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Chlorine 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

Other elements in 2fir:

The structure of Crystal Structure of Dfpr-Viia/Stf also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 2 atoms
Calcium (Ca) 6 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Dfpr-Viia/Stf (pdb code 2fir). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Dfpr-Viia/Stf, PDB code: 2fir:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 2fir

Go back to Chlorine Binding Sites List in 2fir
Chlorine binding site 1 out of 3 in the Crystal Structure of Dfpr-Viia/Stf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1013

b:41.8
occ:1.00
O H:GLY216 3.0 22.6 1.0
NE H:0G7701 3.1 16.2 1.0
C H:GLY216 3.2 20.2 1.0
N H:GLY219 3.2 21.4 1.0
NH2 H:0G7701 3.4 15.8 1.0
O H:HOH461 3.5 43.0 1.0
CA H:GLY216 3.6 17.4 1.0
C H:GLY219 3.6 21.8 1.0
CA H:GLY219 3.7 20.0 1.0
N H:GLY216 3.7 12.8 1.0
CZ1 H:0G7701 3.7 16.5 1.0
O H:GLY219 3.8 24.9 1.0
CG2 H:0G7701 3.8 12.4 1.0
O H:0G7701 3.9 17.2 1.0
N H:GLN217 3.9 23.3 1.0
CD3 H:0G7701 4.1 17.4 1.0
N H:CYS220 4.1 20.0 1.0
C H:GLN217 4.2 22.8 1.0
SG H:CYS220 4.3 22.8 1.0
CA H:GLN217 4.5 22.8 1.0
C H:TRP215 4.7 13.2 1.0
N H:0G7701 4.7 26.5 1.0
CA H:CYS220 4.8 17.7 1.0
C H:0G7701 4.9 22.4 1.0

Chlorine binding site 2 out of 3 in 2fir

Go back to Chlorine Binding Sites List in 2fir
Chlorine binding site 2 out of 3 in the Crystal Structure of Dfpr-Viia/Stf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1014

b:20.6
occ:1.00
N H:ARG84 3.2 20.3 1.0
CD2 H:HIS109 3.4 27.0 1.0
CB H:HIS109 3.7 20.2 1.0
CA H:ARG83 3.7 16.7 1.0
O H:HOH1074 3.7 33.2 1.0
O H:HOH1219 3.8 36.0 1.0
CD H:ARG83 3.8 11.6 1.0
CG H:HIS109 3.9 26.9 1.0
N H:GLN110 3.9 16.8 1.0
CG H:GLN110 3.9 21.2 1.0
C H:ARG83 4.0 17.6 1.0
CB H:GLN110 4.0 17.3 1.0
CG H:ARG84 4.0 29.6 1.0
CB H:ARG83 4.0 17.7 1.0
CB H:ARG84 4.1 23.9 1.0
CA H:ARG84 4.2 19.4 1.0
NE H:ARG84 4.3 46.2 1.0
O H:ARG84 4.5 13.5 1.0
C H:HIS109 4.5 16.6 1.0
CA H:HIS109 4.5 17.1 1.0
CG H:ARG83 4.5 16.2 1.0
CA H:GLN110 4.5 16.9 1.0
NE2 H:HIS109 4.6 29.5 1.0
CD H:ARG84 4.8 37.3 1.0
N H:HIS109 4.8 18.1 1.0
C H:ARG84 4.8 16.2 1.0
O H:SER82 4.9 16.4 1.0
NE H:ARG83 4.9 9.4 1.0
O H:GLN110 5.0 15.6 1.0
N H:ARG83 5.0 17.3 1.0

Chlorine binding site 3 out of 3 in 2fir

Go back to Chlorine Binding Sites List in 2fir
Chlorine binding site 3 out of 3 in the Crystal Structure of Dfpr-Viia/Stf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl1015

b:21.5
occ:1.00
OH T:TYR153 3.2 13.6 1.0
ND2 T:ASN173 3.4 16.8 1.0
N T:GLU130 3.4 19.8 1.0
O T:HOH1128 3.5 36.0 1.0
N T:ARG144 3.5 18.7 1.0
CB T:ARG144 3.6 15.9 1.0
CB T:SER142 3.7 18.1 1.0
N T:LEU143 3.8 17.8 1.0
CA T:ASP129 3.9 21.2 1.0
CB T:LEU143 4.0 16.6 1.0
OG T:SER142 4.0 17.6 1.0
OD1 T:ASN173 4.1 19.1 1.0
O T:GLU130 4.1 22.3 1.0
CE2 T:TYR153 4.1 11.6 1.0
CZ T:TYR153 4.1 12.9 1.0
C T:ASP129 4.1 20.3 1.0
CG T:ASN173 4.1 17.9 1.0
CA T:ARG144 4.2 18.5 1.0
CA T:LEU143 4.3 16.8 1.0
C T:LEU143 4.4 17.5 1.0
CB T:GLU130 4.4 17.0 1.0
CA T:GLU130 4.4 20.8 1.0
CB T:ASP129 4.4 22.2 1.0
CD2 T:LEU151 4.5 13.5 1.0
OD1 T:ASP129 4.5 26.1 1.0
C T:SER142 4.5 18.6 1.0
CA T:SER142 4.6 18.6 1.0
C T:GLU130 4.7 21.5 1.0
O T:GLU128 4.9 16.0 1.0
CG T:ARG144 5.0 14.9 1.0
CG T:ASP129 5.0 27.4 1.0
CG T:GLU130 5.0 17.4 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 Dec 12 09:05:01 2020

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