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Calcium in PDB 3hdb: Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus

Protein crystallography data

The structure of Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus, PDB code: 3hdb was solved by Z.Q.Zhu, L.W.Niu, M.K.Teng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.27 / 2.31
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 111.190, 122.278, 94.721, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.9

Other elements in 3hdb:

The structure of Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus (pdb code 3hdb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus, PDB code: 3hdb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3hdb

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Calcium binding site 1 out of 7 in the Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus


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 Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca621

b:38.3
occ:1.00
 O A:HOH855 2.2 25.4 1.0
O A:CYS388 2.2 47.2 1.0
O A:HOH701 2.3 41.3 1.0
OE2 A:GLU200 2.4 35.6 1.0
OD1 A:ASN391 2.5 45.8 1.0
OD1 A:ASP284 2.5 38.4 1.0
OD2 A:ASP284 2.8 39.6 1.0
CG A:ASP284 3.0 38.4 1.0
CG A:ASN391 3.4 45.2 1.0
C A:CYS388 3.4 47.2 1.0
CD A:GLU200 3.5 35.5 1.0
ND2 A:ASN391 3.7 44.1 1.0
CG A:GLU200 4.0 35.3 1.0
O A:HOH844 4.3 44.0 1.0
CB A:GLU200 4.3 35.7 1.0
N A:ILE389 4.3 46.6 1.0
CA A:ILE389 4.3 46.4 1.0
O A:TYR198 4.4 41.0 1.0
CA A:CYS388 4.4 47.7 1.0
O A:HOH846 4.5 42.6 1.0
CB A:ASP284 4.5 38.2 1.0
OE1 A:GLU200 4.6 37.1 1.0
O A:ASN391 4.6 44.4 1.0
CB A:CYS388 4.6 47.5 1.0
CB A:ASN391 4.8 45.0 1.0
CE A:LYS282 4.9 50.0 1.0
N A:GLU200 4.9 36.6 1.0
C A:ILE389 4.9 46.3 1.0

Calcium binding site 2 out of 7 in 3hdb

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Calcium binding site 2 out of 7 in the Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus


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 Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca622

b:31.3
occ:1.00
 OE2 A:GLU413 2.3 37.5 1.0
O A:LEU408 2.4 37.0 1.0
OD1 A:ASP416 2.4 36.8 1.0
OE2 A:GLU410 2.4 38.8 1.0
O A:LEU403 2.5 39.7 1.0
OD1 A:ASN406 2.5 40.6 1.0
OE1 A:GLU413 2.6 38.4 1.0
CD A:GLU413 2.8 38.2 1.0
CD A:GLU410 3.4 38.4 1.0
C A:LEU403 3.4 40.0 1.0
CG A:ASP416 3.4 36.7 1.0
CG A:ASN406 3.6 39.1 1.0
C A:LEU408 3.6 37.0 1.0
CG A:GLU410 4.0 37.9 1.0
CB A:ASP416 4.0 38.1 1.0
N A:LEU403 4.1 39.7 1.0
ND2 A:ASN406 4.1 38.1 1.0
CA A:CYS404 4.1 39.9 1.0
N A:LEU408 4.1 37.3 1.0
N A:CYS404 4.2 40.0 1.0
CB A:GLU410 4.2 37.0 1.0
CA A:LEU408 4.3 37.0 1.0
N A:GLY405 4.3 39.5 1.0
CG A:GLU413 4.3 37.8 1.0
N A:GLU410 4.3 36.8 1.0
CA A:LEU403 4.4 40.0 1.0
OE1 A:GLU410 4.4 37.4 1.0
N A:ASN406 4.4 38.9 1.0
OD2 A:ASP416 4.4 33.6 1.0
CB A:LEU408 4.5 36.9 1.0
N A:LEU409 4.6 36.7 1.0
C A:CYS404 4.7 39.9 1.0
CB A:ASN406 4.8 39.0 1.0
CA A:LEU409 4.8 36.7 1.0
O A:HOH830 4.9 32.2 1.0
N A:GLU407 4.9 38.5 1.0
C A:LEU409 4.9 36.6 1.0
CA A:GLU410 4.9 37.4 1.0
CA A:ASN406 5.0 38.9 1.0

Calcium binding site 3 out of 7 in 3hdb

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Calcium binding site 3 out of 7 in the Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus


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 Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca623

b:16.4
occ:1.00
 OD1 A:ASP467 2.2 36.3 1.0
OD1 A:ASP482 2.2 36.1 1.0
O A:PRO468 2.3 32.9 1.0
O A:HOH742 2.5 27.5 1.0
OE2 A:GLU470 2.5 28.9 1.0
O A:VAL483 2.6 37.0 1.0
OE1 A:GLU470 2.6 28.5 1.0
CD A:GLU470 2.9 29.5 1.0
CG A:ASP467 3.3 34.2 1.0
CG A:ASP482 3.5 36.1 1.0
C A:PRO468 3.5 32.8 1.0
N A:VAL483 3.6 36.7 1.0
C A:VAL483 3.7 36.9 1.0
OD2 A:ASP467 3.7 34.4 1.0
OD2 A:ASP482 4.1 34.9 1.0
N A:PRO468 4.1 33.6 1.0
CA A:VAL483 4.2 36.8 1.0
C A:ASP467 4.3 33.8 1.0
CA A:PRO468 4.4 33.0 1.0
C A:ASP482 4.4 36.7 1.0
CA A:ASP482 4.4 36.4 1.0
N A:ALA469 4.4 32.4 1.0
CG A:GLU470 4.4 28.8 1.0
CG A:PRO468 4.4 33.6 1.0
CD A:PRO468 4.5 33.8 1.0
CA A:ALA469 4.5 31.8 1.0
CB A:ASP467 4.5 34.1 1.0
O A:HOH745 4.5 30.6 1.0
CB A:ASP482 4.5 36.2 1.0
C A:ALA469 4.6 31.3 1.0
CD1 A:PHE484 4.6 36.2 1.0
CA A:ASP467 4.6 34.0 1.0
O A:ASP467 4.7 33.5 1.0
CD A:ARG460 4.7 32.1 1.0
N A:GLU470 4.7 30.9 1.0
N A:PHE484 4.8 36.9 1.0
CE1 A:PHE484 4.8 36.5 1.0
CB A:VAL483 4.9 36.6 1.0
CB A:PRO468 4.9 33.0 1.0

Calcium binding site 4 out of 7 in 3hdb

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Calcium binding site 4 out of 7 in the Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus


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 Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca654

b:78.5
occ:1.00
 O A:ALA279 3.8 51.6 1.0
O A:LEU278 3.9 50.6 1.0
C A:ALA279 4.1 51.4 1.0
N A:LYS281 4.2 49.8 1.0
C A:GLU280 4.4 50.5 1.0
N A:GLU280 4.6 51.4 1.0
N A:LYS282 4.6 46.8 1.0
C A:LYS281 4.6 48.0 1.0
CA A:ALA279 4.7 51.1 1.0
CA A:LYS281 4.8 49.0 1.0
CA A:GLU280 4.8 51.4 1.0
O A:GLU280 4.8 50.5 1.0
C A:LEU278 4.9 50.6 1.0

Calcium binding site 5 out of 7 in 3hdb

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Calcium binding site 5 out of 7 in the Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus


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 Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca655

b:79.5
occ:1.00
 N A:ASP523 3.0 40.2 1.0
OE1 A:GLU522 3.3 49.6 1.0
CG A:ASP523 3.4 41.2 1.0
OD1 A:ASP523 3.6 44.7 1.0
CB A:ASP523 3.6 40.0 1.0
OD2 A:ASP523 3.6 40.5 1.0
CA A:GLU522 3.7 41.9 1.0
O A:HOH939 3.7 38.4 1.0
C A:GLU522 3.8 41.0 1.0
CA A:ASP523 3.9 39.4 1.0
CB A:GLU522 3.9 42.0 1.0
CD A:GLU522 4.1 48.3 1.0
CG A:GLU522 4.6 45.0 1.0
OE2 A:GLU522 4.9 49.5 1.0
N A:GLU522 5.0 42.1 1.0

Calcium binding site 6 out of 7 in 3hdb

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Calcium binding site 6 out of 7 in the Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus


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 Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca656

b:49.1
occ:1.00
 O A:LEU558 2.7 26.4 1.0
N A:PHE574 2.8 28.1 1.0
O A:GLY583 2.8 27.2 1.0
CA A:MET573 3.4 28.7 1.0
CB A:MET573 3.5 28.8 1.0
CA A:GLY583 3.5 27.7 1.0
C A:MET573 3.5 28.6 1.0
C A:GLY583 3.5 27.3 1.0
C A:LEU558 3.6 26.7 1.0
CD A:ARG557 3.6 23.1 1.0
O A:PHE574 3.7 28.6 1.0
N A:LEU558 3.7 26.9 1.0
CA A:PHE574 3.8 27.8 1.0
CB A:LEU558 3.8 26.6 1.0
CA A:LEU558 3.9 26.6 1.0
CG A:ARG557 3.9 25.1 1.0
CB A:PHE574 4.0 27.7 1.0
CD1 A:LEU513 4.1 36.7 1.0
C A:PHE574 4.2 28.1 1.0
CG A:LEU558 4.5 26.5 1.0
CZ A:PHE514 4.7 36.3 1.0
O A:MET573 4.7 28.3 1.0
C A:ARG557 4.7 26.5 1.0
N A:MET573 4.8 29.8 1.0
N A:TYR559 4.8 27.6 1.0
CD2 A:LEU558 4.8 25.7 1.0
N A:MET584 4.8 26.8 1.0
CE1 A:PHE514 4.8 36.6 1.0
CG A:MET573 4.8 27.3 1.0
O A:LYS572 4.9 30.4 1.0
N A:GLY583 4.9 28.2 1.0
NE A:ARG557 5.0 23.5 1.0

Calcium binding site 7 out of 7 in 3hdb

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Calcium binding site 7 out of 7 in the Crystal Structure of Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus


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 Aahiv, A Metalloproteinase From Venom of Agkistrodon Acutus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca657

b:73.4
occ:1.00
 O A:HOH831 2.5 34.8 1.0
O A:PHE294 2.5 38.7 1.0
O A:GLY296 2.6 43.6 1.0
OD1 A:ASP293 2.7 41.9 1.0
NZ L:LYS1 3.3 59.2 1.0
CG A:ASP293 3.3 38.7 1.0
O A:HOH836 3.3 44.4 1.0
OD2 A:ASP293 3.5 40.2 1.0
C A:PHE294 3.6 38.9 1.0
C A:GLY296 3.8 43.6 1.0
N A:PHE294 4.0 37.3 1.0
N A:GLY296 4.2 42.8 1.0
C A:ASP293 4.3 36.7 1.0
OE1 A:GLN318 4.3 37.5 1.0
CA A:PHE294 4.4 38.0 1.0
C A:ARG295 4.4 42.2 1.0
CB A:ASP293 4.5 36.8 1.0
O A:ILE298 4.6 42.1 1.0
CA A:GLY296 4.6 43.4 1.0
N A:ARG295 4.6 40.3 1.0
CA A:ASP293 4.6 36.4 1.0
CE L:LYS1 4.7 59.3 1.0
N A:SER297 4.7 44.0 1.0
O A:ASP293 4.8 37.1 1.0
NE2 A:GLN318 4.8 39.1 1.0
CA A:ARG295 4.8 41.9 1.0
O A:ARG295 4.8 42.4 1.0
CB A:PHE294 4.8 37.7 1.0
CA A:SER297 4.8 44.5 1.0

Reference:

Z.Zhu, Y.Gao, Z.Zhu, Y.Yu, X.Zhang, J.Zang, M.Teng, L.Niu. Structural Basis of the Autolysis of Aahiv Suggests A Novel Target Recognizing Model For Adam/Reprolysin Family Proteins Biochem.Biophys.Res.Commun. V. 386 159 2009.
ISSN: ISSN 0006-291X
PubMed: 19505434
DOI: 10.1016/J.BBRC.2009.06.004
Page generated: Tue Jul 8 12:57:02 2025

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