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Iodine in PDB 2biv: Crystal Structure of the Wild-Type Mbt Domains of Human SCML2

Protein crystallography data

The structure of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2, PDB code: 2biv was solved by C.M.Santiveri, M.D.Allen, F.Sait, M.Bycroft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.020, 88.206, 186.988, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 22.9

Other elements in 2biv:

The structure of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 (pdb code 2biv). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2, PDB code: 2biv:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 2biv

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Iodine binding site 1 out of 10 in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1244

b:23.2
occ:0.50
 CD1 A:TRP216 3.3 32.9 1.0
N A:TRP216 3.8 24.9 1.0
CG A:TRP216 4.1 30.5 1.0
CB A:TRP216 4.1 26.0 1.0
NE1 A:TRP216 4.3 34.5 1.0
O A:HOH2170 4.4 31.2 1.0
CA A:TYR215 4.4 26.0 1.0
C A:TYR215 4.6 27.6 1.0
CA A:TRP216 4.6 24.9 1.0

Iodine binding site 2 out of 10 in 2biv

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Iodine binding site 2 out of 10 in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1245

b:26.1
occ:0.60
 NE1 A:TRP107 3.7 20.0 1.0
CE2 A:TYR187 3.8 46.0 1.0
CB A:ARG94 3.9 12.2 1.0
CB A:THR89 4.0 19.3 1.0
CD2 A:TYR187 4.0 44.0 1.0
CG2 A:THR89 4.0 18.9 1.0
C A:GLY87 4.0 18.8 1.0
N A:ILE88 4.0 18.3 1.0
CA A:GLY87 4.1 20.4 1.0
O A:ILE88 4.2 17.8 1.0
C A:ILE88 4.3 18.6 1.0
CD A:ARG94 4.3 20.3 1.0
N A:THR89 4.5 16.6 1.0
O A:GLY87 4.6 15.6 1.0
CE2 A:TRP107 4.6 18.6 1.0
O A:HOH2036 4.6 44.4 1.0
CA A:ILE88 4.7 17.9 1.0
CG A:ARG94 4.7 15.5 1.0
CD1 A:TRP107 4.7 17.7 1.0
CZ2 A:TRP107 4.7 19.5 1.0
CA A:THR89 4.8 16.5 1.0
O A:HOH2060 4.9 25.8 1.0
OG1 A:THR89 5.0 21.0 1.0

Iodine binding site 3 out of 10 in 2biv

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Iodine binding site 3 out of 10 in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1246

b:45.9
occ:0.50
 NE A:ARG231 3.7 31.2 1.0
N A:TRP35 3.7 23.0 1.0
CD1 A:TRP35 3.8 15.3 1.0
NH2 A:ARG231 3.8 36.1 1.0
O A:HOH2149 4.1 17.4 1.0
O A:HOH2001 4.1 30.7 1.0
CA A:HIS34 4.1 30.7 1.0
O A:HOH2184 4.2 38.7 1.0
CZ A:ARG231 4.2 33.5 1.0
O A:PHE33 4.3 38.6 1.0
CB A:ARG231 4.4 23.6 1.0
CB A:TRP35 4.4 18.9 1.0
CG A:TRP35 4.4 16.4 1.0
C A:HIS34 4.5 27.1 1.0
CG A:ARG231 4.7 24.1 1.0
CA A:TRP35 4.7 19.9 1.0
ND1 A:HIS34 4.8 34.5 1.0
CD A:ARG231 4.8 26.5 1.0
NE1 A:TRP35 4.8 13.9 1.0
CD2 A:PHE33 4.9 30.1 1.0
N A:HIS34 4.9 34.1 1.0
C A:PHE33 4.9 36.3 1.0

Iodine binding site 4 out of 10 in 2biv

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Iodine binding site 4 out of 10 in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1244

b:35.5
occ:0.50
 NH1 B:ARG231 3.1 37.0 1.0
O B:HOH2089 3.3 27.4 1.0
N B:TRP35 3.5 8.8 1.0
CZ B:ARG231 3.7 33.7 1.0
CD1 B:TRP35 3.7 9.4 1.0
CD B:ARG231 3.8 25.3 1.0
NE B:ARG231 3.9 29.4 1.0
CB B:TRP35 4.0 7.5 1.0
CA B:HIS34 4.2 12.2 1.0
CG B:TRP35 4.2 6.5 1.0
C B:HIS34 4.4 9.2 1.0
CA B:TRP35 4.4 7.1 1.0
O B:HOH2174 4.4 9.9 1.0
NH2 B:ARG231 4.5 31.8 1.0
O B:PHE33 4.6 14.5 1.0
CB B:ARG231 4.6 15.4 1.0
OE1 B:GLU36 4.6 14.5 1.0
CG B:ARG231 4.8 20.3 1.0
NE1 B:TRP35 4.9 8.0 1.0
CD2 B:PHE33 4.9 12.0 1.0
CD2 A:LEU169 4.9 11.8 1.0
CE2 B:PHE33 4.9 8.6 1.0

Iodine binding site 5 out of 10 in 2biv

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Iodine binding site 5 out of 10 in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1245

b:35.1
occ:0.40
 N B:HIS34 3.5 10.8 1.0
O B:HIS34 3.6 8.9 1.0
N B:TYR38 4.0 11.0 1.0
CA B:PHE33 4.0 14.4 1.0
CB B:TYR38 4.0 8.4 1.0
CA B:TYR38 4.1 9.8 1.0
C B:PHE33 4.3 11.1 1.0
CB B:GLU37 4.3 17.2 1.0
CD1 B:PHE33 4.3 11.0 1.0
C B:HIS34 4.3 9.2 1.0
CA B:HIS34 4.3 12.2 1.0
O B:ASP32 4.4 18.0 1.0
C B:GLU37 4.6 9.8 1.0
CB B:HIS34 4.6 17.1 1.0
OE1 B:GLU41 4.6 38.8 1.0
CD1 B:TYR38 4.6 10.9 1.0
CE1 B:PHE33 4.8 13.4 1.0
CG B:PHE33 4.8 12.2 1.0
CG B:TYR38 4.8 11.2 1.0
CD2 B:HIS34 4.8 26.6 1.0
N B:PHE33 4.9 16.3 1.0
CB B:PHE33 4.9 13.3 1.0
C B:ASP32 5.0 17.9 1.0

Iodine binding site 6 out of 10 in 2biv

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Iodine binding site 6 out of 10 in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1247

b:16.8
occ:0.90
 O B:HOH2086 3.3 24.2 1.0
NE1 B:TRP107 3.7 15.5 1.0
CB B:ARG94 4.0 12.2 1.0
CG2 B:THR89 4.0 11.5 1.0
CB B:THR89 4.0 9.0 1.0
C B:GLY87 4.1 12.1 1.0
N B:ILE88 4.1 13.0 1.0
CA B:GLY87 4.1 14.1 1.0
O B:ILE88 4.2 12.0 1.0
CE1 B:TYR187 4.2 14.2 1.0
C B:ILE88 4.3 13.8 1.0
CD1 B:TYR187 4.3 13.1 1.0
CD B:ARG94 4.4 12.7 1.0
CE2 B:TRP107 4.5 12.7 1.0
CZ2 B:TRP107 4.5 14.2 1.0
N B:THR89 4.6 12.1 1.0
O B:GLY87 4.6 12.4 1.0
CA B:ILE88 4.7 14.4 1.0
CD1 B:TRP107 4.8 12.0 1.0
CG B:ARG94 4.8 14.3 1.0
O B:HOH2079 4.9 26.8 1.0
CA B:THR89 4.9 10.6 1.0

