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Zinc in PDB 1q2r: 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: 1q2r 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 / 2.90
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 264.856, 264.856, 55.911, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23

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 1q2r). 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: 1q2r:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1q2r

Go back to Zinc Binding Sites List in 1q2r
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:19.7
occ:1.00
 ND1 A:HIS349 2.1 11.7 1.0
SG A:CYS318 2.2 19.5 1.0
SG A:CYS323 2.3 18.4 1.0
SG A:CYS320 2.4 22.3 1.0
CE1 A:HIS349 2.8 10.8 1.0
CB A:CYS320 2.9 21.8 1.0
CG A:HIS349 3.2 11.2 1.0
CB A:CYS318 3.3 23.6 1.0
CB A:CYS323 3.3 21.2 1.0
CB A:HIS349 3.7 10.8 1.0
N A:CYS323 4.0 21.7 1.0
NE2 A:HIS349 4.0 11.1 1.0
CA A:CYS320 4.1 22.2 1.0
CA A:HIS349 4.1 13.1 1.0
CD2 A:HIS349 4.2 11.1 1.0
N A:CYS320 4.2 24.0 1.0
CA A:CYS323 4.3 22.3 1.0
C A:CYS320 4.6 21.9 1.0
O A:HIS349 4.6 16.2 1.0
O A:CYS320 4.6 21.7 1.0
CA A:CYS318 4.6 24.9 1.0
C A:HIS349 4.8 14.1 1.0
C A:CYS318 4.8 24.7 1.0
O A:CYS318 4.8 23.8 1.0
CB A:VAL322 4.8 19.2 1.0
NE2 A:GLN356 4.9 22.2 1.0

Zinc binding site 2 out of 4 in 1q2r

Go back to Zinc Binding Sites List in 1q2r
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:22.6
occ:1.00
 SG B:CYS318 2.1 26.4 1.0
ND1 B:HIS349 2.1 18.6 1.0
SG B:CYS320 2.2 24.1 1.0
SG B:CYS323 2.2 21.9 1.0
CE1 B:HIS349 2.8 20.3 1.0
CB B:CYS318 3.2 28.0 1.0
CB B:CYS320 3.2 26.8 1.0
CB B:CYS323 3.3 22.5 1.0
CG B:HIS349 3.3 18.6 1.0
CB B:HIS349 3.9 18.9 1.0
N B:CYS323 3.9 23.3 1.0
NE2 B:HIS349 4.0 19.5 1.0
N B:CYS320 4.2 31.3 1.0
CA B:HIS349 4.2 18.4 1.0
CA B:CYS320 4.2 28.6 1.0
CA B:CYS323 4.2 23.9 1.0
CD2 B:HIS349 4.3 18.3 1.0
CA B:CYS318 4.5 29.6 1.0
O B:CYS320 4.6 28.1 1.0
C B:CYS318 4.7 31.2 1.0
CB B:VAL322 4.7 21.4 1.0
C B:CYS320 4.7 27.8 1.0
O B:HIS349 4.8 18.3 1.0
C B:HIS349 4.8 18.5 1.0
CB B:LEU314 4.9 17.5 1.0
O B:CYS318 4.9 30.4 1.0
C B:VAL322 5.0 22.5 1.0

Zinc binding site 3 out of 4 in 1q2r

Go back to Zinc Binding Sites List in 1q2r
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:25.9
occ:1.00
 SG C:CYS323 2.0 18.1 1.0
ND1 C:HIS349 2.1 13.6 1.0
SG C:CYS320 2.2 24.0 1.0
SG C:CYS318 2.3 31.2 1.0
CE1 C:HIS349 2.9 14.7 1.0
CB C:CYS323 3.2 21.4 1.0
CG C:HIS349 3.3 13.4 1.0
CB C:CYS320 3.4 27.0 1.0
CB C:CYS318 3.5 32.4 1.0
CB C:HIS349 3.7 11.4 1.0
CA C:HIS349 3.9 12.9 1.0
N C:CYS323 4.0 22.4 1.0
N C:CYS320 4.1 30.6 1.0
NE2 C:HIS349 4.1 14.2 1.0
CA C:CYS323 4.2 22.9 1.0
CD2 C:HIS349 4.3 13.7 1.0
CA C:CYS320 4.3 26.5 1.0
O C:HIS349 4.4 16.5 1.0
C C:HIS349 4.6 14.5 1.0
NE2 C:GLN356 4.7 20.3 1.0
CA C:CYS318 4.7 33.6 1.0
C C:CYS318 4.8 33.6 1.0
C C:CYS320 4.9 25.0 1.0
CB C:VAL322 5.0 19.6 1.0
N C:HIS319 5.0 33.9 1.0
O C:CYS320 5.0 24.2 1.0

Zinc binding site 4 out of 4 in 1q2r

Go back to Zinc Binding Sites List in 1q2r
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:19.9
occ:1.00
 SG D:CYS318 2.1 32.0 1.0
ND1 D:HIS349 2.1 16.9 1.0
SG D:CYS320 2.1 23.6 1.0
SG D:CYS323 2.3 22.1 1.0
CE1 D:HIS349 2.8 17.2 1.0
CB D:CYS318 3.2 31.6 1.0
CG D:HIS349 3.3 17.0 1.0
CB D:CYS323 3.3 24.6 1.0
CB D:CYS320 3.4 26.5 1.0
CB D:HIS349 3.8 17.2 1.0
NE2 D:HIS349 4.0 17.3 1.0
N D:CYS323 4.1 23.0 1.0
N D:CYS320 4.1 30.0 1.0
CA D:HIS349 4.1 16.6 1.0
CD2 D:HIS349 4.3 16.9 1.0
CA D:CYS320 4.3 26.5 1.0
CA D:CYS323 4.3 24.6 1.0
O D:HIS349 4.4 17.5 1.0
CA D:CYS318 4.5 32.0 1.0
C D:CYS318 4.6 32.7 1.0
C D:HIS349 4.7 16.8 1.0
O D:CYS320 4.8 24.2 1.0
CB D:VAL322 4.8 22.2 1.0
C D:CYS320 4.9 24.6 1.0
N D:HIS319 4.9 33.3 1.0
CB D:LEU314 4.9 20.1 1.0
O D:CYS318 4.9 33.3 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: Mon Jan 25 16:11:54 2021

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