Atomistry » Zinc » PDB 5jf2-5jmz » 5jj4
Atomistry »
  Zinc »
    PDB 5jf2-5jmz »
      5jj4 »

Zinc in PDB 5jj4: Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein

Enzymatic activity of Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein

All present enzymatic activity of Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein:
3.5.4.38;

Protein crystallography data

The structure of Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein, PDB code: 5jj4 was solved by L.C.Pedersen, M.F.Goodman, P.Pham, S.A.Afif, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.48 / 2.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.793, 96.806, 108.692, 90.00, 102.86, 90.00
R / Rfree (%) 18.3 / 23.2

Other elements in 5jj4:

The structure of Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein (pdb code 5jj4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein, PDB code: 5jj4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5jj4

Go back to Zinc Binding Sites List in 5jj4
Zinc binding site 1 out of 3 in the Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein


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 A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1201

b:68.9
occ:1.00
 ND1 C:HIS1056 2.0 45.4 1.0
O C:HOH1307 2.1 59.2 1.0
SG C:CYS1087 2.3 81.0 1.0
SG C:CYS1090 2.3 80.1 1.0
CE1 C:HIS1056 2.9 53.9 1.0
CG C:HIS1056 3.0 53.3 1.0
CB C:CYS1087 3.3 60.7 1.0
CB C:CYS1090 3.3 53.4 1.0
CB C:HIS1056 3.4 48.4 1.0
N C:CYS1087 4.0 50.9 1.0
NE2 C:HIS1056 4.0 56.6 1.0
N C:CYS1090 4.1 58.1 1.0
CD2 C:HIS1056 4.1 55.7 1.0
OE1 C:GLU1058 4.1 73.8 1.0
CA C:CYS1087 4.2 57.8 1.0
CA C:CYS1090 4.3 58.1 1.0
CD C:GLU1058 4.6 71.9 1.0
C C:CYS1087 4.7 63.7 1.0
O C:HOH1312 4.7 33.0 1.0
O C:CYS1087 4.8 67.4 1.0
CA C:HIS1056 4.9 48.2 1.0

Zinc binding site 2 out of 3 in 5jj4

Go back to Zinc Binding Sites List in 5jj4
Zinc binding site 2 out of 3 in the Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein


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 A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1201

b:67.8
occ:1.00
 ND1 A:HIS1056 2.0 56.4 1.0
O A:HOH1306 2.1 70.0 1.0
SG A:CYS1090 2.3 78.8 1.0
SG A:CYS1087 2.3 66.0 1.0
CE1 A:HIS1056 2.8 58.9 1.0
CG A:HIS1056 3.0 59.4 1.0
CB A:CYS1090 3.1 48.9 1.0
CB A:CYS1087 3.3 52.9 1.0
CB A:HIS1056 3.5 57.7 1.0
NE2 A:HIS1056 4.0 63.2 1.0
N A:CYS1087 4.0 46.9 1.0
OE2 A:GLU1058 4.0 58.4 1.0
CD2 A:HIS1056 4.1 63.3 1.0
N A:CYS1090 4.2 49.8 1.0
CA A:CYS1087 4.2 51.5 1.0
CA A:CYS1090 4.3 51.1 1.0
O A:HOH1311 4.6 47.0 1.0
CD A:GLU1058 4.6 61.7 1.0
C A:CYS1087 4.7 57.3 1.0
O A:CYS1087 4.8 60.0 1.0

Zinc binding site 3 out of 3 in 5jj4

Go back to Zinc Binding Sites List in 5jj4
Zinc binding site 3 out of 3 in the Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:71.1
occ:1.00
 ND1 B:HIS1056 2.0 60.0 1.0
O B:HOH1303 2.1 0.7 1.0
SG B:CYS1087 2.3 62.1 1.0
SG B:CYS1090 2.3 77.0 1.0
CE1 B:HIS1056 2.9 62.8 1.0
CG B:HIS1056 3.1 57.0 1.0
CB B:CYS1090 3.1 54.7 1.0
CB B:CYS1087 3.3 54.3 1.0
CB B:HIS1056 3.5 54.5 1.0
OE2 B:GLU1058 3.8 71.6 1.0
N B:CYS1087 3.9 57.2 1.0
NE2 B:HIS1056 4.0 64.5 1.0
CD2 B:HIS1056 4.1 60.4 1.0
CA B:CYS1087 4.2 55.9 1.0
N B:CYS1090 4.2 62.6 1.0
CA B:CYS1090 4.2 58.0 1.0
O B:HOH1311 4.7 47.5 1.0
CD B:GLU1058 4.8 75.7 1.0
C B:CYS1087 4.8 57.7 1.0
O B:CYS1087 4.9 59.3 1.0
CA B:HIS1056 5.0 59.1 1.0

Reference:

P.Pham, S.A.Afif, M.Shimoda, K.Maeda, N.Sakaguchi, L.C.Pedersen, M.F.Goodman. Structural Analysis of the Activation-Induced Deoxycytidine Deaminase Required in Immunoglobulin Diversification. Dna Repair (Amst.) V. 43 48 2016.
ISSN: ISSN 1568-7856
PubMed: 27258794
DOI: 10.1016/J.DNAREP.2016.05.029
Page generated: Sun Oct 27 19:01:06 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy