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Calcium in PDB 1iod: Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X

Enzymatic activity of Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X

All present enzymatic activity of Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X:
3.4.21.6;

Protein crystallography data

The structure of Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X, PDB code: 1iod was solved by H.Mizuno, Z.Fujimoto, H.Atoda, T.Morita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.760, 99.760, 90.420, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 26.7

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X (pdb code 1iod). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X, PDB code: 1iod:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 1iod

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Calcium binding site 1 out of 12 in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X


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 the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:20.3
occ:1.00
 O A:SER41 2.3 18.1 1.0
O A:HOH568 2.4 43.1 1.0
OG A:SER41 2.5 24.8 1.0
OE2 A:GLU47 2.5 27.5 1.0
OE2 A:GLU43 2.6 30.6 1.0
OE1 A:GLU128 2.7 26.1 1.0
OE2 A:GLU128 2.7 21.6 1.0
CD A:GLU128 3.0 18.8 1.0
OE1 A:GLU47 3.1 21.9 1.0
CD A:GLU47 3.2 19.9 1.0
C A:SER41 3.4 17.7 1.0
CB A:SER41 3.6 14.2 1.0
CD A:GLU43 3.7 29.8 1.0
CA A:SER41 3.9 17.9 1.0
N A:SER41 4.0 18.2 1.0
CG A:GLU43 4.1 26.6 1.0
N A:GLU43 4.5 25.2 1.0
CD2 A:HIS12 4.5 29.5 1.0
OH A:TYR14 4.5 15.1 1.0
CG A:GLU128 4.6 16.6 1.0
O A:HOH559 4.6 22.1 1.0
N A:ILE42 4.6 20.4 1.0
CB A:GLU43 4.6 26.6 1.0
CG A:GLU47 4.6 21.5 1.0
OE1 A:GLU43 4.7 36.8 1.0
O A:HOH549 4.8 56.7 1.0
ND2 B:ASN281 4.9 28.6 1.0
O A:HOH533 4.9 23.3 1.0
CA A:ILE42 5.0 23.1 1.0

Calcium binding site 2 out of 12 in 1iod

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Calcium binding site 2 out of 12 in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X


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 the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca511

b:26.4
occ:0.50
 O A:HOH580 2.4 30.1 1.0
O A:SER80 2.5 25.8 1.0
OE2 A:GLU82 2.8 38.0 1.0
OE1 A:GLU82 2.9 34.0 1.0
CD A:GLU82 3.2 35.8 1.0
C A:SER80 3.7 20.0 1.0
CA A:ILE81 4.4 21.6 1.0
N A:ILE81 4.5 21.2 1.0
O A:HOH571 4.5 27.5 1.0
CA A:SER80 4.7 21.2 1.0
CG A:GLU82 4.8 31.8 1.0
CB A:SER80 4.8 21.8 1.0
C A:ILE81 4.8 24.2 1.0
N A:GLU82 5.0 26.6 1.0

Calcium binding site 3 out of 12 in 1iod

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Calcium binding site 3 out of 12 in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X


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 the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca512

b:19.9
occ:0.50
 O A:ASP1 2.3 37.0 1.0
O A:HOH575 2.4 73.8 1.0
OD2 A:ASP1 2.6 51.2 1.0
CG A:ASP1 3.0 45.5 1.0
CB A:ASP1 3.3 43.7 1.0
C A:ASP1 3.4 36.6 1.0
O A:HOH582 3.8 32.5 1.0
OD1 A:ASP1 3.9 46.2 1.0
CA A:ASP1 4.0 41.2 1.0
N A:CYS2 4.5 31.3 1.0
N A:ASP1 4.8 39.4 1.0
CA A:CYS2 4.9 24.6 1.0

Calcium binding site 4 out of 12 in 1iod

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Calcium binding site 4 out of 12 in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X


