Zinc in PDB 8a38: Ring Domain of Human TRIM2

Enzymatic activity of Ring Domain of Human TRIM2

All present enzymatic activity of Ring Domain of Human TRIM2:
2.3.2.27;

Protein crystallography data

The structure of Ring Domain of Human TRIM2, PDB code: 8a38 was solved by C.Perez-Borrajero, B.Murciano, J.Hennig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.87 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 48.71, 48.71, 221.62, 90, 90, 120
R / Rfree (%) 25.8 / 28.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Ring Domain of Human TRIM2 (pdb code 8a38). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Ring Domain of Human TRIM2, PDB code: 8a38:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8a38

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Zinc binding site 1 out of 7 in the Ring Domain of Human TRIM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ring Domain of Human TRIM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:54.1
occ:1.00
 ND1 A:HIS40 2.1 56.6 1.0
SG A:CYS63 2.2 57.5 1.0
SG A:CYS60 2.3 55.5 1.0
SG A:CYS38 2.3 53.0 1.0
CE1 A:HIS40 3.0 67.1 1.0
CG A:HIS40 3.1 61.4 1.0
CB A:CYS60 3.1 59.0 1.0
CB A:CYS63 3.4 51.4 1.0
CB A:CYS38 3.4 47.5 1.0
CB A:HIS40 3.5 55.7 1.0
N A:CYS63 3.7 69.6 1.0
CA A:CYS63 4.1 53.7 1.0
NE2 A:HIS40 4.2 71.9 1.0
CD2 A:HIS40 4.2 57.5 1.0
CB A:VAL62 4.5 56.1 1.0
N A:HIS40 4.5 63.5 1.0
CA A:CYS60 4.6 49.3 1.0
O A:CYS38 4.6 64.3 1.0
CA A:HIS40 4.6 59.9 1.0
CA A:CYS38 4.7 48.8 1.0
C A:CYS63 4.7 65.0 1.0
C A:CYS38 4.8 62.9 1.0
C A:VAL62 4.8 64.1 1.0
N A:VAL62 4.9 58.6 1.0
N A:ARG64 4.9 60.9 1.0
CA A:VAL62 5.0 57.3 1.0
CG1 A:VAL62 5.0 49.1 1.0

Zinc binding site 2 out of 7 in 8a38

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Zinc binding site 2 out of 7 in the Ring Domain of Human TRIM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ring Domain of Human TRIM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:69.7
occ:1.00
 SG A:CYS43 2.3 72.7 1.0
SG A:CYS23 2.3 66.4 1.0
SG A:CYS26 2.3 81.9 1.0
SG A:CYS46 2.4 61.2 1.0
CB A:CYS23 2.9 76.2 1.0
CB A:CYS43 3.3 70.5 1.0
CB A:CYS46 3.5 56.3 1.0
CB A:CYS26 3.6 75.3 1.0
N A:CYS43 3.8 61.4 1.0
N A:CYS26 3.9 76.7 1.0
CA A:CYS43 4.1 66.9 1.0
CA A:CYS23 4.3 71.7 1.0
CA A:CYS26 4.3 68.7 1.0
CB A:ILE25 4.5 63.9 1.0
C A:CYS23 4.8 70.2 1.0
CA A:CYS46 4.8 71.7 1.0
N A:ILE25 4.8 65.3 1.0
C A:ILE25 4.8 75.2 1.0
O A:CYS23 4.9 77.7 1.0
CA A:ILE25 5.0 56.3 1.0
C A:PHE42 5.0 75.9 1.0

Zinc binding site 3 out of 7 in 8a38

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Zinc binding site 3 out of 7 in the Ring Domain of Human TRIM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ring Domain of Human TRIM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:55.1
occ:1.00
 SG B:CYS46 2.3 59.0 1.0
SG B:CYS23 2.4 57.1 1.0
SG B:CYS43 2.4 48.2 1.0
SG B:CYS26 2.4 56.3 1.0
CB B:CYS23 2.9 46.8 1.0
CB B:CYS43 3.0 50.4 1.0
CB B:CYS46 3.4 59.2 1.0
CB B:CYS26 3.5 56.7 1.0
N B:CYS26 3.8 58.7 1.0
N B:CYS43 3.9 55.4 1.0
CA B:CYS43 4.1 59.9 1.0
CA B:CYS26 4.3 64.5 1.0
CA B:CYS23 4.3 53.0 1.0
CB B:ILE25 4.6 54.6 1.0
C B:CYS23 4.8 61.7 1.0
CA B:CYS46 4.8 64.3 1.0
O B:CYS23 4.8 59.5 1.0
C B:ILE25 4.9 60.5 1.0
N B:ILE25 4.9 54.1 1.0

