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Zinc in PDB 5v1u: TBIB1 in Complex with the Tbia(Beta) Leader Peptide

Protein crystallography data

The structure of TBIB1 in Complex with the Tbia(Beta) Leader Peptide, PDB code: 5v1u was solved by J.R.Chekan, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.26 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.155, 48.630, 55.287, 78.30, 66.88, 88.12
R / Rfree (%) 20.1 / 24

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide (pdb code 5v1u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide, PDB code: 5v1u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 5v1u

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Zinc binding site 1 out of 11 in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of TBIB1 in Complex with the Tbia(Beta) Leader Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:36.2
occ:1.00
NE2 A:HIS11 1.9 36.9 1.0
OE1 A:GLU41 2.1 32.3 1.0
CE1 A:HIS11 2.5 31.4 1.0
CD A:GLU41 2.7 30.9 1.0
OE2 A:GLU41 2.8 31.4 1.0
CD2 A:HIS11 3.0 31.0 1.0
ND1 A:HIS11 3.6 28.4 1.0
O A:HOH236 3.9 31.2 1.0
CG A:HIS11 3.9 33.5 1.0
CG A:GLU41 4.1 24.9 1.0
CB A:GLU41 4.5 21.3 1.0
CB A:SER9 4.8 18.8 1.0
OG A:SER38 4.9 31.7 1.0

Zinc binding site 2 out of 11 in 5v1u

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Zinc binding site 2 out of 11 in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of TBIB1 in Complex with the Tbia(Beta) Leader Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:72.4
occ:1.00
OE2 A:GLU82 2.2 56.9 1.0
OD2 A:ASP5 2.5 60.3 1.0
OE1 A:GLU82 2.8 66.7 1.0
CD A:GLU82 2.8 65.9 1.0
CG A:ASP5 3.4 49.1 1.0
N A:ASP5 3.4 29.5 1.0
CB A:ASP5 3.6 34.0 1.0
CA A:ASP5 4.1 29.3 1.0
CG A:GLU82 4.3 52.9 1.0
OG A:SER4 4.4 33.2 1.0
CE A:LYS2 4.4 56.5 1.0
C A:SER4 4.4 28.4 1.0
CA A:SER4 4.5 31.5 1.0
NZ A:LYS2 4.5 61.6 1.0
OD1 A:ASP5 4.6 49.7 1.0
CB A:SER4 5.0 29.0 1.0

Zinc binding site 3 out of 11 in 5v1u

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Zinc binding site 3 out of 11 in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of TBIB1 in Complex with the Tbia(Beta) Leader Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:47.8
occ:1.00
OE2 C:GLU82 2.1 46.7 1.0
OE2 B:GLU82 2.1 38.3 1.0
OD2 C:ASP5 2.2 39.3 1.0
OD2 B:ASP5 2.5 56.3 1.0
OE1 B:GLU82 2.6 48.5 1.0
OE1 C:GLU82 2.7 58.0 1.0
CD B:GLU82 2.7 43.8 1.0
CD C:GLU82 2.7 46.6 1.0
CG C:ASP5 3.2 46.2 1.0
CG B:ASP5 3.4 54.3 1.0
CB C:ASP5 3.5 32.5 1.0
N C:ASP5 3.6 27.9 1.0
CB B:ASP5 3.7 39.0 1.0
N B:ASP5 3.8 20.2 1.0
CG B:GLU82 4.2 38.7 1.0
CG C:GLU82 4.2 37.9 1.0
CA C:ASP5 4.2 30.5 1.0
CE C:LYS2 4.2 47.0 1.0
CE B:LYS2 4.3 40.5 1.0
NZ C:LYS2 4.3 57.0 1.0
NZ B:LYS2 4.3 44.5 1.0
OD1 C:ASP5 4.3 56.6 1.0
CA B:ASP5 4.4 24.9 1.0
OD1 B:ASP5 4.6 64.5 1.0
C C:SER4 4.7 21.7 1.0
CA C:SER4 4.8 24.8 1.0
OG C:SER4 4.8 43.8 1.0
OG B:SER4 4.8 31.8 1.0
C B:SER4 4.8 22.9 1.0
CA B:SER4 4.9 29.8 1.0

Zinc binding site 4 out of 11 in 5v1u

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Zinc binding site 4 out of 11 in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of TBIB1 in Complex with the Tbia(Beta) Leader Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:40.5
occ:1.00
OE2 B:GLU79 1.9 36.0 1.0
OD1 D:ASP67 2.1 26.5 1.0
O B:HOH241 2.2 28.7 1.0
O D:HOH201 2.4 35.2 1.0
O D:HOH211 2.5 24.2 1.0
CD B:GLU79 2.8 38.8 1.0
OE1 B:GLU79 3.0 33.5 1.0
CG D:ASP67 3.2 22.4 1.0
OD2 D:ASP67 3.7 20.8 1.0
O D:HOH234 3.9 30.2 1.0
CG B:GLU79 4.2 31.4 1.0
NE D:ARG66 4.3 46.4 1.0
O B:ASN77 4.4 25.6 1.0
CB H:ALA-15 4.4 25.7 1.0
OD2 D:ASP70 4.4 43.5 1.0
CB D:ASP67 4.5 17.4 1.0
O B:ALA76 4.5 25.2 1.0
NH2 D:ARG66 4.6 45.7 1.0
CA D:ASP67 4.6 16.4 1.0
N D:ASP67 4.9 18.5 1.0
CZ D:ARG66 4.9 42.9 1.0
C B:ASN77 5.0 21.7 1.0

Zinc binding site 5 out of 11 in 5v1u

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Zinc binding site 5 out of 11 in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of TBIB1 in Complex with the Tbia(Beta) Leader Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn103

b:33.6
occ:1.00
NE2 B:HIS11 1.9 32.2 1.0
OE1 B:GLU41 2.3 36.5 1.0
OE2 B:GLU41 2.5 35.0 1.0
CD B:GLU41 2.6 32.6 1.0
CD2 B:HIS11 2.8 24.5 1.0
CE1 B:HIS11 3.0 32.5 1.0
O B:HOH240 3.1 38.3 1.0
CG B:HIS11 3.9 31.4 1.0
ND1 B:HIS11 4.0 30.2 1.0
CG B:GLU41 4.1 24.4 1.0
O B:HOH243 4.4 33.6 1.0
OD1 A:ASN77 4.5 44.4 1.0
CB B:GLU41 4.6 25.4 1.0
CB B:SER9 4.6 18.9 1.0
ND2 A:ASN77 4.8 38.5 1.0

Zinc binding site 6 out of 11 in 5v1u

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Zinc binding site 6 out of 11 in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of TBIB1 in Complex with the Tbia(Beta) Leader Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn104

b:28.3
occ:1.00
OD2 B:ASP51 1.9 24.5 1.0
OE2 B:GLU47 2.0 21.4 1.0
OE1 B:GLU47 2.5 27.5 1.0
CD B:GLU47 2.6 25.9 1.0
CG B:ASP51 2.9 24.3 1.0
OD1 B:ASP51 3.2 22.6 1.0
CG B:GLU47 4.1 24.1 1.0
O B:GLU47 4.1 21.6 1.0
CB B:ASP51 4.3 19.0 1.0
O B:HOH211 4.4 39.4 1.0
C B:GLU47 4.6 22.9 1.0
NH2 B:ARG61 4.7 22.1 1.0
CA B:GLU48 4.8 21.6 1.0
N B:GLU48 4.9 13.5 1.0
CB B:GLU47 5.0 26.6 1.0

Zinc binding site 7 out of 11 in 5v1u

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Zinc binding site 7 out of 11 in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of TBIB1 in Complex with the Tbia(Beta) Leader Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn105

b:36.8
occ:1.00
OE2 B:GLU65 2.2 35.3 1.0
OE1 B:GLU65 2.7 47.8 1.0
CD B:GLU65 2.7 35.1 1.0
O B:HOH235 3.5 38.1 1.0
CG B:GLU65 4.2 20.5 1.0
NE B:ARG61 4.3 23.0 1.0
CD B:ARG61 4.7 15.7 1.0

Zinc binding site 8 out of 11 in 5v1u

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Zinc binding site 8 out of 11 in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of TBIB1 in Complex with the Tbia(Beta) Leader Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:38.6
occ:1.00
OE1 C:GLU41 2.0 31.8 1.0
NE2 C:HIS11 2.1 36.4 1.0
O C:HOH232 2.1 34.4 1.0
CD C:GLU41 2.9 25.5 1.0
CE1 C:HIS11 2.9 28.7 1.0
OE2 C:GLU41 3.1 32.0 1.0
CD2 C:HIS11 3.2 27.4 1.0
O C:HOH205 3.7 48.5 1.0
OG C:SER38 4.0 42.7 1.0
ND1 C:HIS11 4.1 28.9 1.0
CG C:HIS11 4.2 40.7 1.0
CG C:GLU41 4.3 22.8 1.0
CA C:SER38 4.3 24.8 1.0
CB C:SER38 4.6 23.1 1.0
CD1 C:TRP37 4.6 18.1 1.0
CG2 C:VAL16 4.7 30.6 1.0
CB C:GLU41 4.8 27.4 1.0
N C:SER38 4.9 18.1 1.0

Zinc binding site 9 out of 11 in 5v1u

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Zinc binding site 9 out of 11 in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of TBIB1 in Complex with the Tbia(Beta) Leader Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:40.6
occ:1.00
OE2 C:GLU47 2.1 34.0 1.0
OD2 C:ASP51 2.1 36.0 1.0
OE1 C:GLU47 2.4 39.9 1.0
CD C:GLU47 2.5 30.9 1.0
CG C:ASP51 3.2 26.2 1.0
OD1 C:ASP51 3.7 35.9 1.0
O C:HOH231 3.9 35.9 1.0
CG C:GLU47 4.0 29.6 1.0
O C:GLU47 4.2 25.7 1.0
CB C:ASP51 4.5 21.8 1.0
C C:GLU47 4.6 32.8 1.0
CA C:GLU48 4.8 25.4 1.0
NH2 C:ARG61 4.8 30.0 1.0
N C:GLU48 4.9 25.2 1.0
CB C:GLU47 4.9 29.9 1.0

Zinc binding site 10 out of 11 in 5v1u

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Zinc binding site 10 out of 11 in the TBIB1 in Complex with the Tbia(Beta) Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of TBIB1 in Complex with the Tbia(Beta) Leader Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn103

b:52.4
occ:1.00
OE2 C:GLU65 2.6 49.3 1.0
OE1 C:GLU65 3.0 60.5 1.0
CD C:GLU65 3.0 51.0 1.0
CG C:GLU65 4.4 39.8 1.0
NE C:ARG61 4.9 32.4 1.0

Reference:

J.R.Chekan, C.Ongpipattanakul, S.K.Nair. Steric Complementarity Directs Sequence Promiscuous Leader Binding in Ripp Biosynthesis Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1908364116
Page generated: Wed Dec 16 11:07:33 2020

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