Iodine binding site 7 out of 10 in 2biv

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Iodine binding site 7 out of 10 in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1244

b:26.4
occ:0.50
 O C:HOH2131 3.4 30.4 1.0
CB C:TYR187 3.8 19.4 1.0
N C:TYR187 3.8 17.9 1.0
CH2 C:TRP107 3.9 21.9 1.0
CZ3 C:TRP107 3.9 22.9 1.0
CG C:PRO186 4.0 26.2 1.0
CD C:PRO186 4.1 23.0 1.0
O C:HOH2078 4.2 43.9 1.0
C C:ASN185 4.2 18.7 1.0
N C:PRO186 4.2 23.1 1.0
CA C:ASN185 4.3 19.1 1.0
CA C:TYR187 4.4 18.3 1.0
O C:ASN185 4.7 14.9 1.0
C C:PRO186 4.8 21.1 1.0
CB C:ASN185 4.8 16.6 1.0
CA C:PRO186 4.8 22.0 1.0
CZ2 C:TRP107 4.9 19.5 1.0
CE3 C:TRP107 4.9 20.0 1.0
CB C:PRO186 5.0 28.1 1.0

Iodine binding site 8 out of 10 in 2biv

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Iodine binding site 8 out of 10 in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1245

b:21.4
occ:0.80
 O C:HOH2061 3.1 36.0 1.0
NE1 C:TRP107 3.6 20.2 1.0
CG2 C:THR89 3.9 20.5 1.0
CB C:THR89 3.9 19.7 1.0
CB C:ARG94 4.0 17.6 1.0
N C:ILE88 4.0 21.5 1.0
CE1 C:TYR187 4.0 27.6 1.0
C C:GLY87 4.0 21.1 1.0
O C:ILE88 4.1 22.0 1.0
CA C:GLY87 4.2 21.7 1.0
C C:ILE88 4.2 22.2 1.0
CD C:ARG94 4.3 18.0 1.0
N C:THR89 4.5 20.3 1.0
CD1 C:TYR187 4.5 25.5 1.0
O C:GLY87 4.5 22.2 1.0
CD1 C:TRP107 4.6 18.8 1.0
CA C:ILE88 4.6 23.7 1.0
CE2 C:TRP107 4.6 19.4 1.0
CG C:ARG94 4.8 19.2 1.0
CA C:THR89 4.8 18.9 1.0
CZ2 C:TRP107 4.8 19.5 1.0
O C:HOH2052 4.9 33.9 1.0
OG1 C:THR89 5.0 20.4 1.0
CZ C:TYR187 5.0 31.5 1.0

Iodine binding site 9 out of 10 in 2biv

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Iodine binding site 9 out of 10 in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1246

b:46.1
occ:0.50
 O C:HOH2049 3.4 48.2 1.0
CG2 C:ILE86 3.9 33.9 1.0
NH1 C:ARG96 4.0 27.3 1.0
NH2 C:ARG96 4.2 30.4 1.0
CD1 C:ILE86 4.3 32.3 1.0
CZ C:ARG96 4.3 27.6 1.0
O C:HOH2064 4.8 43.3 1.0

Iodine binding site 10 out of 10 in 2biv

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Iodine binding site 10 out of 10 in the Crystal Structure of the Wild-Type Mbt Domains of Human SCML2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of the Wild-Type Mbt Domains of Human SCML2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1248

b:34.0
occ:0.40
 O C:HOH2048 3.1 28.0 1.0
ND2 C:ASN76 4.0 32.6 1.0
CG C:ASN76 4.1 32.8 1.0
OD1 C:ASN76 4.3 29.1 1.0
CB C:ASN76 4.6 31.3 1.0
OG C:SER79 4.9 34.8 1.0
O C:HOH2101 5.0 25.3 1.0

Reference:

C.M.Santiveri, B.C.Lechtenberg, M.D.Allen, A.Sathyamurthy, A.M.Jaulent, S.M.V.Freund, M.Bycroft. The Malignant Brain Tumor Repeats of Human SCML2 Bind to Peptides Containing Monomethylated Lysine. J.Mol.Biol. V. 382 1107 2008.
ISSN: ISSN 0022-2836
PubMed: 18706910
DOI: 10.1016/J.JMB.2008.07.081
Page generated: Sun Aug 11 13:31:20 2024

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