Zinc binding site 4 out of 7 in 8a38

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Zinc binding site 4 out of 7 in the Ring Domain of Human TRIM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ring Domain of Human TRIM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:51.4
occ:1.00
 ND1 B:HIS40 2.0 50.8 1.0
SG B:CYS63 2.2 58.0 1.0
SG B:CYS60 2.2 47.6 1.0
SG B:CYS38 2.3 51.3 1.0
CG B:HIS40 2.9 60.5 1.0
CE1 B:HIS40 3.0 60.5 1.0
CB B:CYS60 3.1 57.0 1.0
CB B:HIS40 3.3 43.6 1.0
CB B:CYS38 3.3 57.4 1.0
CB B:CYS63 3.6 49.8 1.0
N B:CYS63 3.8 51.3 1.0
NE2 B:HIS40 4.0 52.4 1.0
CD2 B:HIS40 4.0 63.8 1.0
CA B:CYS63 4.3 56.2 1.0
N B:HIS40 4.3 46.1 1.0
O B:CYS38 4.4 58.6 1.0
CA B:HIS40 4.4 51.7 1.0
CB B:VAL62 4.5 65.2 1.0
CA B:CYS38 4.5 51.0 1.0
C B:CYS38 4.5 55.9 1.0
CA B:CYS60 4.6 51.2 1.0
C B:VAL62 4.8 64.2 1.0
N B:VAL62 4.9 53.1 1.0
CG1 B:VAL62 5.0 50.2 1.0
C B:CYS63 5.0 53.5 1.0
CA B:VAL62 5.0 48.5 1.0

Zinc binding site 5 out of 7 in 8a38

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Zinc binding site 5 out of 7 in the Ring Domain of Human TRIM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ring Domain of Human TRIM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:73.8
occ:1.00
 SG C:CYS46 2.3 82.9 1.0
SG C:CYS43 2.4 70.8 1.0
SG C:CYS23 2.4 70.0 1.0
SG C:CYS26 2.6 79.4 1.0
CB C:CYS23 3.0 72.7 1.0
CB C:CYS43 3.0 70.0 1.0
CB C:CYS26 3.3 72.8 1.0
CB C:CYS46 3.5 70.5 1.0
N C:CYS26 3.8 72.2 1.0
N C:CYS43 3.8 78.2 1.0
CA C:CYS43 4.0 75.8 1.0
CA C:CYS26 4.2 83.6 1.0
CA C:CYS23 4.5 80.7 1.0
CB C:ILE25 4.6 59.5 1.0
CG2 C:ILE25 4.7 61.3 1.0
C C:ILE25 4.8 69.3 1.0
CA C:CYS46 4.8 69.8 1.0
C C:CYS23 4.9 75.6 1.0
N C:ILE25 5.0 64.9 1.0
O C:CYS23 5.0 76.9 1.0
C C:CYS43 5.0 76.3 1.0
N C:CYS46 5.0 75.4 1.0

Zinc binding site 6 out of 7 in 8a38

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Zinc binding site 6 out of 7 in the Ring Domain of Human TRIM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ring Domain of Human TRIM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:61.8
occ:1.00
 ND1 C:HIS40 2.0 67.8 1.0
SG C:CYS60 2.3 53.3 1.0
SG C:CYS38 2.3 52.7 1.0
CB C:CYS63 2.4 59.3 1.0
CE1 C:HIS40 2.8 63.7 1.0
CB C:CYS60 3.1 72.3 1.0
CG C:HIS40 3.2 58.7 1.0
CB C:CYS38 3.2 52.4 1.0
N C:CYS63 3.4 59.9 1.0
CA C:CYS63 3.5 73.0 1.0
SG C:CYS63 3.6 109.0 1.0
CB C:HIS40 3.7 55.2 1.0
NE2 C:HIS40 4.0 57.1 1.0
CD2 C:HIS40 4.2 59.0 1.0
C C:CYS63 4.5 72.0 1.0
CA C:CYS38 4.5 65.1 1.0
C C:VAL62 4.6 69.0 1.0
CA C:CYS60 4.6 64.8 1.0
O C:CYS38 4.7 66.2 1.0
N C:HIS40 4.7 71.5 1.0
CB C:VAL62 4.7 57.1 1.0
C C:CYS38 4.7 66.8 1.0
CA C:HIS40 4.8 63.6 1.0
N C:ARG64 4.8 73.1 1.0
CB C:GLN65 4.9 52.1 1.0
CG1 C:VAL62 5.0 68.4 1.0

Zinc binding site 7 out of 7 in 8a38

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Zinc binding site 7 out of 7 in the Ring Domain of Human TRIM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ring Domain of Human TRIM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:84.5
occ:1.00
 NE2 C:HIS54 2.0 94.8 1.0
CE1 C:HIS54 2.5 98.2 1.0
CD2 C:HIS54 3.3 85.2 1.0
ND1 C:HIS54 3.8 90.7 1.0
CG C:HIS54 4.2 93.1 1.0
CB C:ALA53 4.7 90.1 1.0

Reference:

C.Perez-Borrajero, J.Hennig. Structural and Biophysical Studies of TRIM2 and TRIM3 To Be Published.
Page generated: Wed Oct 30 17:30:54 2024

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