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Calcium in PDB 1lwu: Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide

Protein crystallography data

The structure of Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide, PDB code: 1lwu was solved by Z.Yang, G.Spraggon, L.Pandi, S.J.Everse, M.Riley, R.F.Doolittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.735, 47.654, 244.650, 88.81, 97.23, 86.17
R / Rfree (%) 24.5 / 28.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide (pdb code 1lwu). 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 Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide, PDB code: 1lwu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1lwu

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Calcium binding site 1 out of 8 in the Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide 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 Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:56.2
occ:1.00
 OD1 B:ASP403 2.0 56.7 1.0
O B:LYS412 2.3 52.5 1.0
O B:TRP405 2.4 60.2 1.0
OD2 B:ASP401 2.4 60.2 1.0
OD1 B:ASP401 3.0 58.8 1.0
CG B:ASP401 3.1 54.5 1.0
CG B:ASP403 3.1 65.2 1.0
C B:TRP405 3.4 56.7 1.0
C B:LYS412 3.5 54.0 1.0
OD2 B:ASP403 3.5 74.5 1.0
N B:TRP405 3.8 43.3 1.0
CB B:TRP405 3.9 49.5 1.0
CA B:TRP405 3.9 50.7 1.0
O B:ASP403 4.2 48.5 1.0
CB B:LYS412 4.3 64.7 1.0
N B:HIS413 4.4 48.2 1.0
CA B:HIS413 4.4 48.4 1.0
CB B:ASP403 4.4 55.9 1.0
O B:ASN406 4.4 31.8 1.0
C B:ASN406 4.4 41.4 1.0
N B:ASN406 4.5 59.7 1.0
CA B:LYS412 4.5 58.7 1.0
C B:ASP403 4.5 59.0 1.0
CG B:TRP405 4.5 48.8 1.0
CB B:ASP401 4.5 50.2 1.0
N B:PRO407 4.6 41.6 1.0
O B:ASP409 4.6 74.8 1.0
N B:ASP403 4.7 44.2 1.0
CA B:PRO407 4.8 53.8 1.0
CA B:ASP403 4.8 50.5 1.0
CE3 B:TRP405 4.8 50.8 1.0
N B:CYS414 4.8 48.4 1.0
CD2 B:TRP405 4.9 53.1 1.0
CA B:ASN406 4.9 48.4 1.0

Calcium binding site 2 out of 8 in 1lwu

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Calcium binding site 2 out of 8 in the Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide 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 Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2

b:52.8
occ:1.00
 OD2 E:ASP401 2.3 48.6 1.0
OD1 E:ASP403 2.4 16.7 1.0
O E:LYS412 2.5 57.4 1.0
O E:TRP405 2.5 51.6 1.0
OD1 E:ASP401 2.9 55.8 1.0
CG E:ASP401 2.9 44.2 1.0
CG E:ASP403 3.5 47.3 1.0
C E:TRP405 3.5 43.5 1.0
C E:LYS412 3.7 49.6 1.0
OD2 E:ASP403 4.0 52.6 1.0
O E:ASN406 4.0 32.8 1.0
N E:TRP405 4.1 41.6 1.0
C E:ASN406 4.1 39.5 1.0
CA E:TRP405 4.2 44.4 1.0
O E:ASP403 4.2 44.5 1.0
N E:PRO407 4.3 37.6 1.0
CB E:TRP405 4.3 18.6 1.0
O E:ASP409 4.3 52.2 1.0
CA E:PRO407 4.3 41.4 1.0
CB E:ASP401 4.4 39.2 1.0
CB E:LYS412 4.4 42.0 1.0
N E:ASN406 4.5 39.6 1.0
N E:HIS413 4.6 40.9 1.0
CA E:HIS413 4.7 30.3 1.0
CA E:LYS412 4.7 50.7 1.0
C E:ASP403 4.7 56.5 1.0
CB E:ASP403 4.8 50.3 1.0
CA E:ASN406 4.8 38.2 1.0
N E:ASP403 4.8 35.7 1.0
CG E:TRP405 4.9 19.7 1.0
C E:PRO407 5.0 47.1 1.0
CA E:ASP403 5.0 46.4 1.0

Calcium binding site 3 out of 8 in 1lwu

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Calcium binding site 3 out of 8 in the Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide 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 Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca3

