Iodine in PDB 6w9d: RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate

Enzymatic activity of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate

All present enzymatic activity of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate:
2.3.2.23; 2.3.2.24; 2.3.2.27;

Protein crystallography data

The structure of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate, PDB code: 6w9d was solved by A.J.Middleton, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.06 / 3.19
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 135.473, 135.473, 51.372, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 28.1

Other elements in 6w9d:

The structure of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate (pdb code 6w9d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate, PDB code: 6w9d:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 6w9d

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Iodine binding site 1 out of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I703

b:76.1
occ:0.91
 N B:HIS595 4.0 93.6 1.0
N B:LYS582 4.1 90.6 1.0
O B:LYS582 4.1 90.9 1.0
CB B:HIS595 4.1 0.5 1.0
N B:VAL594 4.2 95.6 1.0
CD2 B:HIS593 4.3 0.2 1.0
CA B:ASN581 4.4 87.6 1.0
CB B:VAL594 4.5 89.0 1.0
ND2 B:ASN581 4.5 93.1 1.0
CG B:ASN581 4.6 95.0 1.0
CB B:HIS593 4.7 92.7 1.0
CB B:ASN581 4.7 92.5 1.0
CA B:HIS595 4.7 95.4 1.0
CG B:HIS593 4.7 0.8 1.0
CA B:VAL594 4.7 95.0 1.0
C B:ASN581 4.8 91.9 1.0
C B:VAL594 4.9 93.5 1.0
C B:LYS582 4.9 93.9 1.0
CA B:LYS582 5.0 91.4 1.0

Iodine binding site 2 out of 8 in 6w9d

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Iodine binding site 2 out of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I101

b:0.4
occ:1.00
 CB C:LEU8 3.8 79.0 1.0
CG C:LEU8 3.9 78.0 1.0
CD1 C:LEU8 3.9 78.8 1.0
NH1 B:ARG611 3.9 0.6 1.0
CG C:LEU71 4.0 0.8 1.0
N C:LEU8 4.2 86.3 1.0
N C:LEU71 4.3 0.3 1.0
CB C:LEU71 4.4 0.0 1.0
CG2 C:THR9 4.5 87.2 1.0
CA C:LEU8 4.5 83.0 1.0
O C:LEU69 4.6 96.1 1.0
N C:THR9 4.6 83.3 1.0
NH2 B:ARG611 4.7 93.7 1.0
CZ B:ARG611 4.8 96.4 1.0
CD1 C:LEU71 4.8 0.7 1.0
CG2 A:ILE88 4.8 66.3 1.0
CD2 C:LEU71 4.9 96.0 1.0
CA C:VAL70 4.9 95.5 1.0
CA C:LEU71 5.0 0.2 1.0
CB C:THR7 5.0 88.6 1.0

Iodine binding site 3 out of 8 in 6w9d

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Iodine binding site 3 out of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I201

b:0.3
occ:0.81
 CB E:CYS573 4.0 77.0 1.0
CD D:PRO61 4.1 71.0 1.0
CA E:CYS573 4.2 72.3 1.0
N D:ALA2 4.2 74.3 1.0
CE2 D:PHE62 4.6 71.6 1.0
CB D:ARG5 4.6 64.6 1.0
CG D:PRO61 4.6 67.5 1.0
CZ D:PHE62 4.8 73.9 1.0
N E:CYS573 4.8 74.1 1.0
CG1 E:VAL572 4.9 78.8 1.0
O E:VAL572 5.0 83.1 1.0

Iodine binding site 4 out of 8 in 6w9d

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Iodine binding site 4 out of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I703

b:83.3
occ:0.96
 N E:LYS582 3.8 83.2 1.0
ND2 E:ASN581 4.0 91.0 1.0
O E:LYS582 4.0 76.5 1.0
N E:VAL594 4.2 76.2 1.0
N E:HIS595 4.2 91.8 1.0
CA E:ASN581 4.2 81.4 1.0
CD2 E:HIS593 4.3 0.5 1.0
CG E:ASN581 4.5 87.7 1.0
CB E:HIS593 4.5 83.2 1.0
CB E:VAL594 4.5 80.3 1.0
CB E:HIS595 4.5 0.7 1.0
C E:ASN581 4.5 83.3 1.0
CB E:ASN581 4.6 83.9 1.0
CG E:HIS593 4.6 99.5 1.0
CA E:LYS582 4.6 82.0 1.0
C E:LYS582 4.7 79.8 1.0
CA E:VAL594 4.8 75.7 1.0
CB E:LYS582 4.8 84.8 1.0
CA E:HIS593 4.9 81.2 1.0
C E:HIS593 5.0 75.7 1.0

Iodine binding site 5 out of 8 in 6w9d

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Iodine binding site 5 out of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I101

b:0.9
occ:1.00
 NH1 E:ARG611 3.7 94.7 1.0
CG2 F:THR9 3.8 0.8 1.0
CB F:LEU8 4.4 0.8 1.0
N F:THR9 4.4 0.4 1.0
NH2 E:ARG611 4.4 98.5 1.0
N F:LEU8 4.5 97.3 1.0
CZ E:ARG611 4.6 96.0 1.0
CG2 D:ILE88 4.6 58.2 1.0
OG1 F:THR9 4.8 0.9 1.0
CB F:THR7 4.8 89.1 1.0
CB F:THR9 4.8 0.0 1.0
CG F:LEU8 4.9 0.6 1.0
CA F:LEU8 4.9 0.4 1.0

Iodine binding site 6 out of 8 in 6w9d

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Iodine binding site 6 out of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:I201

b:0.7
occ:0.74
 NZ G:LYS4 3.5 0.1 1.0
CG G:LYS4 4.1 92.5 1.0
ND2 G:ASN11 4.1 0.5 1.0
CB G:HIS7 4.1 86.5 1.0
N G:LYS8 4.4 92.7 1.0
CE G:LYS4 4.4 0.4 1.0
O G:LYS4 4.4 82.6 1.0
C G:HIS7 4.6 93.5 1.0
CA G:LYS8 4.6 96.7 1.0
CB G:LYS8 4.8 93.8 1.0
CD G:LYS4 4.9 98.9 1.0
O G:HIS7 4.9 98.3 1.0
CA G:HIS7 5.0 88.2 1.0

Iodine binding site 7 out of 8 in 6w9d

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Iodine binding site 7 out of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I703

b:64.6
occ:0.90
 N H:LYS582 3.7 64.1 1.0
O H:LYS582 3.8 70.2 1.0
N H:HIS595 4.0 66.7 1.0
N H:VAL594 4.1 66.6 1.0
CD2 H:HIS593 4.2 98.4 1.0
CB H:HIS595 4.3 73.7 1.0
CA H:ASN581 4.3 67.7 1.0
ND2 H:ASN581 4.3 68.7 1.0
CB H:VAL594 4.4 66.2 1.0
CB H:HIS593 4.5 85.0 1.0
C H:ASN581 4.6 70.7 1.0
CG H:HIS593 4.6 93.5 1.0
CA H:LYS582 4.6 64.3 1.0
C H:LYS582 4.6 65.1 1.0
CB H:ASN581 4.6 66.5 1.0
CA H:VAL594 4.7 64.3 1.0
CB H:LYS582 4.7 65.2 1.0
CG H:ASN581 4.7 66.7 1.0
CA H:HIS595 4.8 68.9 1.0
C H:VAL594 4.9 64.7 1.0
C H:HIS593 4.9 69.6 1.0
CA H:HIS593 4.9 77.8 1.0

Iodine binding site 8 out of 8 in 6w9d

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Iodine binding site 8 out of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:I101

b:70.0
occ:0.57
 NH1 H:ARG611 3.7 79.5 1.0
CD1 I:LEU71 3.7 89.5 1.0
CD1 I:LEU8 3.8 98.7 1.0
CB I:LEU8 3.8 87.9 1.0
N I:LEU8 4.0 87.9 1.0
CG I:LEU8 4.1 91.8 1.0
NH2 H:ARG611 4.4 71.0 1.0
CA I:LEU8 4.5 86.8 1.0
N I:THR9 4.5 88.4 1.0
CB I:THR7 4.5 81.8 1.0
CZ H:ARG611 4.5 75.6 1.0
N I:LEU71 4.6 89.7 1.0
CG2 I:THR9 4.7 88.4 1.0
O I:LEU69 4.7 91.2 1.0
CB I:LEU71 4.7 92.0 1.0
CG2 G:ILE88 4.7 73.2 1.0
CG I:LEU71 4.7 91.1 1.0

Reference:

A.J.Middleton, J.Zhu, C.L.Day. The Ring Domain of Ring Finger 12 Efficiently Builds Degradative Ubiquitin Chains J.Mol.Biol..
ISSN: ESSN 1089-8638
DOI: 10.1016/J.JMB.2020.05.001
Page generated: Sun Dec 13 19:52:18 2020

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