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Zinc in PDB 3s9c: Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V

Enzymatic activity of Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V

All present enzymatic activity of Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V:
3.4.21.95;

Protein crystallography data

The structure of Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V, PDB code: 3s9c was solved by D.Nakayama, Y.Ben Ammar, S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.21 / 1.80
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 101.200, 101.200, 44.200, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V (pdb code 3s9c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V, PDB code: 3s9c:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3s9c

Go back to Zinc Binding Sites List in 3s9c
Zinc binding site 1 out of 3 in the Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:22.4
occ:1.00
 OE2 A:GLU218 1.9 23.4 1.0
OXT A:ACT901 2.0 22.7 1.0
NE2 A:HIS192 2.0 20.2 1.0
O A:ACT901 2.7 23.4 1.0
C A:ACT901 2.7 23.6 1.0
CD A:GLU218 2.8 22.6 1.0
CD2 A:HIS192 3.0 20.5 1.0
OE1 A:GLU218 3.0 22.0 1.0
CE1 A:HIS192 3.0 20.4 1.0
ND1 A:HIS192 4.1 22.9 1.0
CG A:HIS192 4.1 23.0 1.0
CG A:GLU218 4.1 23.6 1.0
CH3 A:ACT901 4.2 24.0 1.0
CA A:PRO219 4.2 21.5 1.0
SG A:CYS220 4.3 22.7 1.0
N A:CYS220 4.5 21.8 1.0
NZ A:LYS143 4.6 35.2 1.0
SG A:CYS191 4.7 22.6 1.0
CB A:PRO219 4.7 22.0 1.0
C A:PRO219 4.8 22.7 1.0
CB A:GLU218 4.9 23.1 1.0
CA A:GLU218 4.9 22.6 1.0

Zinc binding site 2 out of 3 in 3s9c

Go back to Zinc Binding Sites List in 3s9c
Zinc binding site 2 out of 3 in the Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:38.1
occ:1.00
 OXT A:ACT902 1.9 46.0 1.0
O A:HOH367 2.0 40.0 1.0
NE2 A:HIS156 2.1 29.5 1.0
O A:HOH368 2.2 46.0 1.0
O A:HOH150 2.4 51.4 1.0
C A:ACT902 2.7 48.3 1.0
O A:ACT902 2.8 47.4 1.0
CD2 A:HIS156 3.0 27.4 1.0
CE1 A:HIS156 3.2 29.6 1.0
CH3 A:ACT902 4.1 47.5 1.0
CD1 A:ILE144 4.2 32.2 1.0
CG A:HIS156 4.2 27.3 1.0
O A:HOH319 4.2 44.7 1.0
ND1 A:HIS156 4.3 26.3 1.0
N A:GLU21 4.5 30.5 1.0

Zinc binding site 3 out of 3 in 3s9c

Go back to Zinc Binding Sites List in 3s9c
Zinc binding site 3 out of 3 in the Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Russell'S Viper Venom Serine Proteinase, Rvv-V in Complex with the Fragment (Residues 1533-1546) of Human Factor V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:39.9
occ:1.00
 O A:ACT904 2.0 39.6 1.0
OD1 A:ASN25 2.0 35.4 1.0
NE2 A:HIS117 2.1 34.6 1.0
OXT A:ACT903 2.1 37.1 1.0
O A:ACT903 2.6 35.6 1.0
C A:ACT903 2.7 36.2 1.0
C A:ACT904 2.7 39.5 1.0
OXT A:ACT904 2.8 38.7 1.0
CG A:ASN25 3.0 34.1 1.0
CD2 A:HIS117 3.0 33.3 1.0
CE1 A:HIS117 3.1 33.7 1.0
ND2 A:ASN25 3.4 36.1 1.0
O A:HOH283 3.8 44.9 1.0
CG2 A:THR116 4.1 31.8 1.0
CH3 A:ACT904 4.2 40.1 1.0
CH3 A:ACT903 4.2 38.6 1.0
CG A:HIS117 4.2 31.7 1.0
ND1 A:HIS117 4.2 33.6 1.0
CG2 A:ILE24 4.3 32.4 1.0
O A:HOH388 4.3 56.0 1.0
CB A:ASN25 4.4 33.2 1.0
CG1 A:ILE24 4.7 29.4 1.0
O A:ILE24 4.7 30.5 1.0
CA A:ASN25 4.9 29.9 1.0
C A:ILE24 5.0 30.0 1.0

Reference:

D.Nakayama, Y.Ben Ammar, T.Miyata, S.Takeda. Structural Basis of Coagulation Factor V Recognition For Cleavage By Rvv-V Febs Lett. V. 585 3020 2011.
ISSN: ISSN 0014-5793
PubMed: 21871889
DOI: 10.1016/J.FEBSLET.2011.08.022
Page generated: Wed Dec 16 04:49:35 2020

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