b:57.5
occ:1.00
 OD1 H:ASP403 2.3 56.7 1.0
OD2 H:ASP401 2.4 49.8 1.0
O H:TRP405 2.4 69.0 1.0
O H:LYS412 2.5 62.6 1.0
OD1 H:ASP401 3.0 50.9 1.0
CG H:ASP401 3.0 53.4 1.0
C H:TRP405 3.4 67.7 1.0
CG H:ASP403 3.4 70.1 1.0
C H:LYS412 3.7 61.7 1.0
OD2 H:ASP403 3.9 69.1 1.0
N H:TRP405 3.9 59.7 1.0
CA H:TRP405 4.0 64.6 1.0
O H:ASN406 4.0 59.8 1.0
C H:ASN406 4.1 59.4 1.0
CB H:TRP405 4.1 49.7 1.0
O H:ASP403 4.2 68.1 1.0
N H:PRO407 4.2 59.6 1.0
CA H:PRO407 4.3 68.2 1.0
CB H:LYS412 4.4 67.9 1.0
N H:ASN406 4.4 63.0 1.0
O H:ASP409 4.4 72.4 1.0
CB H:ASP401 4.5 47.1 1.0
C H:ASP403 4.6 70.9 1.0
N H:HIS413 4.6 57.6 1.0
CA H:LYS412 4.7 64.9 1.0
CB H:ASP403 4.7 61.1 1.0
CA H:HIS413 4.7 53.2 1.0
CA H:ASN406 4.7 63.4 1.0
CG H:TRP405 4.8 44.2 1.0
N H:ASP403 4.8 53.2 1.0
CA H:ASP403 4.9 64.0 1.0
CD H:PRO407 5.0 65.7 1.0

Calcium binding site 4 out of 8 in 1lwu

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Calcium binding site 4 out of 8 in the Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide 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 Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca4

b:57.9
occ:1.00
 O K:LYS412 2.2 57.2 1.0
O K:TRP405 2.3 79.1 1.0
OD1 K:ASP403 2.4 55.0 1.0
OD2 K:ASP401 2.4 60.0 1.0
CG K:ASP401 3.1 55.6 1.0
OD1 K:ASP401 3.2 66.6 1.0
C K:TRP405 3.4 66.2 1.0
C K:LYS412 3.4 50.0 1.0
CG K:ASP403 3.5 65.9 1.0
OD2 K:ASP403 3.9 73.7 1.0
CA K:TRP405 4.0 52.9 1.0
N K:TRP405 4.0 47.9 1.0
CB K:LYS412 4.1 57.5 1.0
CB K:TRP405 4.1 40.7 1.0
O K:ASN406 4.1 61.5 1.0
C K:ASN406 4.2 53.6 1.0
O K:ASP409 4.3 81.7 1.0
CA K:LYS412 4.3 55.9 1.0
N K:HIS413 4.3 45.0 1.0
N K:PRO407 4.4 36.0 1.0
N K:ASN406 4.4 70.1 1.0
O K:ASP403 4.4 61.3 1.0
CA K:HIS413 4.4 47.5 1.0
CA K:PRO407 4.5 46.5 1.0
CB K:ASP401 4.6 35.4 1.0
CG K:TRP405 4.7 32.7 1.0
CA K:ASN406 4.7 62.7 1.0
CB K:ASP403 4.8 60.6 1.0
C K:ASP403 4.8 61.2 1.0
CE3 K:TRP405 5.0 36.0 1.0
CD2 K:TRP405 5.0 30.2 1.0

Calcium binding site 5 out of 8 in 1lwu

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Calcium binding site 5 out of 8 in the Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide 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 Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca5

b:82.6
occ:1.00
 OD1 C:ASP316 2.3 0.9 1.0
O C:TYR320 2.5 0.2 1.0
OD2 C:ASP316 2.7 0.7 1.0
CG C:ASP316 2.7 0.9 1.0
OD1 C:ASP318 2.8 86.2 1.0
O C:GLY322 3.0 0.4 1.0
O C:ASP318 3.6 85.5 1.0
C C:TYR320 3.6 0.2 1.0
O C:GLU321 3.9 0.8 1.0
CG C:ASP318 4.0 85.7 1.0
CB C:ASP316 4.0 0.2 1.0
C C:GLU321 4.0 0.3 1.0
C C:GLY322 4.1 0.6 1.0
N C:TYR320 4.1 0.3 1.0
C C:ASP318 4.3 93.9 1.0
N C:GLU321 4.5 0.7 1.0
N C:GLY322 4.5 0.1 1.0
CA C:TYR320 4.5 0.9 1.0
CA C:GLU321 4.5 0.7 1.0
N C:ASP318 4.5 92.2 1.0
OD2 C:ASP318 4.7 83.8 1.0
CA C:GLY322 4.8 0.9 1.0
O C:ASP316 4.8 92.1 1.0
C C:ASP316 4.8 95.0 1.0
CA C:ASP318 4.8 92.6 1.0
CA C:ASP316 5.0 94.5 1.0

