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Cadmium in PDB 2f91: 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti

Enzymatic activity of 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti

All present enzymatic activity of 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti:
3.4.21.4;

Protein crystallography data

The structure of 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti, PDB code: 2f91 was solved by K.Fodor, V.Harmat, C.Hetenyi, J.Kardos, J.Antal, A.Perczel, A.Patthy, G.Katona, L.Graf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.10 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.283, 59.673, 97.302, 90.00, 90.00, 90.00
R / Rfree (%) n/a / 18.2

Other elements in 2f91:

The structure of 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti (pdb code 2f91). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti, PDB code: 2f91:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 2f91

Go back to Cadmium Binding Sites List in 2f91
Cadmium binding site 1 out of 6 in the 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:18.1
occ:1.00
O A:VAL75 2.1 24.3 1.0
OE2 A:GLU70 2.2 14.8 1.0
O A:ASP72 2.2 17.3 1.0
O A:HOH592 2.2 21.7 1.0
OE2 A:GLU80 2.3 17.3 1.0
OE1 A:GLU77 2.5 17.1 1.0
HA A:ASN76 3.1 37.3 1.0
CD A:GLU70 3.2 15.8 1.0
H A:GLU77 3.2 31.9 1.0
C A:VAL75 3.2 25.6 1.0
C A:ASP72 3.3 16.7 1.0
CD A:GLU77 3.4 24.9 1.0
HG2 A:GLU80 3.4 22.9 1.0
CD A:GLU80 3.4 17.8 1.0
OE1 A:GLU70 3.4 19.4 1.0
H A:ASP72 3.5 18.4 1.0
H A:LEU71 3.6 17.0 1.0
HD22 A:ASN76 3.8 44.7 1.0
CG A:GLU80 3.8 19.1 1.0
H A:VAL75 3.8 28.3 1.0
HG3 A:GLU80 3.8 22.9 1.0
HG13 A:VAL75 3.9 46.3 1.0
CA A:ASN76 3.9 31.1 1.0
HG3 A:GLU77 3.9 33.6 1.0
N A:ASN76 4.0 27.8 1.0
N A:GLU77 4.0 26.6 1.0
N A:ASP72 4.0 15.3 1.0
HA A:MET73 4.0 21.0 1.0
HA A:GLU70 4.1 16.9 1.0
HB3 A:ASP72 4.1 20.5 1.0
CG A:GLU77 4.1 28.0 1.0
CA A:ASP72 4.2 15.6 1.0
OE2 A:GLU77 4.2 32.9 1.0
ND2 A:ASN76 4.2 37.2 1.0
N A:MET73 4.3 17.7 1.0
CA A:VAL75 4.3 25.6 1.0
O A:HOH579 4.4 25.4 1.0
N A:VAL75 4.4 23.6 1.0
HG11 A:VAL75 4.4 46.3 1.0
HD21 A:ASN76 4.4 44.7 1.0
N A:LEU71 4.4 14.2 1.0
C A:ASN76 4.5 28.9 1.0
CA A:MET73 4.5 17.5 1.0
OE1 A:GLU80 4.5 20.6 1.0
CG1 A:VAL75 4.5 30.8 1.0
CG A:GLU70 4.6 15.2 1.0
HB2 A:GLU77 4.6 34.8 1.0
CB A:ASP72 4.7 17.1 1.0
C A:MET73 4.7 19.9 1.0
HG3 A:GLU70 4.7 18.2 1.0
H A:ASN76 4.8 33.3 1.0
CB A:GLU77 4.8 29.0 1.0
CG A:ASN76 4.9 37.4 1.0
CA A:GLU70 4.9 14.1 1.0
HB3 A:LEU71 4.9 19.6 1.0
C A:LEU71 4.9 14.1 1.0
CA A:GLU77 4.9 26.8 1.0

