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Zinc in PDB 8rxb: Human UPF1 Ch Domain in Complex with SMG6 Peptide

Enzymatic activity of Human UPF1 Ch Domain in Complex with SMG6 Peptide

All present enzymatic activity of Human UPF1 Ch Domain in Complex with SMG6 Peptide:
3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of Human UPF1 Ch Domain in Complex with SMG6 Peptide, PDB code: 8rxb was solved by L.Langer, J.Basquin, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.44 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.165, 90.677, 92.291, 90, 113.36, 90
R / Rfree (%) 28.1 / 29.5

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Human UPF1 Ch Domain in Complex with SMG6 Peptide (pdb code 8rxb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Human UPF1 Ch Domain in Complex with SMG6 Peptide, PDB code: 8rxb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in 8rxb

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Zinc binding site 1 out of 13 in the Human UPF1 Ch Domain in Complex with SMG6 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human UPF1 Ch Domain in Complex with SMG6 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:45.8
occ:1.00
HD1 E:HIS41 1.3 19.7 1.0
HG E:CYS12 1.9 192.0 1.0
ND1 E:HIS41 2.1 31.2 1.0
SG E:CYS31 2.3 41.6 1.0
SG E:CYS9 2.3 38.6 1.0
SG E:CYS12 2.3 171.4 1.0
HG E:CYS9 2.4 24.2 1.0
HG E:CYS31 2.8 39.2 1.0
CE1 E:HIS41 3.0 62.6 1.0
HB3 E:CYS9 3.1 32.7 1.0
CG E:HIS41 3.1 48.5 1.0
HB2 E:HIS41 3.1 18.8 1.0
CB E:CYS9 3.2 45.5 1.0
HE1 E:HIS41 3.2 57.4 1.0
H E:CYS31 3.2 29.9 1.0
HB2 E:CYS9 3.3 32.7 1.0
HB3 E:CYS31 3.3 39.5 1.0
HE22 E:GLN137 3.4 45.6 1.0
CB E:CYS31 3.4 41.8 1.0
HB2 E:TYR11 3.5 44.1 1.0
H E:CYS12 3.5 43.6 1.0
CB E:HIS41 3.5 30.4 1.0
HB3 E:CYS12 3.5 48.9 1.0
HB3 E:HIS41 3.6 18.8 1.0
CB E:CYS12 3.6 52.4 1.0
HB E:ILE14 3.9 42.8 1.0
N E:CYS31 3.9 33.8 1.0
N E:CYS12 4.0 48.0 1.0
HD11 E:ILE14 4.1 47.5 1.0
NE2 E:GLN137 4.2 55.2 1.0
NE2 E:HIS41 4.2 49.5 1.0
CA E:CYS31 4.2 35.1 1.0
HB2 E:CYS31 4.2 39.5 1.0
CD2 E:HIS41 4.2 39.6 1.0
HE21 E:GLN137 4.3 45.6 1.0
HB2 E:CYS12 4.3 48.9 1.0
H E:ILE14 4.3 36.5 1.0
CA E:CYS12 4.4 50.2 1.0
CB E:TYR11 4.4 54.6 1.0
H E:TYR11 4.4 38.7 1.0
HD2 E:TYR11 4.5 37.2 1.0
H E:GLY13 4.6 45.5 1.0
H E:GLY33 4.6 44.6 1.0
CA E:CYS9 4.6 57.9 1.0
HB3 E:TYR11 4.6 44.1 1.0
C E:CYS31 4.6 31.4 1.0
O E:CYS31 4.7 31.2 1.0
HA E:PHE30 4.8 22.5 1.0
H E:HIS41 4.9 33.6 1.0
CB E:ILE14 4.9 46.3 1.0
C E:CYS12 4.9 46.0 1.0
C E:TYR11 4.9 69.0 1.0
HA E:CYS9 4.9 47.5 1.0
N E:GLY13 4.9 50.4 1.0
CD1 E:ILE14 5.0 50.3 1.0
CA E:HIS41 5.0 37.1 1.0

Zinc binding site 2 out of 13 in 8rxb

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Zinc binding site 2 out of 13 in the Human UPF1 Ch Domain in Complex with SMG6 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human UPF1 Ch Domain in Complex with SMG6 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:49.3
occ:1.00
HG E:CYS69 1.3 89.8 1.0
HG E:CYS72 1.4 33.3 1.0
HG E:CYS99 2.0 40.7 1.0
SG E:CYS99 2.3 46.5 1.0
SG E:CYS72 2.3 42.4 1.0
SG E:CYS69 2.3 84.8 1.0
SG E:CYS95 2.3 36.2 1.0
HG E:CYS95 2.4 35.5 1.0
HB2 E:CYS95 2.9 39.6 1.0
H E:CYS95 3.0 32.0 1.0
HB3 E:CYS69 3.0 43.7 1.0
HB2 E:CYS69 3.0 43.7 1.0
CB E:CYS69 3.0 46.3 1.0
H E:CYS72 3.1 29.8 1.0
CB E:CYS95 3.2 39.8 1.0
HB2 E:CYS99 3.3 31.4 1.0
HB3 E:CYS72 3.4 36.9 1.0
HZ2 A:LYS52 3.4 42.7 1.0
CB E:CYS99 3.4 38.6 1.0
CB E:CYS72 3.5 45.5 1.0
HB3 E:ASN71 3.6 48.7 1.0
HB3 E:CYS74 3.7 50.7 1.0
HB3 E:CYS99 3.7 31.4 1.0
N E:CYS95 3.7 33.1 1.0
N E:CYS72 3.8 39.4 1.0
HB3 E:CYS95 3.9 39.6 1.0
H E:CYS74 4.0 24.7 1.0
HB2 E:CYS74 4.0 50.7 1.0
CA E:CYS95 4.1 34.2 1.0
CA E:CYS72 4.2 36.5 1.0
HD2 E:PRO98 4.2 43.9 1.0
HD22 E:ASN71 4.2 36.3 1.0
NZ A:LYS52 4.3 44.5 1.0
HB2 E:CYS72 4.3 36.9 1.0
H E:CYS99 4.3 39.8 1.0
H E:ASN71 4.3 43.3 1.0
CB E:CYS74 4.3 58.0 1.0
HE2 A:LYS52 4.4 60.8 1.0
H E:GLY73 4.5 31.4 1.0
CA E:CYS69 4.5 33.9 1.0
HA E:LEU94 4.5 36.1 1.0
CB E:ASN71 4.5 58.4 1.0
HZ3 A:LYS52 4.6 42.7 1.0
HA E:CYS95 4.6 33.1 1.0
CA E:CYS99 4.7 41.4 1.0
CE A:LYS52 4.8 59.4 1.0
HE3 A:LYS52 4.8 60.8 1.0
N E:CYS74 4.8 36.2 1.0
HZ1 A:LYS52 4.8 42.7 1.0
C E:CYS72 4.8 44.0 1.0
C E:ASN71 4.8 55.9 1.0
N E:GLY73 4.8 41.1 1.0
HA E:CYS69 4.8 29.0 1.0
HD23 E:LEU94 4.8 47.9 1.0
N E:CYS99 4.9 45.9 1.0
N E:ASN71 4.9 53.5 1.0
C E:LEU94 4.9 44.5 1.0
HD22 E:LEU80 4.9 32.6 1.0
ND2 E:ASN71 5.0 48.3 1.0
CA E:ASN71 5.0 42.2 1.0

Zinc binding site 3 out of 13 in 8rxb

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Zinc binding site 3 out of 13 in the Human UPF1 Ch Domain in Complex with SMG6 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human UPF1 Ch Domain in Complex with SMG6 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn203

b:76.8
occ:1.00
HB2 E:ASN76 3.0 55.8 1.0
HG A:CYS74 3.1 33.4 1.0
HG E:CYS74 3.1 42.1 1.0
HD22 E:ASN76 3.2 39.5 1.0
HD22 A:ASN76 3.4 30.4 1.0
HB2 A:ASN76 3.4 41.0 1.0
CB E:ASN76 3.9 58.1 1.0
ND2 E:ASN76 4.0 44.8 1.0
HB3 E:ASN76 4.0 55.8 1.0
SG E:CYS74 4.1 50.9 1.0
SG A:CYS74 4.1 41.5 1.0
ND2 A:ASN76 4.2 37.1 1.0
CB A:ASN76 4.2 46.2 1.0
HB3 A:ASN76 4.3 41.0 1.0
CG E:ASN76 4.5 45.4 1.0
H E:ASN76 4.6 40.4 1.0
HD21 E:ASN76 4.7 39.5 1.0
H E:ARG75 4.7 34.9 1.0
CG A:ASN76 4.8 40.8 1.0
HD21 A:ASN76 4.8 30.4 1.0
N E:ASN76 4.9 45.0 1.0
CA E:ASN76 4.9 43.5 1.0
H A:ASN76 5.0 37.9 1.0

Zinc binding site 4 out of 13 in 8rxb

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Zinc binding site 4 out of 13 in the Human UPF1 Ch Domain in Complex with SMG6 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human UPF1 Ch Domain in Complex with SMG6 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:42.7
occ:1.00
HD1 A:HIS41 1.2 31.3 1.0
HG A:CYS9 1.7 19.7 1.0
ND1 A:HIS41 2.1 35.7 1.0
SG A:CYS9 2.3 35.4 1.0
SG A:CYS31 2.3 41.1 1.0
SG A:CYS12 2.3 45.7 1.0
HG A:CYS12 2.6 42.1 1.0
HG A:CYS31 2.7 29.9 1.0
CE1 A:HIS41 2.9 46.5 1.0
HE1 A:HIS41 3.0 44.1 1.0
CB A:CYS9 3.1 54.7 1.0
HB2 A:CYS9 3.1 42.3 1.0
HB3 A:CYS9 3.1 42.3 1.0
HB3 A:CYS31 3.1 43.8 1.0
CG A:HIS41 3.2 59.1 1.0
H A:CYS31 3.2 36.7 1.0
HB2 A:HIS41 3.3 31.4 1.0
CB A:CYS31 3.3 52.8 1.0
H A:CYS12 3.4 48.4 1.0
HB3 A:CYS12 3.5 39.5 1.0
HB2 A:TYR11 3.5 38.9 1.0
CB A:CYS12 3.5 43.5 1.0
CB A:HIS41 3.6 35.2 1.0
HD11 A:ILE14 3.8 47.4 1.0
HB3 A:HIS41 3.8 31.4 1.0
HB A:ILE14 3.9 47.8 1.0
N A:CYS12 3.9 50.6 1.0
N A:CYS31 4.0 46.4 1.0
NE2 A:HIS41 4.1 34.7 1.0
HB2 A:CYS31 4.1 43.8 1.0
CA A:CYS31 4.2 46.1 1.0
CD2 A:HIS41 4.2 36.4 1.0
CA A:CYS12 4.3 59.5 1.0
HB2 A:CYS12 4.3 39.5 1.0
H A:ILE14 4.4 50.0 1.0
CB A:TYR11 4.4 43.4 1.0
H A:TYR11 4.5 42.7 1.0
CA A:CYS9 4.5 58.4 1.0
H A:GLY13 4.5 54.5 1.0
HB3 A:TYR11 4.6 38.9 1.0
H A:GLY33 4.7 36.2 1.0
CD1 A:ILE14 4.7 53.3 1.0
C A:CYS31 4.7 40.8 1.0
HA A:CYS9 4.8 46.8 1.0
HD2 A:TYR11 4.8 45.4 1.0
HA A:PHE30 4.8 33.7 1.0
O A:CYS31 4.8 38.8 1.0
CB A:ILE14 4.8 53.6 1.0
C A:CYS12 4.9 60.1 1.0
HG13 A:ILE14 4.9 54.0 1.0
C A:TYR11 4.9 59.2 1.0
O A:GLY33 4.9 36.6 1.0
H A:HIS41 4.9 40.7 1.0
N A:GLY13 4.9 56.5 1.0

Zinc binding site 5 out of 13 in 8rxb

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Zinc binding site 5 out of 13 in the Human UPF1 Ch Domain in Complex with SMG6 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human UPF1 Ch Domain in Complex with SMG6 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:52.1
occ:1.00
HG A:CYS69 1.3 45.1 1.0
HG A:CYS72 2.2 24.1 1.0
SG A:CYS99 2.3 51.9 1.0
SG A:CYS95 2.3 51.6 1.0
SG A:CYS72 2.3 39.1 1.0
SG A:CYS69 2.3 52.0 1.0
HG A:CYS95 2.5 47.3 1.0
HG A:CYS99 2.5 46.8 1.0
HB2 A:CYS95 2.9 37.0 1.0
H A:CYS95 2.9 28.7 1.0
HB3 A:CYS69 3.0 40.9 1.0
HB2 A:CYS69 3.0 40.9 1.0
CB A:CYS69 3.0 48.5 1.0
H A:CYS72 3.1 47.2 1.0
CB A:CYS95 3.2 43.1 1.0
HB2 A:CYS99 3.3 34.3 1.0
HB3 A:CYS72 3.4 50.4 1.0
CB A:CYS99 3.4 41.7 1.0
HB3 A:ASN71 3.4 60.0 1.0
CB A:CYS72 3.5 61.0 1.0
HB3 A:CYS99 3.7 34.3 1.0
N A:CYS95 3.7 36.6 1.0
N A:CYS72 3.8 58.8 1.0
HD21 A:ASN71 3.8 47.4 1.0
HB3 A:CYS74 3.9 28.8 1.0
HB3 A:CYS95 3.9 37.0 1.0
HZ2 E:LYS52 4.0 74.0 1.0
CA A:CYS95 4.0 36.8 1.0
H A:CYS74 4.1 34.5 1.0
HB2 A:CYS74 4.1 28.8 1.0
CA A:CYS72 4.2 61.2 1.0
HE3 E:LYS52 4.2 61.1 1.0
HB2 A:CYS72 4.3 50.4 1.0
H A:ASN71 4.3 52.1 1.0
HD2 A:PRO98 4.3 35.2 1.0
HZ1 E:LYS52 4.3 74.0 1.0
H A:CYS99 4.3 51.9 1.0
CB A:ASN71 4.4 61.3 1.0
CB A:CYS74 4.5 37.7 1.0
HA A:LEU94 4.5 33.5 1.0
H A:GLY73 4.5 61.5 1.0
CA A:CYS69 4.5 56.1 1.0
NZ E:LYS52 4.5 72.7 1.0
HA A:CYS95 4.6 29.1 1.0
ND2 A:ASN71 4.7 50.3 1.0
C A:ASN71 4.8 64.0 1.0
CA A:CYS99 4.8 46.0 1.0
CE E:LYS52 4.8 62.0 1.0
C A:CYS72 4.8 57.9 1.0
HA A:CYS69 4.8 49.7 1.0
N A:GLY73 4.8 60.8 1.0
N A:CYS74 4.9 42.8 1.0
C A:LEU94 4.9 44.3 1.0
HB2 A:ASN71 4.9 60.0 1.0
N A:ASN71 4.9 55.0 1.0
N A:CYS99 4.9 56.0 1.0
CA A:ASN71 4.9 59.5 1.0
HD23 A:LEU94 5.0 32.2 1.0
HE2 E:LYS52 5.0 61.1 1.0

Zinc binding site 6 out of 13 in 8rxb

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Zinc binding site 6 out of 13 in the Human UPF1 Ch Domain in Complex with SMG6 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human UPF1 Ch Domain in Complex with SMG6 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:61.9
occ:1.00
HD1 D:HIS41 1.2 35.1 1.0
HG D:CYS12 1.4 64.8 1.0
ND1 D:HIS41 2.0 46.8 1.0
SG D:CYS12 2.3 72.1 1.0
SG D:CYS31 2.3 62.2 1.0
SG D:CYS9 2.3 58.4 1.0
CE1 D:HIS41 2.8 69.9 1.0
HE1 D:HIS41 2.9 62.5 1.0
HG D:CYS31 3.0 57.0 1.0
HB3 D:CYS9 3.1 53.6 1.0
CB D:CYS9 3.1 63.1 1.0
CG D:HIS41 3.1 69.3 1.0
HB2 D:CYS9 3.1 53.6 1.0
H D:CYS31 3.2 50.9 1.0
HB3 D:CYS31 3.3 56.2 1.0
HG D:CYS9 3.3 47.8 1.0
HB2 D:HIS41 3.3 65.5 1.0
H D:CYS12 3.4 56.8 1.0
CB D:CYS31 3.4 61.2 1.0
HB2 D:TYR11 3.5 60.1 1.0
CB D:HIS41 3.6 71.8 1.0
HD13 D:ILE14 3.7 63.3 1.0
HB3 D:HIS41 3.7 65.5 1.0
CB D:CYS12 3.7 71.8 1.0
HD11 D:ILE14 3.8 63.3 1.0
HB3 D:CYS12 3.8 64.0 1.0
N D:CYS31 4.0 56.6 1.0
N D:CYS12 4.0 65.7 1.0
NE2 D:HIS41 4.0 62.3 1.0
CD2 D:HIS41 4.2 61.3 1.0
HB2 D:CYS31 4.2 56.2 1.0
HB D:ILE14 4.2 72.6 1.0
CD1 D:ILE14 4.2 69.6 1.0
CA D:CYS31 4.2 62.7 1.0
H D:ILE14 4.3 51.5 1.0
H D:GLY13 4.4 62.3 1.0
CA D:CYS12 4.4 73.5 1.0
H D:TYR11 4.4 51.1 1.0
HB2 D:CYS12 4.5 64.0 1.0
CB D:TYR11 4.5 69.7 1.0
CA D:CYS9 4.6 61.1 1.0
C D:CYS31 4.7 60.7 1.0
HB3 D:TYR11 4.8 60.1 1.0
O D:CYS31 4.8 62.0 1.0
H D:GLY33 4.8 63.5 1.0
N D:GLY13 4.8 61.8 1.0
HA D:PHE30 4.8 49.0 1.0
HD12 D:ILE14 4.8 63.3 1.0
HD2 D:TYR11 4.8 59.8 1.0
C D:CYS12 4.8 69.7 1.0
HA D:CYS9 4.9 51.2 1.0
C D:TYR11 4.9 80.1 1.0
H D:HIS41 5.0 55.9 1.0

Zinc binding site 7 out of 13 in 8rxb

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Zinc binding site 7 out of 13 in the Human UPF1 Ch Domain in Complex with SMG6 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human UPF1 Ch Domain in Complex with SMG6 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:44.6
occ:1.00
HG D:CYS69 1.2 37.2 1.0
HG D:CYS72 2.0 31.0 1.0
SG D:CYS99 2.3 44.5 1.0
HG D:CYS99 2.3 51.2 1.0
SG D:CYS69 2.3 43.9 1.0
SG D:CYS72 2.3 41.6 1.0
SG D:CYS95 2.3 53.4 1.0
HG D:CYS95 2.6 54.1 1.0
H D:CYS95 2.9 34.5 1.0
HB2 D:CYS95 2.9 49.8 1.0
HB2 D:CYS69 3.0 40.9 1.0
H D:CYS72 3.0 45.9 1.0
HB3 D:CYS69 3.0 40.9 1.0
CB D:CYS69 3.0 47.0 1.0
HB2 D:CYS99 3.2 39.2 1.0
CB D:CYS95 3.2 49.8 1.0
CB D:CYS99 3.3 34.5 1.0
HB3 D:CYS72 3.4 52.0 1.0
CB D:CYS72 3.5 59.0 1.0
HB3 D:ASN71 3.5 44.2 1.0
HB3 D:CYS99 3.6 39.2 1.0
N D:CYS72 3.7 53.6 1.0
N D:CYS95 3.7 36.9 1.0
HB3 D:CYS74 3.8 60.9 1.0
HZ2 L:LYS52 3.9 64.9 1.0
HB3 D:CYS95 4.0 49.8 1.0
H D:CYS74 4.0 42.8 1.0
CA D:CYS95 4.1 38.1 1.0
CA D:CYS72 4.1 57.7 1.0
HB2 D:CYS74 4.1 60.9 1.0
H D:CYS99 4.2 49.2 1.0
H D:ASN71 4.2 64.8 1.0
HD2 D:PRO98 4.2 50.7 1.0
HB2 D:CYS72 4.3 52.0 1.0
H D:GLY73 4.4 40.2 1.0
HE2 L:LYS52 4.4 80.4 1.0
HA D:LEU94 4.4 35.5 1.0
CB D:CYS74 4.5 57.5 1.0
CB D:ASN71 4.5 42.9 1.0
CA D:CYS69 4.5 48.3 1.0
NZ L:LYS52 4.6 62.4 1.0
HA D:CYS95 4.6 35.8 1.0
CA D:CYS99 4.6 39.8 1.0
HE3 L:LYS52 4.7 80.4 1.0
HZ3 L:LYS52 4.7 64.9 1.0
C D:ASN71 4.7 56.7 1.0
C D:CYS72 4.7 43.1 1.0
N D:GLY73 4.7 43.8 1.0
N D:CYS99 4.8 42.9 1.0
N D:CYS74 4.8 42.1 1.0
CE L:LYS52 4.8 75.5 1.0
HA D:CYS69 4.8 42.5 1.0
N D:ASN71 4.8 60.1 1.0
C D:LEU94 4.8 50.6 1.0
HB2 D:ASN71 4.9 44.2 1.0
CA D:ASN71 4.9 47.6 1.0
HA D:CYS72 5.0 50.6 1.0

Zinc binding site 8 out of 13 in 8rxb

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Zinc binding site 8 out of 13 in the Human UPF1 Ch Domain in Complex with SMG6 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human UPF1 Ch Domain in Complex with SMG6 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:50.5
occ:1.00
HD1 I:HIS41 1.2 40.2 1.0
ND1 I:HIS41 2.1 44.7 1.0
SG I:CYS9 2.3 39.5 1.0
SG I:CYS31 2.3 48.9 1.0
SG I:CYS12 2.3 61.1 1.0
HG I:CYS12 2.6 67.5 1.0
CE1 I:HIS41 2.9 42.7 1.0
HE1 I:HIS41 3.0 37.8 1.0
HG I:CYS31 3.0 47.0 1.0
HB3 I:CYS9 3.2 39.5 1.0
CB I:CYS9 3.2 41.0 1.0
CG I:HIS41 3.2 58.2 1.0
H I:CYS31 3.3 53.7 1.0
HB2 I:CYS9 3.3 39.5 1.0
HG I:CYS9 3.3 37.5 1.0
HB2 I:HIS41 3.4 34.3 1.0
HB3 I:CYS31 3.5 39.4 1.0
H I:CYS12 3.5 52.2 1.0
HB2 I:TYR11 3.5 49.9 1.0
CB I:CYS31 3.5 42.4 1.0
CB I:HIS41 3.7 39.7 1.0
HB3 I:HIS41 3.7 34.3 1.0
CB I:CYS12 3.8 37.9 1.0
HB3 I:CYS12 3.9 39.3 1.0
N I:CYS31 4.0 54.6 1.0
N I:CYS12 4.1 49.0 1.0
NE2 I:HIS41 4.1 37.8 1.0
CD2 I:HIS41 4.3 44.0 1.0
HB2 I:CYS31 4.3 39.4 1.0
CA I:CYS31 4.3 50.9 1.0
H I:GLY13 4.4 50.4 1.0
CB I:TYR11 4.4 50.2 1.0
H I:TYR11 4.4 48.5 1.0
CA I:CYS12 4.4 50.2 1.0
HD11 I:ILE14 4.4 53.7 1.0
H I:ILE14 4.5 57.7 1.0
HB I:ILE14 4.5 65.0 1.0
HB2 I:CYS12 4.5 39.3 1.0
HB3 I:TYR11 4.6 49.9 1.0
CA I:CYS9 4.7 52.3 1.0
HD2 I:TYR11 4.7 54.5 1.0
HA I:PHE30 4.8 36.7 1.0
O I:CYS31 4.8 45.4 1.0
C I:CYS31 4.8 36.8 1.0
N I:GLY13 4.8 52.1 1.0
H I:GLY33 4.9 44.6 1.0
C I:CYS12 4.9 51.0 1.0
C I:TYR11 5.0 61.6 1.0
HA I:CYS9 5.0 52.8 1.0

Zinc binding site 9 out of 13 in 8rxb

Go back to Zinc Binding Sites List in 8rxb
Zinc binding site 9 out of 13 in the Human UPF1 Ch Domain in Complex with SMG6 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human UPF1 Ch Domain in Complex with SMG6 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:47.9
occ:1.00
HG I:CYS69 1.5 35.0 1.0
SG I:CYS99 2.3 57.3 1.0
HG I:CYS72 2.3 24.7 1.0
SG I:CYS72 2.3 43.6 1.0
SG I:CYS95 2.3 49.8 1.0
SG I:CYS69 2.4 41.2 1.0
HG I:CYS99 2.4 53.9 1.0
HG I:CYS95 2.4 47.9 1.0
H I:CYS95 3.0 28.3 1.0
HB2 I:CYS69 3.0 48.5 1.0
HB3 I:CYS69 3.0 48.5 1.0
HB2 I:CYS95 3.0 33.8 1.0
CB I:CYS69 3.1 52.5 1.0
H I:CYS72 3.2 51.2 1.0
CB I:CYS95 3.3 38.0 1.0
HB2 I:CYS99 3.3 38.2 1.0
HB3 I:CYS72 3.4 58.4 1.0
CB I:CYS99 3.4 43.9 1.0
HB3 I:ASN71 3.5 51.3 1.0
CB I:CYS72 3.5 71.8 1.0
HB3 I:CYS99 3.7 38.2 1.0
N I:CYS95 3.8 33.0 1.0
HB3 I:CYS74 3.8 40.3 1.0
N I:CYS72 3.9 65.4 1.0
HD21 I:ASN71 4.0 39.5 1.0
HB3 I:CYS95 4.1 33.8 1.0
H I:CYS74 4.1 36.1 1.0
HB2 I:CYS74 4.2 40.3 1.0
CA I:CYS95 4.2 36.1 1.0
CA I:CYS72 4.3 70.4 1.0
HB2 I:CYS72 4.3 58.4 1.0
HD2 I:PRO98 4.3 48.0 1.0
HA I:LEU94 4.4 40.7 1.0
H I:ASN71 4.4 37.6 1.0
H I:CYS99 4.4 42.8 1.0
CB I:ASN71 4.4 53.1 1.0
CB I:CYS74 4.5 44.7 1.0
CA I:CYS69 4.6 54.7 1.0
H I:GLY73 4.6 45.9 1.0
HA I:CYS95 4.7 31.8 1.0
HD23 I:LEU94 4.7 30.5 1.0
CA I:CYS99 4.8 55.3 1.0
ND2 I:ASN71 4.8 43.6 1.0
C I:ASN71 4.9 61.1 1.0
HA I:CYS69 4.9 51.4 1.0
HB2 I:ASN71 4.9 51.3 1.0
C I:LEU94 4.9 41.7 1.0
C I:CYS72 4.9 55.9 1.0
N I:CYS74 4.9 41.0 1.0
N I:GLY73 5.0 48.6 1.0
N I:ASN71 5.0 41.5 1.0
N I:CYS99 5.0 48.1 1.0

Zinc binding site 10 out of 13 in 8rxb

Go back to Zinc Binding Sites List in 8rxb
Zinc binding site 10 out of 13 in the Human UPF1 Ch Domain in Complex with SMG6 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human UPF1 Ch Domain in Complex with SMG6 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn201

b:62.3
occ:1.00
HD1 L:HIS41 1.2 43.4 1.0
ND1 L:HIS41 2.0 45.5 1.0
SG L:CYS31 2.3 59.7 1.0
SG L:CYS9 2.3 46.5 1.0
SG L:CYS12 2.3 55.2 1.0
HG L:CYS12 2.6 56.1 1.0
CE1 L:HIS41 2.8 61.4 1.0
HE1 L:HIS41 2.9 62.5 1.0
HG L:CYS31 2.9 51.9 1.0
HB3 L:CYS9 3.0 40.0 1.0
CB L:CYS9 3.1 43.5 1.0
HB2 L:CYS9 3.1 40.0 1.0
CG L:HIS41 3.1 54.0 1.0
HG L:CYS9 3.1 43.9 1.0
HB3 L:CYS31 3.2 46.0 1.0
HB2 L:HIS41 3.3 48.5 1.0
H L:CYS31 3.3 46.6 1.0
H L:CYS12 3.3 61.2 1.0
CB L:CYS31 3.4 55.1 1.0
HB2 L:TYR11 3.5 59.1 1.0
HD11 L:ILE14 3.5 58.8 1.0
HB3 L:CYS12 3.5 55.4 1.0
CB L:CYS12 3.6 54.4 1.0
CB L:HIS41 3.6 49.7 1.0
HB3 L:HIS41 3.7 48.5 1.0
HB L:ILE14 3.8 53.8 1.0
N L:CYS12 3.9 59.0 1.0
NE2 L:HIS41 4.0 49.8 1.0
N L:CYS31 4.1 55.3 1.0
HB2 L:CYS31 4.1 46.0 1.0
CD2 L:HIS41 4.2 49.9 1.0
H L:ILE14 4.2 58.4 1.0
CA L:CYS12 4.3 59.7 1.0
CA L:CYS31 4.3 56.0 1.0
HB2 L:CYS12 4.3 55.4 1.0
CB L:TYR11 4.4 59.9 1.0
H L:GLY13 4.4 69.6 1.0
CD1 L:ILE14 4.4 61.4 1.0
H L:TYR11 4.4 49.2 1.0
CA L:CYS9 4.5 55.3 1.0
HB3 L:TYR11 4.6 59.1 1.0
HG13 L:ILE14 4.6 51.3 1.0
HD2 L:TYR11 4.6 65.8 1.0
CB L:ILE14 4.7 57.4 1.0
H L:GLY33 4.7 40.7 1.0
N L:GLY13 4.8 63.0 1.0
C L:CYS12 4.8 62.4 1.0
HD12 L:ILE14 4.8 58.8 1.0
CG1 L:ILE14 4.8 55.2 1.0
C L:CYS31 4.8 46.0 1.0
HA L:CYS9 4.9 54.0 1.0
C L:TYR11 4.9 59.6 1.0
O L:CYS31 4.9 47.7 1.0
HA L:PHE30 4.9 40.2 1.0
N L:ILE14 5.0 61.0 1.0
O L:GLY33 5.0 48.2 1.0
HD13 L:ILE14 5.0 58.8 1.0

Reference:

L.M.Langer, K.Kurscheidt, J.Basquin, F.Bonneau, I.Iermak, C.Basquin, E.Conti. UPF1 Helicase Orchestrates Mutually Exclusive Interactions with the SMG6 Endonuclease and UPF2. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38709891
DOI: 10.1093/NAR/GKAE323
Page generated: Thu Oct 31 10:46:36 2024

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