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Zinc in PDB 2lli: Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex

Zinc Binding Sites:

The binding sites of Zinc atom in the Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex (pdb code 2lli). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex, PDB code: 2lli:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2lli

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Zinc binding site 1 out of 5 in the Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:0.0
occ:1.00
NE2 A:HIS116 2.5 0.0 1.0
SG A:CYS111 2.6 0.0 1.0
SG A:CYS121 2.7 0.0 1.0
HG A:CYS111 2.8 0.0 1.0
SG A:CYS108 2.8 0.0 1.0
HG A:CYS108 3.1 0.0 1.0
CE1 A:HIS116 3.2 0.0 1.0
HE1 A:HIS116 3.3 0.0 1.0
CD2 A:HIS116 3.6 0.0 1.0
HB3 A:TYR107 3.7 0.0 1.0
HB2 A:ASN110 3.8 0.0 1.0
HG A:CYS121 3.8 0.0 1.0
HA A:TYR107 3.8 0.0 1.0
HB3 A:CYS121 3.8 0.0 1.0
HD2 A:HIS116 3.9 0.0 1.0
HD1 A:TYR107 3.9 0.0 1.0
CB A:CYS121 4.0 0.0 1.0
O A:TYR107 4.0 0.0 1.0
C A:TYR107 4.1 0.0 1.0
O A:CYS121 4.2 0.0 1.0
CB A:CYS108 4.3 0.0 1.0
ND1 A:HIS116 4.3 0.0 1.0
CA A:TYR107 4.4 0.0 1.0
HB3 A:CYS108 4.4 0.0 1.0
H A:CYS111 4.4 0.0 1.0
CB A:CYS111 4.5 0.0 1.0
CB A:TYR107 4.5 0.0 1.0
CG A:HIS116 4.5 0.0 1.0
N A:CYS108 4.6 0.0 1.0
HB2 A:CYS121 4.6 0.0 1.0
HD21 A:ASN110 4.8 0.0 1.0
O A:HIS116 4.8 0.0 1.0
CB A:ASN110 4.8 0.0 1.0
N A:CYS111 4.9 0.0 1.0
H A:ASN110 4.9 0.0 1.0
HB3 A:CYS111 4.9 0.0 1.0
CD1 A:TYR107 4.9 0.0 1.0
HB2 A:CYS111 5.0 0.0 1.0
C A:CYS121 5.0 0.0 1.0

Zinc binding site 2 out of 5 in 2lli

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Zinc binding site 2 out of 5 in the Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:0.0
occ:1.00
NE2 A:HIS75 2.5 0.0 1.0
SG A:CYS80 2.6 0.0 1.0
SG A:CYS70 2.8 0.0 1.0
SG A:CYS67 2.9 0.0 1.0
HB2 A:CYS67 2.9 0.0 1.0
CB A:CYS67 3.2 0.0 1.0
HG A:CYS80 3.3 0.0 1.0
HB3 A:CYS67 3.3 0.0 1.0
HG A:CYS70 3.3 0.0 1.0
CE1 A:HIS75 3.4 0.0 1.0
CB A:CYS80 3.4 0.0 1.0
HB3 A:CYS80 3.4 0.0 1.0
HB2 A:CYS80 3.4 0.0 1.0
CD2 A:HIS75 3.5 0.0 1.0
HE1 A:HIS75 3.5 0.0 1.0
HB2 A:CYS70 3.6 0.0 1.0
HD2 A:HIS75 3.7 0.0 1.0
CB A:CYS70 3.8 0.0 1.0
HG A:CYS67 3.9 0.0 1.0
HB3 A:CYS70 4.0 0.0 1.0
ND1 A:HIS75 4.5 0.0 1.0
HB2 A:SER82 4.5 0.0 1.0
CG A:HIS75 4.6 0.0 1.0
HG11 A:VAL65 4.6 0.0 1.0
CA A:CYS67 4.7 0.0 1.0
H A:CYS67 4.8 0.0 1.0
HG12 A:VAL65 4.8 0.0 1.0
CA A:CYS80 4.9 0.0 1.0
H A:CYS70 5.0 0.0 1.0

Zinc binding site 3 out of 5 in 2lli

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Zinc binding site 3 out of 5 in the Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:0.0
occ:1.00
NE2 A:HIS53 2.5 0.0 1.0
SG A:CYS48 2.6 0.0 1.0
SG A:CYS45 2.7 0.0 1.0
HG A:CYS48 2.8 0.0 1.0
SG A:CYS58 2.8 0.0 1.0
HG A:CYS45 3.0 0.0 1.0
HB3 A:CYS58 3.1 0.0 1.0
HG A:CYS58 3.3 0.0 1.0
CB A:CYS58 3.3 0.0 1.0
CE1 A:HIS53 3.4 0.0 1.0
CD2 A:HIS53 3.5 0.0 1.0
HB2 A:CYS58 3.5 0.0 1.0
HE1 A:HIS53 3.6 0.0 1.0
HD2 A:HIS53 3.7 0.0 1.0
HB2 A:CYS48 3.9 0.0 1.0
CB A:CYS48 3.9 0.0 1.0
O A:GLU50 4.1 0.0 1.0
HB3 A:SER46 4.2 0.0 1.0
O A:CYS48 4.3 0.0 1.0
CB A:CYS45 4.4 0.0 1.0
C A:CYS48 4.5 0.0 1.0
ND1 A:HIS53 4.5 0.0 1.0
O A:ASP49 4.6 0.0 1.0
CG A:HIS53 4.6 0.0 1.0
H A:CYS48 4.7 0.0 1.0
H A:SER46 4.7 0.0 1.0
CA A:CYS48 4.7 0.0 1.0
HB2 A:CYS45 4.7 0.0 1.0
HB3 A:CYS48 4.7 0.0 1.0
H A:CYS45 4.8 0.0 1.0
CA A:CYS58 4.8 0.0 1.0
HB3 A:CYS45 4.8 0.0 1.0
O A:CYS58 4.9 0.0 1.0

Zinc binding site 4 out of 5 in 2lli

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Zinc binding site 4 out of 5 in the Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:0.0
occ:1.00
NE2 A:HIS34 2.5 0.0 1.0
SG A:CYS39 2.6 0.0 1.0
SG A:CYS25 2.8 0.0 1.0
HB2 A:CYS25 2.9 0.0 1.0
SG A:CYS28 2.9 0.0 1.0
HB3 A:CYS28 3.0 0.0 1.0
HB2 A:CYS28 3.1 0.0 1.0
CB A:CYS28 3.2 0.0 1.0
HG A:CYS39 3.3 0.0 1.0
CE1 A:HIS34 3.3 0.0 1.0
CB A:CYS25 3.4 0.0 1.0
HE1 A:HIS34 3.4 0.0 1.0
HG A:CYS28 3.5 0.0 1.0
CD2 A:HIS34 3.6 0.0 1.0
HA A:CYS39 3.8 0.0 1.0
HB3 A:CYS25 3.9 0.0 1.0
HD2 A:HIS34 4.0 0.0 1.0
H A:CYS25 4.0 0.0 1.0
HG A:CYS25 4.1 0.0 1.0
CB A:CYS39 4.1 0.0 1.0
HB2 A:CYS39 4.3 0.0 1.0
CA A:CYS39 4.4 0.0 1.0
O A:CYS39 4.5 0.0 1.0
ND1 A:HIS34 4.5 0.0 1.0
CA A:CYS25 4.6 0.0 1.0
N A:CYS25 4.7 0.0 1.0
CG A:HIS34 4.7 0.0 1.0
CA A:CYS28 4.7 0.0 1.0
C A:CYS39 4.8 0.0 1.0
HB3 A:CYS39 4.9 0.0 1.0

Zinc binding site 5 out of 5 in 2lli

Go back to Zinc Binding Sites List in 2lli
Zinc binding site 5 out of 5 in the Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Low Resolution Structure of Rna-Binding Subunit of the Tramp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:0.0
occ:1.00
NE2 A:HIS15 2.5 0.0 1.0
SG A:CYS20 2.6 0.0 1.0
HG A:CYS10 2.7 0.0 1.0
SG A:CYS10 2.8 0.0 1.0
HB2 A:CYS10 2.8 0.0 1.0
SG A:CYS7 2.9 0.0 1.0
HG A:CYS7 3.0 0.0 1.0
CE1 A:HIS15 3.2 0.0 1.0
CD2 A:HIS15 3.2 0.0 1.0
CB A:CYS10 3.3 0.0 1.0
H A:CYS10 3.4 0.0 1.0
HE1 A:HIS15 3.5 0.0 1.0
HD2 A:HIS15 3.5 0.0 1.0
HG A:CYS20 3.6 0.0 1.0
ND1 A:HIS15 4.0 0.0 1.0
CG A:HIS15 4.0 0.0 1.0
HB2 A:CYS20 4.0 0.0 1.0
CB A:CYS20 4.0 0.0 1.0
HB3 A:CYS10 4.1 0.0 1.0
OD1 A:ASN8 4.1 0.0 1.0
HB2 A:ARG13 4.2 0.0 1.0
H A:ASN9 4.3 0.0 1.0
N A:CYS10 4.3 0.0 1.0
H A:ASN8 4.3 0.0 1.0
HD3 A:ARG13 4.3 0.0 1.0
CA A:CYS10 4.4 0.0 1.0
HA A:CYS20 4.5 0.0 1.0
O A:HIS15 4.5 0.0 1.0
CB A:CYS7 4.7 0.0 1.0
HD1 A:HIS15 4.7 0.0 1.0
HB3 A:CYS20 4.8 0.0 1.0
CA A:CYS20 4.9 0.0 1.0

Reference:

P.Holub, J.Lalakova, H.Cerna, J.Pasulka, M.Sarazova, K.Hrazdilova, M.S.Arce, F.Hobor, R.Stefl, S.Vanacova. AIR2P Is Critical For the Assembly and Rna-Binding of the Tramp Complex and the Kow Domain of MTR4P Is Crucial For Exosome Activation. Nucleic Acids Res. V. 40 5679 2012.
ISSN: ISSN 0305-1048
PubMed: 22402490
DOI: 10.1093/NAR/GKS223
Page generated: Wed Dec 16 03:37:53 2020

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