Atomistry » Calcium » PDB 1iqj-1j1n » 1ixx
Atomistry »
  Calcium »
    PDB 1iqj-1j1n »
      1ixx »

Calcium in PDB 1ixx: Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains

Protein crystallography data

The structure of Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains, PDB code: 1ixx was solved by H.Mizuno, Z.Fujimoto, M.Koizumi, H.Kano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 172.200, 85.700, 65.200, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains (pdb code 1ixx). 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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains, PDB code: 1ixx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1ixx

Go back to Calcium Binding Sites List in 1ixx
Calcium binding site 1 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca130

b:35.2
occ:1.00
 O A:SER41 2.5 21.4 1.0
OE2 A:GLU128 2.6 23.9 1.0
OE1 A:GLU128 2.6 24.1 1.0
O A:HOH147 2.6 55.6 1.0
OE2 A:GLU47 2.6 32.8 1.0
OG A:SER41 2.7 27.2 1.0
OE2 A:GLU43 2.7 17.7 1.0
CD A:GLU128 2.9 19.6 1.0
CD A:GLU47 3.5 32.0 1.0
OE1 A:GLU47 3.6 37.6 1.0
C A:SER41 3.6 24.2 1.0
CD A:GLU43 3.8 21.7 1.0
CB A:SER41 3.9 12.6 1.0
OH A:TYR14 4.0 24.7 1.0
CA A:SER41 4.2 18.1 1.0
N A:SER41 4.3 10.2 1.0
CG A:GLU128 4.4 18.3 1.0
OE1 A:GLU43 4.5 25.4 1.0
CG A:GLU43 4.7 19.7 1.0
O A:HOH138 4.7 71.9 1.0
CD2 A:HIS12 4.7 20.7 1.0
N A:ILE42 4.7 20.1 1.0
O A:HOH146 4.8 35.7 1.0
CE2 A:TYR14 4.8 22.3 1.0
CZ A:TYR14 4.9 20.9 1.0
CG A:GLU47 4.9 30.4 1.0
N A:GLU43 4.9 22.1 1.0
CB A:GLU43 5.0 14.2 1.0

Calcium binding site 2 out of 6 in 1ixx

Go back to Calcium Binding Sites List in 1ixx
Calcium binding site 2 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca124

b:27.7
occ:1.00
 O B:SER41 2.3 20.8 1.0
OE1 B:GLN43 2.4 35.0 1.0
OG B:SER41 2.4 31.7 1.0
OE2 B:GLU47 2.5 27.4 1.0
OE2 B:GLU120 2.7 31.1 1.0
OE1 B:GLU120 2.9 32.8 1.0
CD B:GLU120 3.1 27.1 1.0
C B:SER41 3.3 20.4 1.0
CD B:GLU47 3.3 19.4 1.0
OE1 B:GLU47 3.4 21.1 1.0
CB B:SER41 3.6 19.6 1.0
CD B:GLN43 3.6 32.8 1.0
CA B:SER41 3.9 21.7 1.0
N B:SER41 4.1 22.8 1.0
N B:PHE42 4.3 22.9 1.0
NE2 B:GLN43 4.4 30.9 1.0
OH B:TYR14 4.5 18.9 1.0
CG B:GLU120 4.6 20.7 1.0
CA B:PHE42 4.7 26.5 1.0
CG B:GLU47 4.7 19.3 1.0
OD2 A:ASP85 4.7 31.8 1.0
CG B:GLN43 4.7 39.6 1.0
N B:GLN43 4.7 30.8 1.0
O B:HOH137 4.8 28.6 1.0
CB B:GLN43 4.8 40.6 1.0
C B:PHE42 4.9 26.6 1.0
CE2 B:TYR14 4.9 19.1 1.0
CD2 B:HIS12 4.9 28.4 1.0

Calcium binding site 3 out of 6 in 1ixx

Go back to Calcium Binding Sites List in 1ixx
Calcium binding site 3 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca130

b:28.4
occ:1.00
 O C:SER41 2.3 19.4 1.0
O C:HOH145 2.4 41.9 1.0
OG C:SER41 2.4 33.1 1.0
OE2 C:GLU47 2.5 22.9 1.0
OE2 C:GLU43 2.8 43.7 1.0
OE2 C:GLU128 2.8 55.3 1.0
OE1 C:GLU128 2.9 34.5 1.0
OE1 C:GLU47 3.2 28.9 1.0
CD C:GLU128 3.2 41.0 1.0
CD C:GLU47 3.2 15.9 1.0
C C:SER41 3.4 16.9 1.0
CB C:SER41 3.6 25.4 1.0
CD C:GLU43 3.6 34.3 1.0
CG C:GLU43 3.7 26.2 1.0
CA C:SER41 3.9 16.6 1.0
N C:SER41 4.1 16.0 1.0
OH C:TYR14 4.3 45.6 1.0
CB C:GLU43 4.5 20.9 1.0
N C:ILE42 4.5 18.2 1.0
N C:GLU43 4.5 22.2 1.0
CG C:GLU47 4.7 18.7 1.0
CG C:GLU128 4.7 39.1 1.0
OE1 C:GLU43 4.8 44.8 1.0
CE2 C:TYR14 4.9 38.3 1.0
CA C:ILE42 4.9 16.5 1.0

Calcium binding site 4 out of 6 in 1ixx

Go back to Calcium Binding Sites List in 1ixx
Calcium binding site 4 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca124

b:41.4
occ:1.00
 OE1 D:GLN43 2.3 49.3 1.0
O D:SER41 2.3 42.8 1.0
OE2 D:GLU47 2.6 23.8 1.0
OE2 D:GLU120 2.6 36.5 1.0
OG D:SER41 2.7 56.9 1.0
OE1 D:GLU47 3.3 25.5 1.0
OE1 D:GLU120 3.3 38.2 1.0
CD D:GLU47 3.3 21.5 1.0
CD D:GLU120 3.4 32.5 1.0
C D:SER41 3.5 35.1 1.0
CD D:GLN43 3.5 42.7 1.0
CB D:SER41 3.9 45.5 1.0
CA D:SER41 4.1 37.1 1.0
NE2 D:GLN43 4.2 31.8 1.0
OH D:TYR14 4.3 31.3 1.0
N D:SER41 4.3 34.8 1.0
N D:PHE42 4.5 36.0 1.0
N D:GLN43 4.6 40.3 1.0
CB D:GLN43 4.6 40.1 1.0
CG D:GLN43 4.7 41.5 1.0
CA D:PHE42 4.7 38.1 1.0
CG D:GLU47 4.8 20.4 1.0
CG D:GLU120 4.8 26.0 1.0
C D:PHE42 4.9 39.8 1.0
CE2 D:TYR14 5.0 31.2 1.0
CD2 D:HIS12 5.0 36.5 1.0

Calcium binding site 5 out of 6 in 1ixx

Go back to Calcium Binding Sites List in 1ixx
Calcium binding site 5 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca130

b:25.9
occ:1.00
 O E:SER41 2.4 25.0 1.0
OE1 E:GLU128 2.6 21.8 1.0
OG E:SER41 2.6 22.8 1.0
OE2 E:GLU47 2.6 11.1 1.0
OE2 E:GLU43 2.6 24.4 1.0
OE2 E:GLU128 2.8 24.3 1.0
CD E:GLU128 3.0 12.3 1.0
OE1 E:GLU47 3.1 7.1 1.0
CD E:GLU47 3.2 7.7 1.0
C E:SER41 3.5 18.1 1.0
CD E:GLU43 3.6 20.8 1.0
CB E:SER41 3.7 9.7 1.0
CG E:GLU43 3.8 18.6 1.0
O E:HOH154 4.0 37.7 1.0
CA E:SER41 4.0 17.2 1.0
N E:SER41 4.2 19.4 1.0
OH E:TYR14 4.3 21.7 1.0
CB E:GLU43 4.5 16.3 1.0
CG E:GLU128 4.5 12.7 1.0
N E:ILE42 4.6 14.5 1.0
O E:HOH139 4.6 27.4 1.0
N E:GLU43 4.6 16.3 1.0
CG E:GLU47 4.7 13.0 1.0
OE1 E:GLU43 4.8 26.5 1.0
O E:HOH136 4.9 26.7 1.0
CA E:ILE42 5.0 12.0 1.0

Calcium binding site 6 out of 6 in 1ixx

Go back to Calcium Binding Sites List in 1ixx
Calcium binding site 6 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca124

b:39.5
occ:1.00
 OE1 F:GLN43 2.3 46.8 1.0
OG F:SER41 2.6 34.6 1.0
OE2 F:GLU47 2.7 15.2 1.0
O F:SER41 2.7 24.4 1.0
OE2 F:GLU120 2.7 42.4 1.0
OE1 F:GLU47 3.2 6.5 1.0
CD F:GLU47 3.3 9.1 1.0
OE1 F:GLU120 3.4 43.3 1.0
CD F:GLU120 3.4 39.4 1.0
CD F:GLN43 3.6 38.0 1.0
C F:SER41 3.6 25.6 1.0
CB F:SER41 3.8 22.4 1.0
CA F:SER41 4.2 22.8 1.0
OH F:TYR14 4.3 22.9 1.0
NE2 F:GLN43 4.3 39.3 1.0
N F:SER41 4.4 29.0 1.0
CG F:GLN43 4.6 41.0 1.0
N F:GLN43 4.7 26.9 1.0
OD2 E:ASP85 4.7 36.7 1.0
N F:PHE42 4.7 21.8 1.0
CB F:GLN43 4.7 35.1 1.0
CG F:GLU47 4.7 14.3 1.0
CD2 F:HIS12 4.8 25.2 1.0
CE2 F:TYR14 4.8 23.3 1.0
CG F:GLU120 4.8 38.0 1.0
NE2 F:HIS12 4.9 20.7 1.0
CA F:PHE42 5.0 14.2 1.0

Reference:

H.Mizuno, Z.Fujimoto, M.Koizumi, H.Kano, H.Atoda, T.Morita. Structure of Coagulation Factors IX/X-Binding Protein, A Heterodimer of C-Type Lectin Domains. Nat.Struct.Biol. V. 4 438 1997.
ISSN: ISSN 1072-8368
PubMed: 9187649
DOI: 10.1038/NSB0697-438
Page generated: Thu Jul 11 10:28:03 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy