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Zinc in PDB 1vq2: Crystal Structure of T4-Bacteriophage Deoxycytidylate Deaminase, Mutant R115E

Enzymatic activity of Crystal Structure of T4-Bacteriophage Deoxycytidylate Deaminase, Mutant R115E

All present enzymatic activity of Crystal Structure of T4-Bacteriophage Deoxycytidylate Deaminase, Mutant R115E:
3.5.4.12;

Protein crystallography data

The structure of Crystal Structure of T4-Bacteriophage Deoxycytidylate Deaminase, Mutant R115E, PDB code: 1vq2 was solved by R.Almog, F.Maley, G.F.Maley, R.Maccoll, P.Van Roey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.59 / 2.20
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 114.528, 114.528, 76.950, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 24.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of T4-Bacteriophage Deoxycytidylate Deaminase, Mutant R115E (pdb code 1vq2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of T4-Bacteriophage Deoxycytidylate Deaminase, Mutant R115E, PDB code: 1vq2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1vq2

Go back to Zinc Binding Sites List in 1vq2
Zinc binding site 1 out of 2 in the Crystal Structure of T4-Bacteriophage Deoxycytidylate Deaminase, Mutant R115E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of T4-Bacteriophage Deoxycytidylate Deaminase, Mutant R115E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:35.1
occ:1.00
ND1 A:HIS104 2.1 31.1 1.0
O4 A:DDN308 2.2 36.0 1.0
SG A:CYS135 2.4 33.1 1.0
SG A:CYS132 2.4 35.2 1.0
CG A:HIS104 3.0 30.5 1.0
CE1 A:HIS104 3.0 29.9 1.0
CB A:CYS135 3.2 30.6 1.0
C4 A:DDN308 3.3 39.1 1.0
CB A:HIS104 3.3 29.5 1.0
CB A:CYS132 3.5 34.5 1.0
C5 A:DDN308 3.6 39.1 1.0
O A:HOH419 3.7 32.3 1.0
N3 A:DDN308 3.7 39.5 1.0
N A:CYS132 3.8 34.2 1.0
OE2 A:GLU106 4.0 29.5 1.0
N A:CYS135 4.0 32.9 1.0
NE2 A:HIS104 4.1 31.7 1.0
CD2 A:HIS104 4.1 31.1 1.0
C6 A:DDN308 4.2 39.4 1.0
C2 A:DDN308 4.2 39.8 1.0
CA A:CYS135 4.2 32.6 1.0
CA A:CYS132 4.2 34.8 1.0
OE1 A:GLU106 4.3 30.2 1.0
CD A:GLU106 4.4 30.2 1.0
N1 A:DDN308 4.6 40.8 1.0
O A:CYS132 4.7 35.2 1.0
O2 A:DDN308 4.7 39.1 1.0
C A:CYS132 4.7 35.3 1.0
CA A:HIS104 4.9 29.0 1.0
C A:PRO131 4.9 34.1 1.0
CA A:PRO131 5.0 34.3 1.0

Zinc binding site 2 out of 2 in 1vq2

Go back to Zinc Binding Sites List in 1vq2
Zinc binding site 2 out of 2 in the Crystal Structure of T4-Bacteriophage Deoxycytidylate Deaminase, Mutant R115E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of T4-Bacteriophage Deoxycytidylate Deaminase, Mutant R115E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:33.2
occ:1.00
OE2 A:GLU102 2.0 33.8 1.0
SG A:CYS19 2.2 29.5 1.0
NE2 A:HIS94 2.2 33.6 1.0
SG A:CYS49 2.4 34.0 1.0
CD A:GLU102 2.8 33.3 1.0
OE1 A:GLU102 3.0 34.1 1.0
CD2 A:HIS94 3.1 34.3 1.0
CE1 A:HIS94 3.3 34.1 1.0
CB A:CYS19 3.3 32.6 1.0
CB A:CYS49 3.3 35.2 1.0
CA A:CYS19 3.6 33.2 1.0
O3' A:DDN308 3.8 42.1 1.0
N A:CYS20 3.8 35.0 1.0
OG A:SER98 4.1 34.8 1.0
C A:CYS19 4.2 34.0 1.0
CG A:GLU102 4.3 33.6 1.0
CG A:HIS94 4.3 35.3 1.0
ND1 A:HIS94 4.3 34.0 1.0
N A:SER21 4.4 36.5 1.0
CB A:SER98 4.4 34.1 1.0
CZ3 A:TRP97 4.6 30.6 1.0
CB A:SER21 4.7 36.5 1.0
CA A:CYS49 4.7 36.7 1.0
SG A:CYS20 4.7 37.4 1.0
C3' A:DDN308 4.7 42.2 1.0
N A:CYS19 4.9 33.1 1.0
CE3 A:TRP97 5.0 31.4 1.0
CA A:CYS20 5.0 35.6 1.0

Reference:

R.Almog, F.Maley, G.F.Maley, R.Maccoll, P.Van Roey. Three-Dimensional Structure of the R115E Mutant of T4-Bacteriophage 2'-Deoxycytidylate Deaminase Biochemistry V. 43 13715 2004.
ISSN: ISSN 0006-2960
PubMed: 15504034
DOI: 10.1021/BI048928H
Page generated: Wed Dec 16 03:08:09 2020

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