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Calcium in PDB 2e3x: Crystal Structure of Russell'S Viper Venom Metalloproteinase

Enzymatic activity of Crystal Structure of Russell'S Viper Venom Metalloproteinase

All present enzymatic activity of Crystal Structure of Russell'S Viper Venom Metalloproteinase:
3.4.24.58;

Protein crystallography data

The structure of Crystal Structure of Russell'S Viper Venom Metalloproteinase, PDB code: 2e3x was solved by T.Igarashi, S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.60 / 2.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.350, 91.730, 152.930, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 27.3

Other elements in 2e3x:

The structure of Crystal Structure of Russell'S Viper Venom Metalloproteinase also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Russell'S Viper Venom Metalloproteinase (pdb code 2e3x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Russell'S Viper Venom Metalloproteinase, PDB code: 2e3x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2e3x

Go back to Calcium Binding Sites List in 2e3x
Calcium binding site 1 out of 5 in the Crystal Structure of Russell'S Viper Venom Metalloproteinase


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 Russell'S Viper Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:55.3
occ:1.00
 OE2 A:GLU14 2.3 76.3 1.0
OD2 A:ASP96 2.4 64.7 1.0
O A:CYS200 2.4 58.7 1.0
OD1 A:ASP96 2.7 52.6 1.0
CG A:ASP96 2.9 47.4 1.0
CD A:GLU14 3.0 80.3 1.0
CG A:GLU14 3.2 72.0 1.0
C A:CYS200 3.6 56.5 1.0
O A:ASN203 4.0 68.6 1.0
OE1 A:GLU14 4.1 72.3 1.0
O A:PHE12 4.3 57.5 1.0
CB A:GLU14 4.3 55.9 1.0
CB A:ASP96 4.4 47.0 1.0
CA A:CYS200 4.4 53.8 1.0
N A:ILE201 4.4 51.7 1.0
CA A:ILE201 4.4 55.5 1.0
N A:GLU14 4.7 44.7 1.0
CB A:CYS200 4.7 66.7 1.0

Calcium binding site 2 out of 5 in 2e3x

Go back to Calcium Binding Sites List in 2e3x
Calcium binding site 2 out of 5 in the Crystal Structure of Russell'S Viper Venom Metalloproteinase


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 Russell'S Viper Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:76.3
occ:1.00
 OE2 A:GLU225 2.2 0.9 1.0
OD1 A:ASN218 2.2 80.4 1.0
OE1 A:GLU225 2.3 0.4 1.0
O A:ILE220 2.3 72.8 1.0
O A:VAL215 2.4 77.9 1.0
OE1 A:GLU222 2.4 69.5 1.0
CD A:GLU225 2.6 0.0 1.0
OD2 A:ASP228 2.7 68.6 1.0
CG A:ASN218 3.1 79.3 1.0
C A:ILE220 3.4 69.0 1.0
ND2 A:ASN218 3.4 69.7 1.0
C A:VAL215 3.5 68.8 1.0
CD A:GLU222 3.5 81.0 1.0
CG A:ASP228 3.7 81.9 1.0
CG A:GLU222 4.0 76.7 1.0
N A:GLU222 4.0 72.2 1.0
N A:ILE220 4.1 58.5 1.0
CG A:GLU225 4.1 93.8 1.0
CA A:ILE220 4.1 63.4 1.0
CB A:GLU222 4.1 76.5 1.0
N A:VAL215 4.1 56.9 1.0
CB A:ASP228 4.2 72.7 1.0
CB A:ILE220 4.2 54.7 1.0
CA A:CYS216 4.3 88.7 1.0
N A:CYS216 4.3 75.5 1.0
N A:TRP221 4.3 67.4 1.0
CA A:VAL215 4.4 57.6 1.0
CB A:ASN218 4.5 66.5 1.0
CA A:TRP221 4.5 75.8 1.0
N A:ASN218 4.5 88.3 1.0
C A:TRP221 4.6 72.3 1.0
OE2 A:GLU222 4.6 89.9 1.0
N A:GLY217 4.7 91.5 1.0
OD1 A:ASP228 4.7 87.1 1.0
CA A:GLU222 4.7 76.7 1.0
C A:CYS216 4.8 91.2 1.0
CB A:GLU225 4.9 82.9 1.0
CA A:ASN218 4.9 80.0 1.0
CB A:VAL215 5.0 53.3 1.0
CG2 A:ILE220 5.0 48.8 1.0

Calcium binding site 3 out of 5 in 2e3x

Go back to Calcium Binding Sites List in 2e3x
Calcium binding site 3 out of 5 in the Crystal Structure of Russell'S Viper Venom Metalloproteinase


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 Russell'S Viper Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:56.8
occ:1.00
 O A:VAL280 2.2 64.8 1.0
OD2 A:ASP294 2.5 66.8 1.0
OE1 A:GLU282 2.5 67.9 1.0
OD2 A:ASP279 2.5 85.4 1.0
O A:GLN295 2.6 73.6 1.0
OE2 A:GLU282 2.7 71.1 1.0
CD A:GLU282 2.9 73.5 1.0
C A:VAL280 3.3 65.4 1.0
CG A:ASP294 3.4 72.0 1.0
CG A:ASP279 3.4 75.6 1.0
C A:GLN295 3.6 69.8 1.0
OD1 A:ASP279 3.7 81.6 1.0
N A:GLN295 3.7 64.5 1.0
N A:VAL280 3.9 74.2 1.0
CD A:ARG272 3.9 62.5 1.0
OD1 A:ASP294 4.0 67.0 1.0
CA A:VAL280 4.2 68.2 1.0
N A:PRO281 4.2 58.1 1.0
CA A:GLN295 4.3 65.1 1.0
CA A:PRO281 4.4 53.9 1.0
C A:ASP294 4.4 63.0 1.0
CA A:ASP294 4.4 61.3 1.0
CG A:GLU282 4.4 75.6 1.0
CB A:ASP294 4.5 59.1 1.0
CG A:ARG272 4.5 61.5 1.0
C A:PRO281 4.5 54.2 1.0
O A:ARG273 4.5 69.4 1.0
N A:LEU296 4.6 67.8 1.0
CB A:VAL280 4.8 67.9 1.0
CB A:ASP279 4.8 78.7 1.0
N A:GLU282 4.8 51.3 1.0
O A:ARG272 4.8 55.9 1.0
CA A:LEU296 4.9 64.8 1.0
CD2 A:LEU296 4.9 48.9 1.0
C A:ASP279 4.9 77.1 1.0
O A:PRO281 4.9 59.7 1.0

Calcium binding site 4 out of 5 in 2e3x

Go back to Calcium Binding Sites List in 2e3x
Calcium binding site 4 out of 5 in the Crystal Structure of Russell'S Viper Venom Metalloproteinase


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 Russell'S Viper Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:89.3
occ:1.00
 OD1 A:ASN51 2.5 74.6 1.0
OE1 A:GLU219 2.5 80.5 1.0
OE2 A:GLU219 2.7 82.6 1.0
CD A:GLU219 3.0 86.4 1.0
CG A:ASN51 3.7 68.2 1.0
CG A:GLU219 4.5 76.2 1.0
O A:ASN48 4.5 58.1 1.0
ND2 A:ASN51 4.5 69.0 1.0
CB A:ASN51 4.7 65.9 1.0
CA A:ASN51 4.7 62.9 1.0
NE2 A:HIS53 4.9 87.1 1.0
OD1 A:ASN48 5.0 84.7 1.0

Calcium binding site 5 out of 5 in 2e3x

Go back to Calcium Binding Sites List in 2e3x
Calcium binding site 5 out of 5 in the Crystal Structure of Russell'S Viper Venom Metalloproteinase


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 Russell'S Viper Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:86.7
occ:1.00
 O B:GLY86 2.5 73.2 1.0
OE1 B:GLU82 2.8 59.6 1.0
OE2 B:GLU82 3.0 75.7 1.0
CD B:GLU82 3.3 67.8 1.0
C B:GLY86 3.6 66.3 1.0
CA B:GLY86 4.2 61.1 1.0
N B:SER87 4.7 60.8 1.0
CG B:GLU82 4.8 63.5 1.0
CA B:SER87 5.0 64.0 1.0
C B:SER87 5.0 60.1 1.0

Reference:

S.Takeda, T.Igarashi, H.Mori. Crystal Structure of Rvv-X: An Example of Evolutionary Gain of Specificity By Adam Proteinases. Febs Lett. V. 581 5859 2007.
ISSN: ISSN 0014-5793
PubMed: 18060879
DOI: 10.1016/J.FEBSLET.2007.11.062
Page generated: Fri Jul 12 10:04:22 2024

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