Atomistry » Cadmium » PDB 2eil-2mhu » 2f91
Atomistry »
  Cadmium »
    PDB 2eil-2mhu »
      2f91 »

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: Fri Jul 19 14:49:50 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy