Calcium 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 / R_free (%)*	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:

Zinc

(Zn)

3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Variant Human Activation-Induced Deoxycytidine Deaminase As An Mbp Fusion Protein, PDB code: 5jj4:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5jj4

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Calcium Binding Sites List in 5jj4

Calcium 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 Calcium with other atoms in the Ca 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:Ca1202 b:0.7 occ:1.00	O	C:GLN325	2.5	80.1	1.0
	O	C:GLY327	2.8	64.8	1.0
	C	C:GLN325	3.7	77.0	1.0
	C	C:GLY327	4.0	61.7	1.0
	O	C:LYS326	4.1	66.8	1.0
	C	C:LYS326	4.2	70.7	1.0
	CA	C:GLN325	4.6	75.8	1.0
	N	C:GLY327	4.6	67.8	1.0
	N	C:LYS326	4.6	75.3	1.0
	CA	C:LYS326	4.7	76.5	1.0
	O	C:ALA324	4.9	62.4	1.0
	CA	C:GLY327	4.9	64.3	1.0
	N	C:GLU328	4.9	61.0	1.0
	CA	C:GLU328	4.9	63.4	1.0

Calcium binding site 2 out of 3 in 5jj4

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Calcium Binding Sites List in 5jj4

Calcium 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 Calcium with other atoms in the Ca 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:Ca1202 b:0.9 occ:1.00	O	A:GLN325	2.7	94.5	1.0
	O	A:GLY327	2.8	85.7	1.0
	C	A:GLN325	3.8	92.7	1.0
	C	A:GLY327	4.0	82.6	1.0
	O	A:LYS326	4.1	89.9	1.0
	C	A:LYS326	4.3	87.7	1.0
	CA	A:GLN325	4.5	92.8	1.0
	N	A:LYS326	4.7	90.6	1.0
	O	A:ALA324	4.7	77.9	1.0
	N	A:GLY327	4.7	83.8	1.0
	CA	A:LYS326	4.8	88.4	1.0
	CA	A:GLU328	4.8	83.9	1.0
	N	A:GLU328	4.9	82.7	1.0
	CA	A:GLY327	5.0	80.5	1.0
	OE1	A:GLN325	5.0	0.1	1.0

Calcium binding site 3 out of 3 in 5jj4

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Calcium Binding Sites List in 5jj4

Calcium 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 Calcium with other atoms in the Ca 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:Ca1202 b:0.9 occ:1.00	O	B:GLY327	2.2	0.3	1.0
	O	B:GLN325	2.6	97.4	1.0
	C	B:GLY327	3.4	0.2	1.0
	C	B:GLN325	3.7	98.3	1.0
	O	B:HOH1308	3.9	64.3	1.0
	O	B:ALA324	4.1	93.0	1.0
	N	B:GLU328	4.1	96.5	1.0
	CA	B:GLU328	4.2	90.7	1.0
	N	B:GLY327	4.2	0.2	1.0
	CA	B:GLN325	4.3	97.6	1.0
	CA	B:GLY327	4.4	99.4	1.0
	C	B:LYS326	4.5	0.9	1.0
	N	B:LYS326	4.7	99.9	1.0
	O	B:LYS326	4.9	0.9	1.0
	CB	B:GLU328	5.0	86.2	1.0
	CA	B:LYS326	5.0	0.6	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 Jul 9 07:08:04 2025

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