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Iodine in PDB 3pe9: Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules

Protein crystallography data

The structure of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules, PDB code: 3pe9 was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.128, 103.281, 45.632, 90.00, 106.53, 90.00
R / Rfree (%) 18.2 / 22.9

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Iodine atom in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules (pdb code 3pe9). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 17 binding sites of Iodine where determined in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules, PDB code: 3pe9:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 17 in 3pe9

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Iodine binding site 1 out of 17 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I99

b:16.9
occ:0.45
 I A:IOD99 0.0 16.9 0.5
I A:IOD99 1.1 31.8 0.5
OG1 A:THR24 3.5 20.0 1.0
NZ A:LYS3 3.6 30.4 1.0
CA A:ALA25 3.6 22.7 1.0
N A:ALA25 3.6 21.9 1.0
OG A:SER26 3.7 32.8 1.0
CG A:MET1 3.7 29.9 1.0
C A:THR24 3.8 19.2 1.0
C A:ALA25 3.8 24.0 1.0
N A:SER26 3.9 26.4 1.0
O A:THR24 3.9 18.9 1.0
CG A:LYS3 3.9 23.2 1.0
CB A:THR24 4.1 19.4 1.0
O A:MET1 4.1 22.4 1.0
CD A:LYS3 4.1 26.7 1.0
SD A:MET1 4.3 35.8 1.0
N A:LYS3 4.4 18.7 1.0
CB A:SER26 4.4 30.6 1.0
C A:MET1 4.4 24.3 1.0
CE A:LYS3 4.4 29.7 1.0
O A:ALA25 4.4 23.0 1.0
CE A:MET1 4.4 33.9 1.0
CA A:VAL2 4.5 19.0 1.0
C A:VAL2 4.5 19.7 1.0
CB A:LYS3 4.6 18.0 1.0
CA A:THR24 4.6 17.5 1.0
N A:VAL2 4.6 22.1 1.0
CA A:SER26 4.7 30.5 1.0
CB A:MET1 4.8 29.5 1.0

Iodine binding site 2 out of 17 in 3pe9

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Iodine binding site 2 out of 17 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I99

b:31.8
occ:0.45
 I A:IOD99 0.0 31.8 0.5
I A:IOD99 1.1 16.9 0.5
OG1 A:THR24 3.0 20.0 1.0
CB A:THR24 3.5 19.4 1.0
NZ A:LYS3 3.7 30.4 1.0
N A:ALA25 3.9 21.9 1.0
CD A:LYS3 3.9 26.7 1.0
C A:THR24 3.9 19.2 1.0
OG A:SER26 4.0 32.8 1.0
CG A:LYS3 4.1 23.2 1.0
CA A:ALA25 4.2 22.7 1.0
O A:THR24 4.2 18.9 1.0
C A:ALA25 4.3 24.0 1.0
CE A:LYS3 4.3 29.7 1.0
CA A:THR24 4.4 17.5 1.0
N A:SER26 4.5 26.4 1.0
CB A:LYS3 4.6 18.0 1.0
O A:HOH988 4.6 20.3 1.0
CG A:MET1 4.6 29.9 1.0
O A:ALA25 4.7 23.0 1.0
CB A:SER26 4.7 30.6 1.0
CG2 A:THR24 4.7 18.6 1.0
CE A:MET1 4.8 33.9 1.0
O A:HOH951 4.9 12.8 1.0
N A:LYS3 4.9 18.7 1.0
SD A:MET1 4.9 35.8 1.0

Iodine binding site 3 out of 17 in 3pe9

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Iodine binding site 3 out of 17 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I100

b:29.1
occ:0.30
 O A:HOH1017 2.6 27.0 1.0
O A:HOH195 3.2 13.9 1.0
CB A:ASN62 3.8 14.8 1.0
C A:HIS63 3.8 10.6 1.0
N A:HIS63 3.8 11.2 1.0
C A:ASN62 4.0 12.5 1.0
N A:GLU64 4.0 13.0 1.0
CA A:HIS63 4.0 10.2 1.0
O A:HIS63 4.1 11.5 1.0
CD A:LYS83 4.3 20.6 1.0
O A:ASN62 4.4 12.3 1.0
CG A:LYS83 4.4 11.6 1.0
CA A:ASN62 4.4 12.2 1.0
CG A:ASN62 4.5 18.8 1.0
CE A:LYS83 4.6 25.4 1.0
OD1 A:ASN62 4.6 16.8 1.0
CB A:GLU64 4.6 15.0 1.0
CA A:GLU64 4.7 12.3 1.0
CB A:LYS83 4.9 9.1 1.0

Iodine binding site 4 out of 17 in 3pe9

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Iodine binding site 4 out of 17 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I99

b:28.4
occ:0.40
 I B:IOD99 0.0 28.4 0.4
I B:IOD99 2.2 56.7 0.2
O B:HOH111 3.3 11.9 1.0
O B:HOH764 3.4 7.1 0.5
C B:HIS63 3.8 6.2 1.0
N B:HIS63 3.9 9.8 1.0
CD B:LYS83 3.9 25.1 1.0
O B:HIS63 4.0 7.4 1.0
CB B:ASN62 4.0 13.3 1.0
N B:GLU64 4.0 5.5 0.5
N B:GLU64 4.1 6.4 0.5
CA B:HIS63 4.1 6.0 1.0
C B:ASN62 4.1 9.8 1.0
CG B:LYS83 4.2 18.8 1.0
CB B:GLU64 4.3 8.4 0.5
O B:ASN62 4.5 11.7 1.0
CA B:GLU64 4.6 6.7 0.5
CA B:ASN62 4.6 11.1 1.0
CA B:GLU64 4.6 5.3 0.5
CB B:GLU64 4.7 6.1 0.5
CB B:LYS83 4.7 13.3 1.0
CG B:ASN62 4.7 17.1 1.0
CE B:LYS83 4.8 31.6 1.0
OD1 B:ASN62 4.8 17.7 1.0
NZ B:LYS83 4.9 37.0 1.0

Iodine binding site 5 out of 17 in 3pe9

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Iodine binding site 5 out of 17 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I99

b:56.7
occ:0.20
 I B:IOD99 0.0 56.7 0.2
O B:HOH764 1.7 7.1 0.5
I B:IOD99 2.2 28.4 0.4
O B:ASN62 3.6 11.7 1.0
OD1 B:ASP40 3.7 16.4 1.0
CA B:HIS63 3.7 6.0 1.0
C B:ASN62 3.8 9.8 1.0
N B:HIS63 3.9 9.8 1.0
N B:GLU64 3.9 5.5 0.5
N B:GLU64 4.0 6.4 0.5
C B:HIS63 4.0 6.2 1.0
CB B:ASN62 4.3 13.3 1.0
CG B:ASP40 4.5 8.3 1.0
CB B:GLU64 4.7 8.4 0.5
CA B:ASN62 4.7 11.1 1.0
O B:HIS63 4.7 7.4 1.0
CB B:GLU64 4.8 6.1 0.5
CA B:GLU64 4.9 5.3 0.5
CA B:GLU64 4.9 6.7 0.5

Iodine binding site 6 out of 17 in 3pe9

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Iodine binding site 6 out of 17 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I100

b:10.2
occ:0.35
 I B:IOD100 0.0 10.2 0.3
I B:IOD100 0.9 17.5 0.3
O B:HOH974 3.4 21.7 1.0
CB B:LYS87 3.8 8.6 1.0
CE B:LYS87 3.9 22.7 1.0
CG B:LYS87 4.0 7.8 1.0
N B:GLN88 4.0 12.5 1.0
CA B:LYS87 4.1 9.5 1.0
CD B:LYS87 4.6 16.7 1.0
C B:LYS87 4.6 10.2 1.0
CE2 B:PHE85 4.7 10.6 1.0
CB B:GLN88 4.8 16.7 1.0
O B:HOH310 4.9 18.2 1.0

Iodine binding site 7 out of 17 in 3pe9

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Iodine binding site 7 out of 17 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I100

b:17.5
occ:0.35
 I B:IOD100 0.0 17.5 0.3
I B:IOD100 0.9 10.2 0.3
O B:HOH974 2.8 21.7 1.0
N B:GLN88 3.6 12.5 1.0
CB B:LYS87 3.9 8.6 1.0
CE B:LYS87 4.0 22.7 1.0
CB B:GLN88 4.1 16.7 1.0
O B:HOH310 4.1 18.2 1.0
CA B:LYS87 4.2 9.5 1.0
CG B:LYS87 4.3 7.8 1.0
C B:LYS87 4.4 10.2 1.0
CA B:GLN88 4.5 14.6 1.0
CG B:GLN88 4.6 17.7 1.0
O B:HOH935 4.8 29.1 1.0
CD B:LYS87 4.8 16.7 1.0

