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Zinc in PDB 7yh3: TRAPPC3 From Thorarchaeota SMTZ1-45

Protein crystallography data

The structure of TRAPPC3 From Thorarchaeota SMTZ1-45, PDB code: 7yh3 was solved by R.C.Robinson, L.T.Tran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.48 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.387, 62.06, 69.324, 90, 100.46, 90
R / Rfree (%) 21.6 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the TRAPPC3 From Thorarchaeota SMTZ1-45 (pdb code 7yh3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the TRAPPC3 From Thorarchaeota SMTZ1-45, PDB code: 7yh3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7yh3

Go back to Zinc Binding Sites List in 7yh3
Zinc binding site 1 out of 4 in the TRAPPC3 From Thorarchaeota SMTZ1-45


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of TRAPPC3 From Thorarchaeota SMTZ1-45 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:11.6
occ:1.00
 SG A:CYS100 2.3 10.8 1.0
SG A:CYS150 2.4 10.2 1.0
SG A:CYS103 2.4 12.4 1.0
SG A:CYS117 2.4 93.8 1.0
CB A:CYS100 2.8 17.4 1.0
CB A:CYS103 3.5 10.4 1.0
CB A:CYS117 3.5 62.3 1.0
CB A:CYS150 3.6 18.9 1.0
N A:CYS103 4.0 11.9 1.0
OG A:SER142 4.2 18.0 1.0
CA A:CYS100 4.3 11.0 1.0
CA A:CYS103 4.3 13.3 1.0
NE2 A:GLN139 4.4 7.5 1.0
CZ2 A:TRP152 4.4 11.3 1.0
CB A:TRP102 4.6 9.3 1.0
CH2 A:TRP152 4.7 10.3 1.0
C A:CYS100 4.7 10.8 1.0
O A:HOH648 4.7 10.2 1.0
O A:HOH644 4.7 17.8 1.0
O A:CYS100 4.8 16.1 1.0
N A:TRP102 4.8 9.9 1.0
C A:TRP102 4.8 13.4 1.0
CA A:CYS117 4.9 13.9 1.0
CA A:CYS150 4.9 20.5 1.0
N A:LYS143 4.9 13.9 1.0
CA A:TRP102 5.0 10.3 1.0

Zinc binding site 2 out of 4 in 7yh3

Go back to Zinc Binding Sites List in 7yh3
Zinc binding site 2 out of 4 in the TRAPPC3 From Thorarchaeota SMTZ1-45


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of TRAPPC3 From Thorarchaeota SMTZ1-45 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:8.1
occ:1.00
 SG B:CYS117 2.2 7.6 1.0
SG B:CYS103 2.4 9.7 1.0
SG B:CYS150 2.4 9.4 1.0
SG B:CYS100 2.4 9.6 1.0
CB B:CYS100 3.0 21.8 1.0
CB B:CYS103 3.4 11.7 1.0
CB B:CYS117 3.5 7.2 1.0
CB B:CYS150 3.6 10.5 1.0
N B:CYS103 4.0 7.1 1.0
OG B:SER142 4.2 11.2 1.0
NE2 B:GLN139 4.2 11.7 1.0
CA B:CYS103 4.3 7.3 1.0
CA B:CYS100 4.4 8.8 1.0
CZ2 B:TRP152 4.5 8.3 1.0
CH2 B:TRP152 4.6 10.1 1.0
O B:HOH661 4.6 16.1 1.0
O B:HOH671 4.6 8.2 1.0
N B:LYS143 4.6 14.7 1.0
CB B:TRP102 4.7 6.4 1.0
C B:CYS100 4.8 8.3 1.0
CA B:CYS117 4.9 6.8 1.0
C B:TRP102 4.9 6.6 1.0
N B:TRP102 4.9 6.9 1.0
CA B:CYS150 4.9 10.7 1.0
O B:CYS100 5.0 9.8 1.0

Zinc binding site 3 out of 4 in 7yh3

Go back to Zinc Binding Sites List in 7yh3
Zinc binding site 3 out of 4 in the TRAPPC3 From Thorarchaeota SMTZ1-45


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of TRAPPC3 From Thorarchaeota SMTZ1-45 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:12.6
occ:1.00
 SG C:CYS117 2.4 15.2 1.0
SG C:CYS150 2.4 11.8 1.0
SG C:CYS100 2.4 12.4 1.0
SG C:CYS103 2.5 13.3 1.0
CB C:CYS100 3.0 10.6 1.0
CB C:CYS117 3.4 9.5 1.0
CB C:CYS103 3.4 12.4 1.0
CB C:CYS150 3.6 12.1 1.0
N C:CYS103 3.9 9.0 1.0
OG C:SER142 4.2 12.6 1.0
NE2 C:GLN139 4.2 13.3 1.0
CA C:CYS103 4.3 12.0 1.0
CA C:CYS100 4.4 11.8 1.0
CZ2 C:TRP152 4.5 20.2 1.0
CB C:TRP102 4.5 10.8 1.0
O C:HOH662 4.6 18.8 1.0
CH2 C:TRP152 4.7 12.6 1.0
O C:HOH691 4.7 20.7 1.0
C C:TRP102 4.8 13.4 1.0
N C:TRP102 4.8 7.8 1.0
CA C:CYS117 4.8 23.5 1.0
C C:CYS100 4.8 9.9 1.0
CB C:SER142 4.9 12.9 1.0
N C:LYS143 4.9 12.0 1.0
CA C:TRP102 4.9 8.3 1.0
O C:CYS100 4.9 10.9 1.0
CA C:CYS150 5.0 20.8 1.0

Zinc binding site 4 out of 4 in 7yh3

Go back to Zinc Binding Sites List in 7yh3
Zinc binding site 4 out of 4 in the TRAPPC3 From Thorarchaeota SMTZ1-45


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of TRAPPC3 From Thorarchaeota SMTZ1-45 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:13.7
occ:1.00
 SG D:CYS117 2.2 13.7 1.0
SG D:CYS100 2.4 17.1 1.0
SG D:CYS103 2.4 15.1 1.0
SG D:CYS150 2.5 17.4 1.0
CB D:CYS100 3.0 20.7 1.0
CB D:CYS117 3.4 13.2 1.0
CB D:CYS103 3.5 16.5 1.0
O D:HOH605 3.6 22.1 1.0
CB D:CYS150 3.6 12.9 1.0
N D:CYS103 3.9 15.5 1.0
OG D:SER142 4.3 15.3 1.0
CA D:CYS103 4.4 21.6 1.0
NE2 D:GLN139 4.4 12.7 1.0
CA D:CYS100 4.4 21.4 1.0
CZ2 D:TRP152 4.5 14.4 1.0
CH2 D:TRP152 4.6 12.0 1.0
CB D:TRP102 4.6 17.1 1.0
O D:HOH707 4.7 20.6 1.0
N D:TRP102 4.7 15.5 1.0
C D:CYS100 4.8 16.2 1.0
CA D:CYS117 4.8 13.0 1.0
C D:TRP102 4.8 24.2 1.0
N D:LYS143 4.9 14.5 1.0
CD1 D:TRP102 4.9 14.1 1.0
O D:HOH698 4.9 18.9 1.0
CA D:TRP102 5.0 15.3 1.0
CA D:CYS150 5.0 12.8 1.0

Reference:

L.T.Tran, R.C.Robinson. TRAPPC3 From Thorarchaeota SMTZ1-45 To Be Published.
Page generated: Fri Aug 22 07:05:47 2025

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