Cadmium binding site 2 out of 6 in 2f91

Go back to Cadmium Binding Sites List in 2f91
Cadmium binding site 2 out of 6 in the 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:7.6
occ:0.80
OD2 A:ASP135 2.3 11.4 1.0
CL A:CL408 2.4 11.8 0.8
OD1 A:ASP135 2.5 8.9 1.0
CL A:CL407 2.6 11.4 0.8
CG A:ASP135 2.8 8.2 1.0
HD3 A:PRO161 3.6 10.8 1.0
HB3 A:PRO161 3.6 9.8 1.0
HG23 A:THR159 4.1 17.0 1.0
O A:HOH655 4.1 27.6 1.0
O A:HOH620 4.2 27.7 1.0
CB A:ASP135 4.2 8.8 1.0
CD A:PRO161 4.3 9.0 1.0
HG3 A:PRO161 4.4 10.6 1.0
CB A:PRO161 4.4 8.1 1.0
O A:HOH413 4.5 9.1 1.0
HB3 A:ASP135 4.5 10.6 1.0
O A:HOH725 4.5 26.7 0.5
N A:PRO161 4.5 8.0 1.0
HB2 A:ASP135 4.7 10.6 1.0
CG A:PRO161 4.7 8.8 1.0
HZ1 A:LYS188 4.7 33.4 1.0
HA A:VAL160 4.8 9.8 1.0
HA A:PRO161 4.8 8.3 1.0
HG21 A:THR159 4.9 17.0 1.0
CA A:PRO161 4.9 6.9 1.0
HA A:ASP135 4.9 11.0 1.0
C A:VAL160 4.9 7.6 1.0
CG2 A:THR159 5.0 11.3 1.0
HG11 A:VAL185 5.0 17.6 1.0

Cadmium binding site 3 out of 6 in 2f91

Go back to Cadmium Binding Sites List in 2f91
Cadmium binding site 3 out of 6 in the 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:13.9
occ:0.47
O A:HOH705 2.3 40.7 1.0
O A:HOH627 2.3 26.8 1.0
OE1 A:GLU60E 2.4 19.6 1.0
OE2 A:GLU60E 2.4 19.4 1.0
O A:HOH633 2.5 33.6 1.0
O A:HOH433 2.5 19.5 1.0
CD A:GLU60E 2.8 17.7 1.0
HD2 A:LYS87 3.2 23.4 1.0
HZ3 A:LYS87 3.7 31.9 1.0
O A:HOH492 4.1 27.1 1.0
CD A:LYS87 4.2 19.5 1.0
CG A:GLU60E 4.3 15.9 1.0
HE3 A:LYS87 4.4 22.7 1.0
NZ A:LYS87 4.5 21.3 1.0
CE A:LYS87 4.6 18.9 1.0
HD3 A:LYS87 4.7 23.4 1.0
O A:HOH609 4.7 18.7 0.5
HG3 A:GLU60E 4.7 19.1 1.0
HG2 A:GLU60E 4.8 19.1 1.0
HA A:GLU60E 4.8 16.6 1.0
HG3 A:LYS87 4.8 21.1 1.0
HB3 A:LYS87 4.9 17.2 1.0
HB3 A:GLU60E 5.0 16.9 1.0
HZ2 A:LYS87 5.0 31.9 1.0
HZ1 A:LYS87 5.0 31.9 1.0

Cadmium binding site 4 out of 6 in 2f91

Go back to Cadmium Binding Sites List in 2f91
Cadmium binding site 4 out of 6 in the 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:27.1
occ:0.69
O A:HOH597 1.6 30.5 1.0
OD2 A:ASP21 2.2 19.2 1.0
O A:HOH595 2.2 16.7 1.0
O A:HOH687 2.6 43.6 1.0
OD1 A:ASP21 2.6 17.1 1.0
CG A:ASP21 2.7 15.5 1.0
CB A:ASP21 4.2 13.9 1.0
HE21 A:GLN156 4.3 17.8 1.0
O A:HOH513 4.3 25.7 1.0
HB2 A:ASP21 4.4 16.6 1.0
HB3 A:ASP21 4.6 16.6 1.0
H A:ASP21 4.7 15.9 1.0
HG12 A:VAL154 4.8 30.7 1.0
HB A:VAL154 4.8 22.0 1.0
O A:HOH683 4.8 55.7 1.0
HG23 A:VAL154 4.9 29.8 1.0

