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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: Wed Dec 16 06:25:19 2020

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