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 the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:34.5
occ:1.00
 OE1 B:GLN243 2.3 46.1 1.0
O B:HOH554 2.4 30.1 1.0
OE2 B:GLU247 2.5 27.5 1.0
OE2 B:GLU320 2.6 36.8 1.0
O B:SER241 2.6 29.9 1.0
O B:HOH529 2.7 44.5 1.0
OE1 B:GLU320 2.8 36.0 1.0
OG B:SER241 3.0 38.7 1.0
CD B:GLU320 3.1 37.5 1.0
OE1 B:GLU247 3.2 27.8 1.0
CD B:GLU247 3.2 25.9 1.0
CD B:GLN243 3.5 42.0 1.0
C B:SER241 3.6 25.2 1.0
CB B:SER241 4.1 30.1 1.0
NE2 B:GLN243 4.2 44.8 1.0
CA B:SER241 4.3 27.2 1.0
N B:SER241 4.3 27.3 1.0
OH B:TYR214 4.4 37.9 1.0
N B:PHE242 4.6 23.7 1.0
CG B:GLU320 4.6 35.6 1.0
CG B:GLN243 4.6 37.9 1.0
N B:GLN243 4.6 27.9 1.0
CG B:GLU247 4.7 23.9 1.0
CA B:PHE242 4.8 24.0 1.0
CD2 B:HIS212 4.8 39.4 1.0
CB B:GLN243 4.8 30.3 1.0
O B:HOH513 4.9 26.2 1.0
CE2 B:TYR214 5.0 30.8 1.0
C B:PHE242 5.0 23.9 1.0

Calcium binding site 5 out of 12 in 1iod

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Calcium binding site 5 out of 12 in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X


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 the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca503

b:13.5
occ:1.00
 OE21 G:CGU425 2.3 16.1 1.0
OE11 G:CGU425 2.3 16.5 1.0
OE12 G:CGU429 2.3 17.4 1.0
O B:HOH505 2.4 22.7 1.0
OE2 A:GLU98 2.4 17.7 1.0
OE22 G:CGU429 2.5 10.3 1.0
CD1 G:CGU429 3.1 16.8 1.0
CD2 G:CGU425 3.1 15.3 1.0
CD1 G:CGU425 3.2 16.1 1.0
CG G:CGU429 3.3 13.0 1.0
CD A:GLU98 3.3 17.5 1.0
CD2 G:CGU429 3.3 12.2 1.0
CG G:CGU425 3.3 17.7 1.0
OE1 A:GLU98 3.3 15.4 1.0
NH2 G:ARG428 3.9 22.4 1.0
O G:HOH47 4.0 13.8 1.0
OE11 G:CGU429 4.2 20.6 1.0
OE22 G:CGU425 4.3 22.3 1.0
OH B:TYR298 4.3 18.5 1.0
OE12 G:CGU425 4.4 14.6 1.0
O G:HOH62 4.4 40.4 1.0
OE21 G:CGU429 4.5 14.5 1.0
CA G:CA504 4.5 14.3 1.0
NZ A:LYS100 4.6 10.8 1.0
CG A:GLU98 4.7 14.3 1.0
CB G:CGU429 4.8 11.0 1.0
NH1 B:ARG307 4.8 15.5 1.0
CB G:CGU425 4.9 13.2 1.0
O G:CGU425 4.9 20.8 1.0
CZ G:ARG428 5.0 23.5 1.0

Calcium binding site 6 out of 12 in 1iod

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Calcium binding site 6 out of 12 in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X


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 the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca504

b:14.3
occ:1.00
 O G:HOH62 2.4 40.4 1.0
OE22 G:CGU407 2.4 8.1 1.0
OE22 G:CGU429 2.4 10.3 1.0
OE12 G:CGU407 2.4 13.2 1.0
O G:HOH47 2.4 13.8 1.0
OE11 G:CGU426 2.4 11.8 1.0
OE21 G:CGU429 2.8 14.5 1.0
CD2 G:CGU429 2.9 12.2 1.0
CD1 G:CGU407 3.3 13.1 1.0
CD2 G:CGU407 3.4 9.3 1.0
CD1 G:CGU426 3.4 14.3 1.0
OE12 G:CGU426 3.7 10.3 1.0
CG G:CGU407 3.8 10.9 1.0
O G:HOH78 4.0 36.8 1.0
CA G:CA505 4.1 9.4 1.0
OE11 G:CGU407 4.2 8.1 1.0
O G:HOH115 4.2 24.2 1.0
ND2 G:ASN402 4.3 11.7 1.0
O B:HOH505 4.4 22.7 1.0
CG G:CGU429 4.4 13.0 1.0
CB G:CGU407 4.5 13.2 1.0
OE11 G:CGU425 4.5 16.5 1.0
CA G:CA503 4.5 13.5 1.0
OE21 G:CGU407 4.6 13.6 1.0
CD1 G:CGU425 4.6 16.1 1.0
OD1 G:ASN402 4.7 17.3 1.0
O G:HOH59 4.8 39.5 1.0
CG G:CGU426 4.8 13.6 1.0
O G:HOH125 4.8 11.9 1.0
CG G:ASN402 4.9 13.8 1.0
CG G:CGU425 4.9 17.7 1.0
OE12 G:CGU425 5.0 14.6 1.0

