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Zinc 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:

Iodine (I) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate, PDB code: 6w9d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6w9d

Go back to Zinc Binding Sites List in 6w9d
Zinc binding site 1 out of 6 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn701

b:68.5
occ:1.00
 ND1 B:HIS593 2.2 0.5 1.0
SG B:CYS573 2.4 66.3 1.0
SG B:CYS596 2.4 74.3 1.0
SG B:CYS570 2.4 76.7 1.0
CG B:HIS593 3.0 0.8 1.0
CB B:CYS570 3.2 85.2 1.0
CB B:HIS593 3.2 92.7 1.0
CE1 B:HIS593 3.3 0.3 1.0
CB B:CYS596 3.4 75.4 1.0
CB B:CYS573 3.5 60.5 1.0
N B:CYS573 3.7 59.6 1.0
CA B:CYS573 4.2 60.3 1.0
CD2 B:HIS593 4.2 0.2 1.0
N B:HIS593 4.3 85.9 1.0
NE2 B:HIS593 4.3 0.3 1.0
CB B:VAL572 4.3 72.2 1.0
CA B:HIS593 4.4 86.2 1.0
CA B:CYS570 4.6 88.7 1.0
C B:VAL572 4.8 70.8 1.0
CA B:CYS596 4.8 81.2 1.0
O B:CYS570 4.8 86.9 1.0
C B:CYS570 4.8 88.0 1.0
N B:VAL572 4.9 80.3 1.0
CA B:VAL572 4.9 73.4 1.0
CG1 B:VAL572 5.0 65.0 1.0
N B:CYS596 5.0 82.4 1.0

Zinc binding site 2 out of 6 in 6w9d

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Zinc binding site 2 out of 6 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn702

b:1.0
occ:1.00
 CD2 B:HIS590 2.2 90.5 1.0
SG B:CYS610 2.3 0.1 1.0
SG B:CYS607 2.3 95.6 1.0
SG B:CYS588 2.4 0.3 1.0
CB B:CYS607 2.8 99.0 1.0
NE2 B:HIS590 2.9 91.4 1.0
CB B:CYS588 3.0 0.4 1.0
CG B:HIS590 3.3 91.2 1.0
CB B:CYS610 3.5 0.2 1.0
N B:CYS610 3.7 91.6 1.0
CE1 B:HIS590 4.0 92.6 1.0
CB B:HIS590 4.0 89.9 1.0
CA B:CYS610 4.1 95.3 1.0
ND1 B:HIS590 4.2 93.5 1.0
O B:CYS588 4.3 1.0 1.0
NH1 B:ARG612 4.3 0.2 1.0
CA B:CYS607 4.3 98.1 1.0
CA B:CYS588 4.4 0.7 1.0
N B:ARG611 4.5 91.5 1.0
CB B:ARG612 4.5 0.7 1.0
N B:ARG612 4.5 0.1 1.0
C B:CYS610 4.5 96.4 1.0
OH B:TYR592 4.6 99.9 1.0
C B:CYS588 4.6 1.0 1.0
C B:CYS607 4.8 95.1 1.0
CB B:ILE609 4.9 79.0 1.0
C B:ILE609 4.9 88.7 1.0
N B:ILE609 4.9 84.0 1.0
CD1 B:LEU586 5.0 87.4 1.0

Zinc binding site 3 out of 6 in 6w9d

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Zinc binding site 3 out of 6 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
E:Zn701

b:75.9
occ:1.00
 ND1 E:HIS593 2.1 96.8 1.0
SG E:CYS570 2.3 78.6 1.0
SG E:CYS573 2.4 80.6 1.0
SG E:CYS596 2.5 99.8 1.0
CB E:CYS570 2.9 80.5 1.0
CG E:HIS593 2.9 99.5 1.0
CB E:HIS593 3.0 83.2 1.0
CE1 E:HIS593 3.2 0.6 1.0
CB E:CYS573 3.6 77.0 1.0
CB E:CYS596 3.6 93.8 1.0
N E:CYS573 3.9 74.1 1.0
N E:HIS593 4.1 80.8 1.0
CD2 E:HIS593 4.1 0.5 1.0
CA E:HIS593 4.2 81.2 1.0
NE2 E:HIS593 4.2 0.4 1.0
CA E:CYS570 4.3 79.0 1.0
CA E:CYS573 4.4 72.3 1.0
CB E:VAL572 4.5 77.2 1.0
O E:CYS570 4.7 79.7 1.0
C E:CYS570 4.8 75.4 1.0
CA E:CYS596 4.9 91.3 1.0
C E:VAL572 5.0 75.6 1.0
N E:CYS596 5.0 94.5 1.0

Zinc binding site 4 out of 6 in 6w9d

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Zinc binding site 4 out of 6 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn702

b:69.2
occ:1.00
 ND1 E:HIS590 2.0 1.0 1.0
SG E:CYS607 2.3 83.5 1.0
SG E:CYS610 2.3 89.8 1.0
SG E:CYS588 2.5 91.6 1.0
CE1 E:HIS590 2.5 0.2 1.0
CB E:CYS607 3.0 89.2 1.0
CG E:HIS590 3.0 0.1 1.0
CB E:CYS610 3.1 92.9 1.0
N E:CYS610 3.3 90.8 1.0
CB E:CYS588 3.4 0.5 1.0
NE2 E:HIS590 3.6 0.1 1.0
CB E:HIS590 3.7 0.6 1.0
CA E:CYS610 3.8 94.4 1.0
CD2 E:HIS590 3.9 0.3 1.0
CB E:ILE609 4.2 78.6 1.0
C E:ILE609 4.4 89.9 1.0
NH1 E:ARG612 4.4 0.6 1.0
O E:CYS588 4.4 0.8 1.0
CA E:CYS607 4.5 90.2 1.0
OH E:TYR592 4.5 96.6 1.0
C E:CYS610 4.5 99.1 1.0
N E:ILE609 4.5 83.0 1.0
N E:ARG611 4.6 91.8 1.0
CA E:ILE609 4.6 82.6 1.0
CA E:CYS588 4.7 0.1 1.0
CG2 E:ILE609 4.7 84.8 1.0
C E:CYS607 4.8 87.0 1.0
C E:CYS588 4.8 0.5 1.0
N E:HIS590 5.0 0.3 1.0
CA E:HIS590 5.0 0.8 1.0
CD1 E:LEU586 5.0 92.8 1.0

Zinc binding site 5 out of 6 in 6w9d

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Zinc binding site 5 out of 6 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
H:Zn701

b:66.8
occ:1.00
 ND1 H:HIS593 2.1 97.5 1.0
SG H:CYS596 2.4 66.3 1.0
SG H:CYS573 2.4 62.1 1.0
SG H:CYS570 2.4 51.3 1.0
CG H:HIS593 2.9 93.5 1.0
CB H:HIS593 3.0 85.0 1.0
CB H:CYS570 3.1 55.5 1.0
CE1 H:HIS593 3.3 99.7 1.0
CB H:CYS596 3.4 64.7 1.0
CB H:CYS573 3.5 63.1 1.0
N H:CYS573 3.9 69.2 1.0
CD2 H:HIS593 4.1 98.4 1.0
N H:HIS593 4.1 76.0 1.0
CA H:HIS593 4.2 77.8 1.0
NE2 H:HIS593 4.3 0.4 1.0
CA H:CYS573 4.3 63.1 1.0
CA H:CYS570 4.5 60.5 1.0
CB H:VAL572 4.6 66.3 1.0
O H:CYS570 4.7 71.0 1.0
CA H:CYS596 4.8 68.6 1.0
C H:CYS570 4.8 68.0 1.0
N H:CYS596 4.9 67.8 1.0
C H:VAL572 5.0 71.8 1.0

Zinc binding site 6 out of 6 in 6w9d

Go back to Zinc Binding Sites List in 6w9d
Zinc binding site 6 out of 6 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
H:Zn702

b:64.4
occ:1.00
 ND1 H:HIS590 2.0 98.1 1.0
SG H:CYS610 2.3 89.3 1.0
SG H:CYS588 2.4 65.8 1.0
SG H:CYS607 2.4 71.3 1.0
CE1 H:HIS590 2.6 99.9 1.0
CB H:CYS607 3.1 72.8 1.0
CB H:CYS588 3.1 70.9 1.0
CG H:HIS590 3.2 92.8 1.0
CB H:CYS610 3.3 86.5 1.0
N H:CYS610 3.7 67.2 1.0
NE2 H:HIS590 3.8 99.0 1.0
CB H:HIS590 3.9 83.8 1.0
CA H:CYS610 4.0 77.2 1.0
CD2 H:HIS590 4.1 97.2 1.0
O H:CYS588 4.3 87.2 1.0
CA H:CYS588 4.5 75.1 1.0
OH H:TYR592 4.5 75.5 1.0
CA H:CYS607 4.6 74.2 1.0
C H:CYS588 4.6 82.7 1.0
C H:CYS610 4.7 78.9 1.0
N H:ARG611 4.7 70.5 1.0
CB H:ILE609 4.7 66.2 1.0
C H:ILE609 4.8 69.7 1.0
N H:HIS590 4.9 82.8 1.0
N H:ARG612 5.0 85.2 1.0
N H:ILE609 5.0 69.7 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: Tue Oct 29 09:15:06 2024

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