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Zinc in PDB 1q2s: Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate

Enzymatic activity of Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate

All present enzymatic activity of Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate:
2.4.2.29;

Protein crystallography data

The structure of Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate, PDB code: 1q2s was solved by W.Xie, X.Liu, R.H.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.20
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 261.961, 261.961, 55.549, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate (pdb code 1q2s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate, PDB code: 1q2s:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1q2s

Go back to Zinc Binding Sites List in 1q2s
Zinc binding site 1 out of 4 in the Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:22.7
occ:1.00
 SG A:CYS323 2.1 27.9 1.0
ND1 A:HIS349 2.2 15.0 1.0
SG A:CYS318 2.2 25.4 1.0
SG A:CYS320 2.4 34.5 1.0
CB A:CYS320 2.8 36.5 1.0
CE1 A:HIS349 2.9 14.2 1.0
CB A:CYS323 3.3 31.1 1.0
CG A:HIS349 3.3 15.7 1.0
CB A:CYS318 3.3 35.9 1.0
CB A:HIS349 3.8 16.7 1.0
CA A:CYS320 4.0 38.0 1.0
N A:CYS323 4.0 33.4 1.0
CA A:HIS349 4.0 17.4 1.0
N A:CYS320 4.1 38.5 1.0
NE2 A:HIS349 4.1 14.7 1.0
CA A:CYS323 4.2 32.5 1.0
CD2 A:HIS349 4.3 14.9 1.0
O A:HIS349 4.4 16.4 1.0
C A:CYS320 4.5 38.6 1.0
O A:CYS320 4.6 38.7 1.0
C A:HIS349 4.6 17.6 1.0
CA A:CYS318 4.7 38.5 1.0
CB A:VAL322 4.8 33.4 1.0
C A:CYS318 4.9 39.0 1.0
CD1 A:LEU314 4.9 31.1 1.0

Zinc binding site 2 out of 4 in 1q2s

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Zinc binding site 2 out of 4 in the Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:16.2
occ:1.00
 ND1 B:HIS349 2.0 18.8 1.0
SG B:CYS323 2.2 20.8 1.0
SG B:CYS318 2.3 35.8 1.0
SG B:CYS320 2.3 17.2 1.0
CE1 B:HIS349 2.7 17.8 1.0
CB B:CYS320 3.0 25.3 1.0
CG B:HIS349 3.2 17.6 1.0
CB B:CYS323 3.3 23.6 1.0
CB B:CYS318 3.4 38.6 1.0
N B:CYS320 3.8 32.5 1.0
CB B:HIS349 3.8 17.2 1.0
N B:CYS323 3.9 25.3 1.0
CA B:CYS320 3.9 28.5 1.0
NE2 B:HIS349 3.9 17.1 1.0
CD2 B:HIS349 4.2 17.2 1.0
CA B:CYS323 4.2 25.7 1.0
CA B:HIS349 4.2 16.9 1.0
O B:CYS320 4.5 28.6 1.0
C B:CYS320 4.5 28.6 1.0
C B:CYS318 4.6 39.4 1.0
CA B:CYS318 4.6 39.6 1.0
CB B:VAL322 4.7 22.9 1.0
O B:HIS349 4.8 15.6 1.0
O B:CYS318 4.8 39.1 1.0
N B:HIS319 4.9 39.4 1.0
CB B:LEU314 4.9 28.9 1.0
C B:HIS349 4.9 16.6 1.0
C B:HIS319 5.0 36.2 1.0

Zinc binding site 3 out of 4 in 1q2s

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Zinc binding site 3 out of 4 in the Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:19.9
occ:1.00
 ND1 C:HIS349 1.9 7.2 1.0
SG C:CYS323 2.1 11.2 1.0
SG C:CYS320 2.2 12.4 1.0
SG C:CYS318 2.2 20.7 1.0
CE1 C:HIS349 2.8 5.7 1.0
CG C:HIS349 3.1 8.6 1.0
CB C:CYS318 3.2 28.9 1.0
CB C:CYS320 3.3 18.6 1.0
CB C:CYS323 3.5 16.4 1.0
CB C:HIS349 3.5 10.1 1.0
CA C:HIS349 3.9 12.3 1.0
NE2 C:HIS349 4.0 5.9 1.0
CD2 C:HIS349 4.1 6.3 1.0
N C:CYS323 4.2 17.7 1.0
N C:CYS320 4.2 25.7 1.0
CA C:CYS320 4.3 21.2 1.0
O C:HIS349 4.4 13.3 1.0
CA C:CYS323 4.5 17.9 1.0
O C:CYS320 4.5 20.8 1.0
C C:HIS349 4.5 13.0 1.0
CA C:CYS318 4.6 32.5 1.0
C C:CYS320 4.7 20.9 1.0
CD1 C:LEU314 4.9 26.5 1.0
CB C:VAL322 4.9 16.3 1.0
NE2 C:GLN356 4.9 24.4 1.0
C C:CYS318 4.9 33.0 1.0
CB C:LEU314 5.0 24.6 1.0
N C:HIS319 5.0 32.7 1.0

Zinc binding site 4 out of 4 in 1q2s

Go back to Zinc Binding Sites List in 1q2s
Zinc binding site 4 out of 4 in the Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn404

b:24.8
occ:1.00
 ND1 D:HIS349 1.8 17.4 1.0
SG D:CYS320 2.2 14.0 1.0
SG D:CYS323 2.3 5.5 1.0
SG D:CYS318 2.3 23.8 1.0
CE1 D:HIS349 2.5 17.0 1.0
CB D:CYS320 3.0 20.0 1.0
CG D:HIS349 3.1 17.4 1.0
CB D:CYS323 3.4 13.1 1.0
CB D:CYS318 3.4 31.0 1.0
NE2 D:HIS349 3.7 17.6 1.0
CB D:HIS349 3.7 17.5 1.0
N D:CYS323 3.9 16.1 1.0
CD2 D:HIS349 4.0 16.9 1.0
CA D:HIS349 4.0 16.2 1.0
CA D:CYS320 4.1 21.4 1.0
N D:CYS320 4.2 26.3 1.0
CA D:CYS323 4.3 16.8 1.0
O D:HIS349 4.5 15.5 1.0
C D:CYS320 4.6 20.3 1.0
C D:HIS349 4.7 15.8 1.0
O D:CYS320 4.7 19.3 1.0
CA D:CYS318 4.7 32.3 1.0
CB D:VAL322 4.8 16.2 1.0
C D:CYS318 4.9 32.1 1.0
CB D:LEU314 4.9 27.2 1.0
NE2 D:GLN356 4.9 33.0 1.0

Reference:

W.Xie, X.Liu, R.H.Huang. Chemical Trapping and Crystal Structure of A Catalytic Trna Guanine Transglycosylase Covalent Intermediate Nat.Struct.Biol. V. 10 781 2003.
ISSN: ISSN 1072-8368
PubMed: 12949492
DOI: 10.1038/NSB976
Page generated: Wed Dec 16 03:01:32 2020

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