Calcium binding site 7 out of 12 in 1iod

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Calcium binding site 7 out of 12 in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X


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 the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca505

b:9.4
occ:1.00
 O G:HOH63 2.4 16.9 1.0
O G:HOH102 2.4 6.8 1.0
O G:HOH125 2.4 11.9 1.0
OE12 G:CGU426 2.4 10.3 1.0
OE21 G:CGU429 2.5 14.5 1.0
OE12 G:CGU407 2.5 13.2 1.0
OE22 G:CGU416 2.5 9.0 1.0
OE11 G:CGU407 2.7 8.1 1.0
CD1 G:CGU407 3.0 13.1 1.0
CD1 G:CGU426 3.5 14.3 1.0
CD2 G:CGU416 3.5 8.4 1.0
CA G:CA506 3.6 12.6 1.0
CD2 G:CGU429 3.7 12.2 1.0
OE21 G:CGU416 3.7 4.8 1.0
OE11 G:CGU426 3.9 11.8 1.0
CA G:CA504 4.1 14.3 1.0
CB G:CGU429 4.2 11.0 1.0
OE12 G:CGU406 4.2 15.9 1.0
CA G:GLY411 4.3 17.8 1.0
CG G:CGU407 4.5 10.9 1.0
CG G:CGU429 4.6 13.0 1.0
OE22 G:CGU429 4.6 10.3 1.0
O G:HOH115 4.7 24.2 1.0
O G:CGU426 4.7 17.8 1.0
CG G:CGU426 4.7 13.6 1.0
CA G:CGU426 4.7 15.5 1.0
OD1 G:ASN402 4.8 17.3 1.0
CB G:CGU426 4.8 14.9 1.0
N G:GLY411 4.9 17.2 1.0
O B:HOH528 4.9 31.3 1.0
CG G:CGU416 4.9 7.4 1.0
OE22 G:CGU426 5.0 10.6 1.0

Calcium binding site 8 out of 12 in 1iod

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Calcium binding site 8 out of 12 in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X


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 the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca506

b:12.6
occ:1.00
 OD1 G:ASN402 2.3 17.3 1.0
OE12 G:CGU416 2.3 12.4 1.0
OE11 G:CGU407 2.4 8.1 1.0
OE22 G:CGU416 2.4 9.0 1.0
OE22 G:CGU426 2.5 10.6 1.0
OE12 G:CGU426 2.5 10.3 1.0
OE11 G:CGU406 2.5 22.5 1.0
OE12 G:CGU406 2.9 15.9 1.0
CD1 G:CGU406 3.1 17.6 1.0
CD1 G:CGU416 3.2 12.0 1.0
O G:ALA401 3.2 14.1 1.0
CD1 G:CGU426 3.3 14.3 1.0
CD2 G:CGU416 3.4 8.4 1.0
CD1 G:CGU407 3.4 13.1 1.0
CD2 G:CGU426 3.5 11.2 1.0
CG G:ASN402 3.5 13.8 1.0
CA G:CA505 3.6 9.4 1.0
CG G:CGU416 3.8 7.4 1.0
C G:ALA401 3.9 12.0 1.0
CA G:CA507 3.9 12.1 1.0
CG G:CGU426 3.9 13.6 1.0
OE11 G:CGU416 4.0 12.7 1.0
O G:HOH102 4.2 6.8 1.0
OE12 G:CGU407 4.2 13.2 1.0
CA G:ASN402 4.2 14.3 1.0
OE11 G:CGU426 4.3 11.8 1.0
CG G:CGU407 4.3 10.9 1.0
N G:ASN402 4.3 11.7 1.0
N G:ALA401 4.3 4.1 1.0
ND2 G:ASN402 4.4 11.7 1.0
CB G:ASN402 4.4 14.2 1.0
CB G:CGU416 4.5 11.1 1.0
OE21 G:CGU416 4.5 4.8 1.0
OE21 G:CGU426 4.6 14.4 1.0
CG G:CGU406 4.6 18.2 1.0
CB G:CGU426 4.7 14.9 1.0
CA G:ALA401 4.7 5.6 1.0
O G:HOH63 4.9 16.9 1.0
OE22 G:CGU420 5.0 14.7 1.0

