C:ASN325 5.0 62.8 1.0

Calcium binding site 2 out of 6 in 2h43

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Calcium binding site 2 out of 6 in the Crystal Structure of Human Fragment D Complexed with Ala-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 Human Fragment D Complexed with Ala-His-Arg-Pro- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:52.9
occ:1.00
 OD1 B:ASP383 2.7 58.0 1.0
O B:TRP385 2.7 77.9 1.0
OD1 B:ASP381 2.8 43.0 1.0
OD2 B:ASP381 2.9 44.9 1.0
CG B:ASP381 3.2 52.1 1.0
C B:TRP385 3.5 79.6 1.0
CG B:ASP383 3.7 65.2 1.0
OD2 B:ASP383 4.1 65.2 1.0
O B:ASP383 4.1 60.1 1.0
N B:LEU386 4.2 86.9 1.0
CA B:LEU386 4.2 90.5 1.0
N B:TRP385 4.3 72.8 1.0
CA B:TRP385 4.4 74.8 1.0
N B:THR387 4.5 83.9 1.0
C B:ASP383 4.6 63.9 1.0
CB B:ASP381 4.7 52.9 1.0
CB B:TRP385 4.8 78.1 1.0
C B:LEU386 4.8 86.9 1.0
N B:ASP383 4.8 50.6 1.0
CG B:GLN393 4.9 32.3 1.0
CB B:ASP383 4.9 61.8 1.0
O B:THR387 4.9 88.8 1.0

Calcium binding site 3 out of 6 in 2h43

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Calcium binding site 3 out of 6 in the Crystal Structure of Human Fragment D Complexed with Ala-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 Human Fragment D Complexed with Ala-His-Arg-Pro- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:0.4
occ:1.00
 OD2 B:ASP261 3.0 53.5 1.0
O B:GLY263 3.0 34.6 1.0
OE1 C:GLU132 3.3 72.7 1.0
NE2 C:GLN136 3.4 33.7 1.0
CD C:GLU132 3.5 71.9 1.0
OE2 C:GLU132 3.6 69.1 1.0
CG B:ASP261 4.2 51.9 1.0
C B:GLY263 4.2 33.4 1.0
CD C:GLN136 4.4 55.1 1.0
CG C:GLU132 4.4 63.0 1.0
OE1 C:GLN136 4.7 59.1 1.0
OD1 B:ASP261 4.7 57.0 1.0
OH B:TYR378 4.8 56.3 1.0
CE2 B:TYR378 4.9 47.9 1.0

Calcium binding site 4 out of 6 in 2h43

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Calcium binding site 4 out of 6 in the Crystal Structure of Human Fragment D Complexed with Ala-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 Human Fragment D Complexed with Ala-His-Arg-Pro- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2

b:58.5
occ:1.00
 OD1 E:ASP381 2.6 42.4 1.0
OD1 E:ASP383 2.6 59.9 1.0
OD2 E:ASP381 2.8 43.1 1.0
O E:TRP385 2.8 100.0 1.0
CG E:ASP381 3.1 51.6 1.0
CG E:ASP383 3.6 74.2 1.0
C E:TRP385 3.6 93.7 1.0
OD2 E:ASP383 3.9 76.9 1.0
O E:ASP383 4.1 76.6 1.0
N E:TRP385 4.2 89.2 1.0
N E:LEU386 4.2 95.3 1.0
CA E:LEU386 4.3 97.9 1.0
CA E:TRP385 4.4 88.9 1.0
N E:THR387 4.5 94.1 1.0
CB E:ASP381 4.6 46.0 1.0
C E:ASP383 4.6 78.8 1.0
CG E:GLN393 4.6 53.0 1.0
CB E:TRP385 4.7 88.9 1.0
N E:ASP383 4.8 71.8 1.0
CB E:ASP383 4.8 75.1 1.0
C E:LEU386 4.9 95.5 1.0
CG2 E:THR387 4.9 67.4 1.0
CA E:ASP383 5.0 76.7 1.0

Calcium binding site 5 out of 6 in 2h43

Go back to Calcium Binding Sites List in 2h43
Calcium binding site 5 out of 6 in the Crystal Structure of Human Fragment D Complexed with Ala-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 Human Fragment D Complexed with Ala-His-Arg-Pro- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca3

b:0.3
occ:1.00
 O E:GLY263 2.9 53.5 1.0
OE1 F:GLU132 3.1 64.8 1.0
OD2 E:ASP261 3.7 51.5 1.0
C E:GLY263 3.8 51.7 1.0
CA E:GLY263 4.1 40.5 1.0
CD F:GLU132 4.4 65.3 1.0
OD1 E:ASP261 4.4 56.4 1.0
CE2 E:TYR378 4.4 52.7 1.0
CG E:ASP261 4.5 48.4 1.0
N E:GLY263 4.9 44.5 1.0

Calcium binding site 6 out of 6 in 2h43

Go back to Calcium Binding Sites List in 2h43
Calcium binding site 6 out of 6 in the Crystal Structure of Human Fragment D Complexed with Ala-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 Human Fragment D Complexed with Ala-His-Arg-Pro- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1

b:62.8
occ:1.00
 O F:PHE322 2.6 63.7 1.0
OD2 F:ASP318 2.7 54.3 1.0
OD1 F:ASP318 2.7 46.3 1.0
O F:GLY324 2.8 65.0 1.0
OD2 F:ASP320 2.8 72.1 1.0
CG F:ASP318 3.0 50.4 1.0
O F:GLU323 3.4 80.1 1.0
C F:PHE322 3.8 68.2 1.0
C F:GLY324 3.9 72.2 1.0
C F:GLU323 3.9 83.2 1.0
CG F:ASP320 4.0 66.5 1.0
O F:ASP320 4.2 60.8 1.0
CB F:ASP318 4.3 43.1 1.0
OD1 F:ASP320 4.5 74.1 1.0
N F:PHE322 4.5 62.9 1.0
N F:GLY324 4.5 84.6 1.0
CA F:GLY324 4.6 77.8 1.0
N F:GLU323 4.7 73.4 1.0
CA F:PHE322 4.7 67.0 1.0
CA F:GLU323 4.7 80.5 1.0
C F:ASP320 4.7 60.1 1.0
N F:ASP320 4.8 47.5 1.0
N F:ASN325 4.9 71.0 1.0

Reference:

R.F.Doolittle, A.Chen, L.Pandi. Differences in Binding Specificity For the Homologous Gamma- and Beta-Chain "Holes" on Fibrinogen: Exclusive Binding of Ala-His-Arg-Pro-Amide By the Beta-Chain Hole. Biochemistry V. 45 13962 2006.
ISSN: ISSN 0006-2960
PubMed: 17115691
DOI: 10.1021/BI061219E
Page generated: Fri Jul 12 11:00:44 2024

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