Calcium binding site 6 out of 8 in 1lwu

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Calcium binding site 6 out of 8 in the Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide 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 Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca6

b:94.7
occ:1.00
 OD1 F:ASP318 2.1 92.0 1.0
O F:TYR320 2.1 0.4 1.0
OD1 F:ASP316 2.2 0.5 1.0
O F:GLY322 2.4 0.7 1.0
OD2 F:ASP316 2.4 0.8 1.0
CG F:ASP316 2.6 0.7 1.0
C F:TYR320 3.3 0.4 1.0
CG F:ASP318 3.3 90.8 1.0
O F:ASP318 3.5 92.6 1.0
C F:GLY322 3.6 0.7 1.0
N F:TYR320 3.8 0.1 1.0
OD2 F:ASP318 3.9 96.7 1.0
C F:GLU321 4.0 1.0 1.0
O F:GLU321 4.0 0.3 1.0
CA F:TYR320 4.0 0.9 1.0
C F:ASP318 4.0 98.1 1.0
CB F:ASP316 4.1 93.4 1.0
N F:GLY322 4.2 0.3 1.0
N F:ASP318 4.3 84.9 1.0
N F:GLU321 4.3 0.7 1.0
CA F:GLY322 4.4 0.2 1.0
CB F:ASP318 4.4 88.8 1.0
CB F:TYR320 4.4 0.5 1.0
CA F:ASP318 4.4 92.3 1.0
N F:SER323 4.5 0.4 1.0
CA F:GLU321 4.5 0.9 1.0
CA F:SER323 4.6 0.2 1.0
N F:LYS319 4.8 0.6 1.0
C F:ASP316 4.9 81.9 1.0
C F:LYS319 4.9 0.9 1.0
CD1 F:TYR320 4.9 98.4 1.0
CA F:ASP316 5.0 85.3 1.0

Calcium binding site 7 out of 8 in 1lwu

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Calcium binding site 7 out of 8 in the Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide 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 Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca7

b:0.8
occ:1.00
 O I:TYR320 2.2 0.5 1.0
OD1 I:ASP316 2.2 96.8 1.0
OD1 I:ASP318 2.3 99.6 1.0
OD2 I:ASP316 2.5 91.6 1.0
O I:GLY322 2.6 0.2 1.0
CG I:ASP316 2.6 94.1 1.0
C I:TYR320 3.3 0.2 1.0
O I:ASP318 3.5 92.4 1.0
CG I:ASP318 3.5 98.8 1.0
C I:GLY322 3.7 0.4 1.0
N I:TYR320 3.9 0.6 1.0
O I:GLU321 3.9 0.3 1.0
C I:GLU321 4.0 0.7 1.0
CB I:ASP316 4.1 89.8 1.0
C I:ASP318 4.1 91.7 1.0
CA I:TYR320 4.1 0.8 1.0
OD2 I:ASP318 4.2 98.2 1.0
N I:GLY322 4.2 1.0 1.0
N I:GLU321 4.3 0.1 1.0
N I:ASP318 4.4 81.7 1.0
CA I:GLU321 4.5 0.9 1.0
CA I:GLY322 4.5 0.2 1.0
CA I:ASP318 4.6 90.5 1.0
CB I:ASP318 4.6 92.3 1.0
CB I:TYR320 4.6 0.3 1.0
N I:SER323 4.7 0.2 1.0
CA I:SER323 4.8 0.4 1.0
C I:ASP316 4.9 73.2 1.0
N I:LYS319 4.9 92.7 1.0
CA I:ASP316 5.0 81.5 1.0
O I:ASP316 5.0 65.9 1.0

Calcium binding site 8 out of 8 in 1lwu

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Calcium binding site 8 out of 8 in the Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide 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 8 of Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca8

b:93.6
occ:1.00
 OD1 L:ASP316 2.1 0.8 1.0
CG L:ASP316 2.6 97.5 1.0
OD2 L:ASP316 2.7 87.8 1.0
O L:TYR320 2.8 0.3 1.0
OD1 L:ASP318 3.0 89.3 1.0
O L:GLY322 3.3 0.7 1.0
O L:ASP318 3.6 92.5 1.0
CB L:ASP316 3.9 93.4 1.0
C L:TYR320 3.9 0.6 1.0
O L:GLU321 4.0 0.1 1.0
CG L:ASP318 4.1 94.6 1.0
C L:GLU321 4.3 0.8 1.0
C L:GLY322 4.3 0.3 1.0
C L:ASP318 4.4 97.2 1.0
N L:TYR320 4.4 0.8 1.0
N L:ASP318 4.5 90.3 1.0
O L:ASP316 4.5 82.0 1.0
C L:ASP316 4.6 91.5 1.0
N L:GLY322 4.7 0.4 1.0
N L:GLU321 4.7 0.8 1.0
CA L:GLU321 4.8 0.6 1.0
CA L:TYR320 4.8 0.1 1.0
OD2 L:ASP318 4.8 88.3 1.0
CA L:ASP316 4.8 91.8 1.0
CA L:ASP318 4.9 95.8 1.0
CA L:GLY322 5.0 0.4 1.0

Reference:

Z.Yang, G.Spraggon, L.Pandi, S.J.Everse, M.Riley, R.F.Doolittle. Crystal Structure of Fragment D From Lamprey Fibrinogen Complexed with the Peptide Gly-His-Arg-Pro-Amide. Biochemistry V. 41 10218 2002.
ISSN: ISSN 0006-2960
PubMed: 12162736
DOI: 10.1021/BI020299T
Page generated: Thu Jul 11 12:10:33 2024

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