Calcium binding site 9 out of 12 in 1iod

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Calcium binding site 9 out of 12 in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca507

b:12.1
occ:1.00
 O G:HOH123 2.4 20.7 1.0
OE22 G:CGU406 2.4 18.9 1.0
OE11 G:CGU406 2.4 22.5 1.0
O G:ALA401 2.4 14.1 1.0
OE22 G:CGU420 2.4 14.7 1.0
OE12 G:CGU416 2.4 12.4 1.0
OE11 G:CGU416 2.5 12.7 1.0
OE21 G:CGU420 2.6 12.8 1.0
CD1 G:CGU416 2.8 12.0 1.0
CD2 G:CGU420 2.8 10.2 1.0
CD1 G:CGU406 3.0 17.6 1.0
CD2 G:CGU406 3.3 19.5 1.0
C G:ALA401 3.6 12.0 1.0
CG G:CGU406 3.6 18.2 1.0
OE12 G:CGU406 3.7 15.9 1.0
CA G:CA506 3.9 12.6 1.0
N G:ALA401 4.2 4.1 1.0
O G:HOH149 4.2 21.9 1.0
OE21 G:CGU406 4.3 21.6 1.0
CG G:CGU416 4.4 7.4 1.0
CG G:CGU420 4.4 13.1 1.0
CB G:CGU406 4.4 15.4 1.0
CA G:ALA401 4.4 5.6 1.0
N G:ASN402 4.5 11.7 1.0
CA G:ASN402 4.6 14.3 1.0
NE G:ARG415 4.6 8.2 1.0
O G:HOH143 4.7 19.4 1.0
O G:ARG415 4.7 10.5 1.0
CA G:CA508 4.8 19.1 1.0
CB G:ALA401 4.8 2.0 1.0
OE22 G:CGU426 4.8 10.6 1.0
CA G:CGU416 4.8 12.2 1.0
N G:SER403 4.9 17.8 1.0
O G:HOH168 4.9 30.1 1.0
CG G:ARG415 5.0 4.3 1.0
CB G:CGU416 5.0 11.1 1.0

Calcium binding site 10 out of 12 in 1iod

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Calcium binding site 10 out of 12 in the Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the Complex Between the Coagulation Factor X Binding Protein From Snake Venom and the Gla Domain of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca508

b:19.1
occ:1.00
 OE11 G:CGU420 2.4 16.5 1.0
OE21 G:CGU420 2.5 12.8 1.0
O G:HOH143 2.5 19.4 1.0
O G:HOH37 2.5 11.5 1.0
O G:HOH149 2.6 21.9 1.0
CD1 G:CGU420 3.3 12.7 1.0
CD2 G:CGU420 3.4 10.2 1.0
CG G:CGU420 3.5 13.1 1.0
OE12 G:CGU420 4.5 19.0 1.0
O G:ARG415 4.5 10.5 1.0
OE22 G:CGU420 4.5 14.7 1.0
O G:HOH190 4.6 28.5 1.0
O G:HOH84 4.6 26.9 1.0
OE22 G:CGU406 4.6 18.9 1.0
CG G:ARG415 4.7 4.3 1.0
O G:HOH123 4.7 20.7 1.0
CA G:CA507 4.8 12.1 1.0

Reference:

H.Mizuno, Z.Fujimoto, H.Atoda, T.Morita. Crystal Structure of An Anticoagulant Protein in Complex with the Gla Domain of Factor X. Proc.Natl.Acad.Sci.Usa V. 98 7230 2001.
ISSN: ISSN 0027-8424
PubMed: 11404471
DOI: 10.1073/PNAS.131179698
Page generated: Thu Jul 11 10:22:46 2024

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