Atomistry » Zinc » PDB 6vr7-6wcz » 6w9d
Atomistry »
  Zinc »
    PDB 6vr7-6wcz »
      6w9d »

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

Go back to Zinc Binding Sites List in 6w9d
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

Go back to Zinc Binding Sites List in 6w9d
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

Go back to Zinc Binding Sites List in 6w9d
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

Go back to Zinc Binding Sites List in 6w9d
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy