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Chlorine in PDB 3g4r: Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity

Protein crystallography data

The structure of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity, PDB code: 3g4r was solved by J.E.Knapp, R.Pahl, J.Cohen, J.C.Nichols, K.Schulten, Q.H.Gibson, V.Srajer, W.E.Royer Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.10 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.140, 43.940, 83.530, 90.00, 121.89, 90.00
R / Rfree (%) 20 / 21.9

Other elements in 3g4r:

The structure of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity (pdb code 3g4r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity, PDB code: 3g4r:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3g4r

Go back to Chlorine Binding Sites List in 3g4r
Chlorine binding site 1 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl150

b:20.9
occ:0.30
 CL1 A:DCE150 0.0 20.9 0.3
C1 A:DCE150 1.8 19.3 0.3
C1 A:DCE150 2.1 42.6 0.7
CL1 A:DCE150 2.5 42.5 0.7
C2 A:DCE150 2.7 21.1 0.3
C2 A:DCE150 3.0 42.8 0.7
CD2 A:LEU36 3.4 16.8 1.0
SD A:MET74 3.7 14.4 1.0
CL2 A:DCE150 4.0 41.7 0.7
CE A:MET74 4.0 15.4 1.0
CD1 A:LEU36 4.0 17.0 1.0
CG A:LEU36 4.1 16.8 1.0
CD1 A:LEU77 4.1 12.1 1.0
CB A:LEU36 4.2 13.5 1.0
CL2 A:DCE150 4.3 18.9 0.3
CG2 A:ILE25 4.5 19.2 1.0
O A:ASN32 4.7 12.3 1.0
CG1 A:ILE118 5.0 11.7 1.0

Chlorine binding site 2 out of 8 in 3g4r

Go back to Chlorine Binding Sites List in 3g4r
Chlorine binding site 2 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl150

b:42.5
occ:0.70
 CL1 A:DCE150 0.0 42.5 0.7
C1 A:DCE150 1.2 19.3 0.3
C1 A:DCE150 1.8 42.6 0.7
C2 A:DCE150 2.4 21.1 0.3
CL1 A:DCE150 2.5 20.9 0.3
C2 A:DCE150 2.7 42.8 0.7
CL2 A:DCE150 3.0 18.9 0.3
CZ3 A:TRP22 3.1 14.7 1.0
CD1 A:LEU77 3.2 12.1 1.0
CE3 A:TRP22 3.7 12.6 1.0
CG2 A:ILE25 4.1 19.2 1.0
CH2 A:TRP135 4.1 13.9 1.0
CE A:MET74 4.2 15.4 1.0
CZ3 A:TRP135 4.2 14.3 1.0
CH2 A:TRP22 4.2 14.4 1.0
SD A:MET74 4.3 14.4 1.0
CL2 A:DCE150 4.3 41.7 0.7
CG A:LEU77 4.5 11.7 1.0
CZ2 A:TRP135 4.5 14.8 1.0
CB A:LEU77 4.6 9.7 1.0
CE3 A:TRP135 4.7 14.6 1.0
CB A:ILE25 4.9 17.7 1.0
CE2 A:TRP135 5.0 14.0 1.0

Chlorine binding site 3 out of 8 in 3g4r

Go back to Chlorine Binding Sites List in 3g4r
Chlorine binding site 3 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl150

b:18.9
occ:0.30
 CL2 A:DCE150 0.0 18.9 0.3
C2 A:DCE150 1.6 42.8 0.7
C2 A:DCE150 1.8 21.1 0.3
C1 A:DCE150 2.6 42.6 0.7
C1 A:DCE150 2.7 19.3 0.3
CL2 A:DCE150 2.8 41.7 0.7
CL1 A:DCE150 3.0 42.5 0.7
CE2 A:TRP135 3.5 14.0 1.0
CZ2 A:TRP135 3.6 14.8 1.0
CG1 A:ILE25 3.7 19.4 1.0
NE1 A:TRP135 3.7 12.4 1.0
CD2 A:LEU122 3.8 13.4 1.0
CG2 A:ILE25 3.8 19.2 1.0
CB A:ILE25 3.9 17.7 1.0
CD2 A:TRP135 4.0 13.1 1.0
CH2 A:TRP135 4.2 13.9 1.0
CG A:LEU122 4.3 12.9 1.0
CD1 A:TRP135 4.3 13.5 1.0
CL1 A:DCE150 4.3 20.9 0.3
CE3 A:TRP22 4.5 12.6 1.0
CG A:TRP135 4.5 12.9 1.0
CE3 A:TRP135 4.6 14.6 1.0
CZ3 A:TRP135 4.6 14.3 1.0
CD1 A:ILE25 4.7 20.5 1.0
CZ3 A:TRP22 4.8 14.7 1.0
CD1 A:LEU122 4.9 14.4 1.0
OG A:SER21 4.9 12.4 1.0
CG2 A:ILE118 5.0 12.5 1.0

Chlorine binding site 4 out of 8 in 3g4r

Go back to Chlorine Binding Sites List in 3g4r
Chlorine binding site 4 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl150

b:41.7
occ:0.70
 CL2 A:DCE150 0.0 41.7 0.7
C2 A:DCE150 1.8 42.8 0.7
C2 A:DCE150 2.0 21.1 0.3
C1 A:DCE150 2.7 42.6 0.7
CL2 A:DCE150 2.8 18.9 0.3
O A:ILE118 3.1 12.3 1.0
CG A:LEU122 3.3 12.9 1.0
C1 A:DCE150 3.4 19.3 0.3
CG2 A:ILE118 3.5 12.5 1.0
CA A:ILE118 3.8 11.1 1.0
CB A:VAL121 3.8 14.2 1.0
N A:LEU122 3.8 12.6 1.0
CD2 A:LEU122 3.8 13.4 1.0
C A:ILE118 3.8 11.7 1.0
CG1 A:VAL121 4.0 14.3 1.0
CL1 A:DCE150 4.0 20.9 0.3
CB A:ILE118 4.1 10.7 1.0
CD1 A:LEU122 4.2 14.4 1.0
CB A:LEU122 4.2 13.3 1.0
CA A:LEU122 4.3 13.3 1.0
CL1 A:DCE150 4.3 42.5 0.7
C A:VAL121 4.4 14.2 1.0
CG1 A:ILE118 4.4 11.7 1.0
CA A:VAL121 4.6 14.0 1.0
CG2 A:ILE25 4.8 19.2 1.0
CG1 A:ILE25 4.8 19.4 1.0
CG2 A:VAL121 4.8 16.0 1.0
CD1 A:ILE25 5.0 20.5 1.0

Chlorine binding site 5 out of 8 in 3g4r

Go back to Chlorine Binding Sites List in 3g4r
Chlorine binding site 5 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl151

b:21.0
occ:0.33
 CL1 B:DCE151 0.0 21.0 0.3
C1 B:DCE151 1.8 20.6 0.3
C2 B:DCE151 2.4 43.5 0.7
CL2 B:DCE151 2.5 41.8 0.7
C2 B:DCE151 2.7 19.1 0.3
C1 B:DCE151 3.3 42.7 0.7
CD2 B:LEU122 3.4 13.2 1.0
NE1 B:TRP135 3.5 11.4 1.0
CE2 B:TRP135 3.5 11.3 1.0
CG1 B:ILE25 3.7 15.4 1.0
CG B:LEU122 3.7 12.2 1.0
CZ2 B:TRP135 3.8 11.9 1.0
CB B:ILE25 4.0 13.1 1.0
CD1 B:TRP135 4.1 10.1 1.0
CG2 B:ILE25 4.1 14.3 1.0
CD2 B:TRP135 4.1 10.4 1.0
CL1 B:DCE151 4.3 42.4 0.7
CL2 B:DCE151 4.3 18.4 0.3
CD1 B:LEU122 4.4 13.6 1.0
CG B:TRP135 4.4 10.0 1.0
CH2 B:TRP135 4.5 11.6 1.0
OG B:SER21 4.5 10.2 1.0
CB B:SER21 4.7 11.7 1.0
CE3 B:TRP22 4.8 10.2 1.0
CE3 B:TRP135 4.8 10.4 1.0
CD1 B:ILE25 4.8 16.6 1.0
O B:SER21 4.9 11.6 1.0
CB B:LEU122 5.0 12.5 1.0
CZ3 B:TRP135 5.0 11.5 1.0
CG2 B:ILE118 5.0 12.9 1.0

Chlorine binding site 6 out of 8 in 3g4r

Go back to Chlorine Binding Sites List in 3g4r
Chlorine binding site 6 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl151

b:42.4
occ:0.67
 CL1 B:DCE151 0.0 42.4 0.7
CL2 B:DCE151 1.7 18.4 0.3
C1 B:DCE151 1.8 42.7 0.7
C2 B:DCE151 2.1 19.1 0.3
C2 B:DCE151 2.7 43.5 0.7
C1 B:DCE151 3.0 20.6 0.3
CD1 B:LEU77 3.3 10.8 1.0
SD B:MET74 3.4 11.9 1.0
CZ3 B:TRP22 3.4 11.4 1.0
CE B:MET74 3.4 12.3 1.0
CG2 B:ILE25 4.0 14.3 1.0
CH2 B:TRP22 4.3 11.1 1.0
CL1 B:DCE151 4.3 21.0 0.3
CL2 B:DCE151 4.3 41.8 0.7
CE3 B:TRP22 4.3 10.2 1.0
CD2 B:LEU36 4.4 14.8 1.0
CG B:LEU77 4.8 8.5 1.0

Chlorine binding site 7 out of 8 in 3g4r

Go back to Chlorine Binding Sites List in 3g4r
Chlorine binding site 7 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl151

b:18.4
occ:0.33
 CL2 B:DCE151 0.0 18.4 0.3
C1 B:DCE151 1.0 42.7 0.7
CL1 B:DCE151 1.7 42.4 0.7
C2 B:DCE151 1.8 19.1 0.3
C2 B:DCE151 2.5 43.5 0.7
C1 B:DCE151 2.7 20.6 0.3
CD2 B:LEU36 3.5 14.8 1.0
CL2 B:DCE151 3.5 41.8 0.7
CD1 B:LEU77 3.6 10.8 1.0
CG1 B:ILE118 4.0 12.5 1.0
CD1 B:LEU36 4.0 16.4 1.0
CL1 B:DCE151 4.3 21.0 0.3
CG B:LEU36 4.4 14.4 1.0
CD1 B:ILE118 4.5 13.1 1.0
SD B:MET74 4.6 11.9 1.0
CZ3 B:TRP22 4.9 11.4 1.0
CB B:ILE118 5.0 10.9 1.0
CB B:LEU36 5.0 11.8 1.0
CE B:MET74 5.0 12.3 1.0

Chlorine binding site 8 out of 8 in 3g4r

Go back to Chlorine Binding Sites List in 3g4r
Chlorine binding site 8 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Dichloroethane Bound to the XE4 Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl151

b:41.8
occ:0.67
 CL2 B:DCE151 0.0 41.8 0.7
C1 B:DCE151 1.6 20.6 0.3
C2 B:DCE151 1.8 43.5 0.7
CL1 B:DCE151 2.5 21.0 0.3
C1 B:DCE151 2.7 42.7 0.7
C2 B:DCE151 2.8 19.1 0.3
O B:ILE118 3.2 12.5 1.0
CG B:LEU122 3.3 12.2 1.0
CG2 B:ILE118 3.4 12.9 1.0
CL2 B:DCE151 3.5 18.4 0.3
CA B:ILE118 3.8 10.7 1.0
C B:ILE118 3.8 10.7 1.0
N B:LEU122 3.9 11.9 1.0
CD1 B:LEU122 4.0 13.6 1.0
CD2 B:LEU122 4.0 13.2 1.0
CB B:ILE118 4.0 10.9 1.0
CB B:VAL121 4.0 12.3 1.0
CB B:LEU122 4.2 12.5 1.0
CG1 B:VAL121 4.2 14.5 1.0
CG1 B:ILE118 4.2 12.5 1.0
CL1 B:DCE151 4.3 42.4 0.7
CA B:LEU122 4.3 12.6 1.0
C B:VAL121 4.6 13.1 1.0
CA B:VAL121 4.8 12.7 1.0
CG2 B:ILE25 4.9 14.3 1.0
CG1 B:ILE25 4.9 15.4 1.0

Reference:

J.E.Knapp, R.Pahl, J.Cohen, J.C.Nichols, K.Schulten, Q.H.Gibson, V.Srajer, W.E.Royer. Ligand Migration and Cavities Within Scapharca Dimeric Hbi: Studies By Time-Resolved Crystallo-Graphy, Xe Binding, and Computational Analysis. Structure V. 17 1494 2009.
ISSN: ISSN 0969-2126
PubMed: 19913484
DOI: 10.1016/J.STR.2009.09.004
Page generated: Sat Jul 20 19:59:09 2024

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