Iodine binding site 8 out of 17 in 3pe9

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Iodine binding site 8 out of 17 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:40.8
occ:0.50
 O B:HOH1030 2.3 23.0 1.0
OG1 B:THR24 2.9 34.7 1.0
CG B:MET1 3.6 27.0 0.5
CA B:ALA25 3.6 39.3 1.0
CE B:MET1 3.7 31.2 0.5
CG B:LYS3 3.7 25.8 1.0
N B:ALA25 3.7 37.6 1.0
C B:THR24 3.7 36.0 1.0
O B:THR24 3.7 36.4 1.0
CB B:THR24 3.8 33.8 1.0
O B:HOH1025 3.8 21.0 0.5
C B:ALA25 3.8 40.6 1.0
OG B:SER26 3.8 47.9 1.0
N B:SER26 4.0 43.1 1.0
O B:MET1 4.0 26.0 0.5
CD B:LYS3 4.1 30.4 1.0
C B:MET1 4.4 25.1 0.5
O B:ALA25 4.4 38.8 1.0
N B:LYS3 4.4 21.3 1.0
CA B:THR24 4.5 33.5 1.0
CA B:VAL2 4.5 24.6 1.0
CB B:SER26 4.5 45.1 1.0
SD B:MET1 4.5 31.5 0.5
N B:VAL2 4.6 24.4 1.0
C B:VAL2 4.8 22.5 1.0
CA B:SER26 4.8 45.0 1.0
CB B:MET1 4.9 26.7 0.5
CB B:LYS3 4.9 21.7 1.0

Iodine binding site 9 out of 17 in 3pe9

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Iodine binding site 9 out of 17 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I99

b:15.4
occ:0.70
 OG1 C:THR24 3.4 13.7 1.0
O C:HOH473 3.4 12.8 1.0
OG C:SER26 3.6 25.6 1.0
CA C:ALA25 3.7 17.4 1.0
N C:ALA25 3.8 16.5 1.0
NZ C:LYS3 3.8 21.1 1.0
C C:ALA25 3.8 19.4 1.0
C C:THR24 3.9 14.6 1.0
N C:SER26 3.9 22.9 1.0
O C:THR24 3.9 12.8 1.0
CG C:MET1 4.0 28.8 1.0
CB C:THR24 4.0 15.2 1.0
SD C:MET1 4.1 40.8 1.0
CD C:LYS3 4.1 20.4 1.0
CG C:LYS3 4.1 17.0 1.0
O C:HOH486 4.3 17.4 1.0
O C:MET1 4.4 20.9 1.0
CB C:SER26 4.4 27.3 1.0
O C:ALA25 4.5 19.6 1.0
N C:LYS3 4.5 12.9 1.0
CE C:LYS3 4.6 24.0 1.0
CB C:LYS3 4.6 14.2 1.0
CA C:THR24 4.6 13.2 1.0
C C:MET1 4.7 19.2 1.0
C C:VAL2 4.8 12.4 1.0
CA C:VAL2 4.8 13.4 1.0
CA C:SER26 4.8 26.1 1.0
N C:VAL2 4.9 16.6 1.0
O C:HOH123 5.0 16.0 1.0

Iodine binding site 10 out of 17 in 3pe9

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Iodine binding site 10 out of 17 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I100

b:19.9
occ:0.25
 I C:IOD100 0.0 19.9 0.2
I C:IOD100 1.1 12.5 0.2
O C:HOH810 2.7 17.9 1.0
O C:HOH479 2.8 12.2 1.0
N C:GLN88 3.4 11.1 1.0
CB C:GLN88 3.8 13.2 1.0
CB C:LYS87 3.8 10.1 1.0
CA C:LYS87 4.1 10.6 1.0
O C:HOH530 4.2 14.5 1.0
CE C:LYS87 4.2 24.0 1.0
CA C:GLN88 4.2 12.5 1.0
C C:LYS87 4.2 11.2 1.0
CG C:LYS87 4.4 8.3 1.0
O C:HOH912 4.8 31.0 1.0
O C:HOH741 4.8 42.4 1.0
OE1 C:GLN88 4.9 22.9 1.0
O C:GLN88 4.9 11.8 1.0
CD C:LYS87 4.9 16.6 1.0

Reference:

R.Brunecky, M.Alahuhta, Y.J.Bomble, Q.Xu, J.O.Baker, S.Y.Ding, M.E.Himmel, V.V.Lunin. Structure and Function of the Clostridium Thermocellum Cellobiohydrolase A X1-Module Repeat: Enhancement Through Stabilization of the Cbha Complex. Acta Crystallogr.,Sect.D V. 68 292 2012.
ISSN: ISSN 0907-4449
PubMed: 22349231
DOI: 10.1107/S0907444912001680
Page generated: Sun Aug 11 16:03:11 2024

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