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Zinc in PDB 2fir: Crystal Structure of Dfpr-Viia/Stf

Enzymatic activity of Crystal Structure of Dfpr-Viia/Stf

All present enzymatic activity of Crystal Structure of Dfpr-Viia/Stf:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Dfpr-Viia/Stf, PDB code: 2fir was solved by S.P.Bajaj, A.E.Schmidt, K.Padmanabhan, M.S.Bajaj, D.Prevost, H.Schreuder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.020, 80.980, 126.330, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 28.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dfpr-Viia/Stf (pdb code 2fir). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Dfpr-Viia/Stf, PDB code: 2fir:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2fir

Go back to Zinc Binding Sites List in 2fir
Zinc binding site 1 out of 2 in the Crystal Structure of Dfpr-Viia/Stf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1011

b:49.6
occ:1.00
O H:HOH1132 2.5 73.6 1.0
O H:HOH1135 2.6 99.1 1.0
OE1 H:GLU80 3.0 26.8 1.0
O H:HOH1136 3.1 25.9 1.0
ND1 H:HIS76 3.2 26.7 1.0
CE1 H:HIS76 3.5 27.7 1.0
OG H:SER82 3.7 19.8 1.0
CB H:GLU80 3.8 16.1 1.0
O H:HOH1120 3.9 26.8 1.0
CG1 H:VAL67 4.0 9.7 1.0
CD H:GLU80 4.0 26.5 1.0
O H:HOH1137 4.1 36.8 1.0
CG H:GLU80 4.5 20.6 1.0
CG H:HIS76 4.5 26.6 1.0
OE1 H:GLU70 4.6 18.6 1.0
NE2 H:HIS76 4.7 31.6 1.0
CG2 H:VAL67 4.8 12.8 1.0
O H:HOH1166 4.9 53.4 1.0
O H:HOH1227 4.9 45.8 1.0

Zinc binding site 2 out of 2 in 2fir

Go back to Zinc Binding Sites List in 2fir
Zinc binding site 2 out of 2 in the Crystal Structure of Dfpr-Viia/Stf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1012

b:42.5
occ:1.00
NZ H:LYS24 2.6 20.3 1.0
O H:HOH1052 2.8 18.7 1.0
O H:GLY69 2.9 13.3 1.0
O H:HOH1081 3.2 12.1 1.0
ND1 H:HIS117 3.3 10.9 1.0
CG H:LYS24 3.6 12.7 1.0
CB H:HIS117 3.7 11.8 1.0
CE H:LYS24 3.7 18.4 1.0
C H:GLY69 3.7 12.3 1.0
CB H:ASP79 3.7 15.1 1.0
OD1 H:ASP79 3.7 17.1 1.0
CG H:HIS117 3.7 6.2 1.0
CA H:GLY69 4.1 13.0 1.0
CD H:LYS24 4.2 15.6 1.0
CG H:ASP79 4.2 16.5 1.0
CE1 H:HIS117 4.3 10.2 1.0
O H:HOH1026 4.4 14.3 1.0
N H:GLY25 4.5 12.7 1.0
O H:GLU70 4.6 17.0 1.0
CB H:HIS71 4.6 13.1 1.0
O H:HIS117 4.7 12.9 1.0
N H:GLU70 4.7 12.7 1.0
C H:GLU70 4.8 14.9 1.0
OD1 H:ASP77 4.8 17.8 1.0
CA H:HIS117 4.8 12.0 1.0
CD2 H:HIS117 4.8 5.8 1.0
CA H:GLY25 4.9 14.6 1.0
CB H:LYS24 4.9 12.5 1.0

Reference:

S.P.Bajaj, A.E.Schmidt, S.Agah, M.S.Bajaj, K.Padmanabhan. High Resolution Structures of P-Aminobenzamidine- and Benzamidine-Viia/Soluble Tissue Factor: Unpredicted Conformation of the 192-193 Peptide Bond and Mapping of CA2+, MG2+, Na+ and ZN2+ Sites in Factor Viia J.Biol.Chem. V. 281 24873 2006.
ISSN: ISSN 0021-9258
PubMed: 16757484
DOI: 10.1074/JBC.M509971200
Page generated: Sat Sep 26 01:54:00 2020
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