Cadmium binding site 5 out of 6 in 2f91

Go back to Cadmium Binding Sites List in 2f91
Cadmium binding site 5 out of 6 in the 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:6.8
occ:0.54
O A:ASP178 2.3 7.3 1.0
O A:MET180 2.3 8.6 1.0
OE1 A:GLU231 2.3 9.1 1.0
OD2 A:ASP165 2.3 9.8 1.0
O A:HOH577 2.4 11.9 1.0
O A:HOH576 2.4 9.8 1.0
OD1 A:ASP165 2.7 11.1 1.0
CG A:ASP165 2.9 8.9 1.0
C A:ASP178 3.3 6.7 1.0
HA A:ASP178 3.3 8.3 1.0
C A:MET180 3.5 6.7 1.0
CD A:GLU231 3.5 8.7 1.0
HA A:ILE181 3.6 10.6 1.0
H A:MET180 3.8 7.8 1.0
CA A:ASP178 3.9 6.9 1.0
HB A:ILE181 3.9 12.3 1.0
O A:HOH528 4.0 27.2 1.0
N A:MET180 4.1 6.5 1.0
OE2 A:GLU231 4.1 13.3 1.0
HE1 A:TYR234 4.1 11.4 1.0
O A:LEU177 4.2 7.6 1.0
HB2 A:GLU231 4.2 8.2 1.0
O A:HOH468 4.2 13.2 1.0
O A:HOH574 4.3 15.6 1.0
CA A:ILE181 4.3 8.8 1.0
N A:ILE181 4.3 7.2 1.0
CB A:ASP165 4.4 8.2 1.0
N A:SER179 4.4 6.7 1.0
HB3 A:ASP178 4.4 8.4 1.0
O A:HOH602 4.5 19.2 1.0
CA A:MET180 4.5 6.6 1.0
HG13 A:ILE181 4.5 13.1 1.0
HA A:SER179 4.5 7.7 1.0
OH A:TYR234 4.5 10.1 1.0
CB A:ILE181 4.6 10.3 1.0
CE1 A:TYR234 4.6 9.5 1.0
O A:HOH582 4.7 32.3 1.0
CG A:GLU231 4.7 7.7 1.0
C A:SER179 4.7 5.6 1.0
HB2 A:ASP165 4.7 9.8 1.0
CB A:ASP178 4.8 7.0 1.0
HB3 A:GLU231 4.8 8.2 1.0
CB A:GLU231 4.8 6.9 1.0
CA A:SER179 4.8 6.4 1.0
HB3 A:ASP165 4.8 9.8 1.0
CZ A:TYR234 4.8 8.7 1.0
HD13 A:ILE181 4.9 23.9 1.0
H A:ASP165 5.0 8.7 1.0
N A:ASP178 5.0 7.0 1.0
C A:LEU177 5.0 6.6 1.0

Cadmium binding site 6 out of 6 in 2f91

Go back to Cadmium Binding Sites List in 2f91
Cadmium binding site 6 out of 6 in the 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of 1.2A Resolution Structure of A Crayfish Trypsin Complexed with A Peptide Inhibitor, Sgti within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd406

b:40.5
occ:0.43
OE2 A:GLU125 2.3 32.3 1.0
OE1 A:GLU125 2.5 31.8 1.0
CD A:GLU125 2.6 28.0 1.0
O A:HOH719 2.7 58.4 1.0
CG A:GLU125 4.1 22.4 1.0
O A:HOH625 4.2 34.7 1.0
HG2 A:GLU125 4.5 26.9 1.0
HG3 A:GLU125 4.6 26.9 1.0
HB2 A:GLU125 4.9 19.4 1.0
HB3 A:GLU125 4.9 19.4 1.0
CB A:GLU125 5.0 16.1 1.0

Reference:

K.Fodor, V.Harmat, R.Neutze, L.Szilagyi, L.Graf, G.Katona. Enzyme:Substrate Hydrogen Bond Shortening During the Acylation Phase of Serine Protease Catalysis. Biochemistry V. 45 2114 2006.
ISSN: ISSN 0006-2960
PubMed: 16475800
DOI: 10.1021/BI0517133
Page generated: Sat Dec 12 08:17:01 2020

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