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Calcium in PDB 5w0u: Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp

Enzymatic activity of Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp

All present enzymatic activity of Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp:
3.5.4.38;

Protein crystallography data

The structure of Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp, PDB code: 5w0u was solved by Q.Qiao, L.Wang, H.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 153.94 / 2.90
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.005, 39.777, 153.935, 90.00, 90.14, 90.00
R / Rfree (%) 25.1 / 28.1

Other elements in 5w0u:

The structure of Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp (pdb code 5w0u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp, PDB code: 5w0u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5w0u

Go back to Calcium Binding Sites List in 5w0u
Calcium binding site 1 out of 2 in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp


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 Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:0.3
occ:1.00
N B:ASN101 0.6 0.2 1.0
CA B:LYS103 0.6 99.6 1.0
CD1 B:ILE179 0.9 0.1 1.0
CG1 B:ILE179 1.0 0.0 1.0
C B:LYS103 1.0 92.9 1.0
CB B:THR81 1.0 94.3 1.0
C B:TYR100 1.0 0.5 1.0
O B:ALA370 1.1 0.9 1.0
CG2 B:ILE179 1.1 0.2 1.0
N B:LYS103 1.1 91.9 1.0
CA B:THR81 1.3 89.5 1.0
O B:TYR100 1.5 1.0 1.0
N B:LEU104 1.5 89.1 1.0
CG2 B:THR81 1.7 82.6 1.0
O B:LYS103 1.7 90.4 1.0
O B:THR81 1.8 88.5 1.0
CB B:ILE179 1.9 0.3 1.0
CA B:ASN101 1.9 0.7 1.0
N B:GLY102 2.0 0.8 1.0
C B:THR81 2.1 84.6 1.0
OG1 B:THR81 2.1 0.6 1.0
CB B:LYS103 2.1 0.2 1.0
CA B:TYR100 2.1 95.4 1.0
C B:ALA370 2.1 0.6 1.0
O B:ILE80 2.3 87.8 1.0
C B:GLY102 2.4 95.9 1.0
N B:TYR100 2.5 93.1 1.0
C B:ASN101 2.5 0.9 1.0
NE2 B:GLN336 2.5 99.1 1.0
CD1 B:TYR1064 2.6 0.9 1.0
N B:THR81 2.6 86.6 1.0
CE1 B:TYR1064 2.7 0.8 1.0
CD B:GLN336 2.7 0.5 1.0
N B:ALA371 2.8 0.6 1.0
CG2 B:ILE334 2.8 81.9 1.0
CG B:GLN336 2.9 0.6 1.0
CG B:LYS103 2.9 0.9 1.0
CA B:GLY102 2.9 95.5 1.0
OD1 B:ASP1045 2.9 1.0 1.0
NH2 B:ARG1063 2.9 0.4 1.0
CA B:ALA371 2.9 0.0 1.0
CB B:ASN101 3.0 0.0 1.0
C B:ILE80 3.0 82.9 1.0
O B:ASN368 3.0 0.8 1.0
CA B:LEU104 3.1 83.2 1.0
OE1 B:GLN336 3.1 0.1 1.0
CA B:ILE179 3.1 0.6 1.0
CB B:GLN336 3.2 91.2 1.0
O B:GLY102 3.2 0.5 1.0
OE2 B:GLU79 3.2 0.9 1.0
O B:THR367 3.2 0.1 1.0
CA B:ALA370 3.2 0.1 1.0
OH B:TYR1031 3.2 86.2 1.0
CD1 B:ILE334 3.3 96.4 1.0
OD2 B:ASP1045 3.3 83.7 1.0
O B:GLY175 3.3 0.5 1.0
N B:ALA370 3.3 0.5 1.0
N B:PRO82 3.3 76.9 1.0
CD B:ARG1063 3.3 0.2 1.0
CB B:TYR100 3.4 93.0 1.0
O B:PHE1046 3.4 92.0 1.0
CB B:ALA371 3.4 0.9 1.0
CG B:LEU104 3.4 82.1 1.0
CB B:LEU104 3.5 83.2 1.0
CZ B:ARG1063 3.5 0.7 1.0
C B:ARG99 3.5 91.3 1.0
CB B:ILE334 3.5 79.5 1.0
O B:ASN101 3.6 1.0 1.0
CG B:ASP1045 3.6 0.2 1.0
CG B:TYR100 3.6 97.7 1.0
CG B:ARG99 3.7 96.5 1.0
CE1 B:PHE1046 3.7 90.4 1.0
OH B:TYR1064 3.7 0.3 1.0
CZ B:TYR1064 3.7 0.1 1.0
CG B:GLU79 3.8 95.2 1.0
O B:LEU104 3.8 91.7 1.0
O B:ILE179 3.8 0.4 1.0
CG B:TYR1064 3.8 0.2 1.0
NH1 B:ARG1063 3.8 0.6 1.0
C B:LEU104 3.8 82.3 1.0
CZ B:PHE1046 3.8 0.9 1.0
CD B:GLU79 3.9 0.7 1.0
NE B:ARG1063 3.9 0.9 1.0
OD2 B:ASP1067 3.9 0.8 1.0
OE2 B:GLU372 3.9 0.9 1.0
N B:ILE179 3.9 0.2 1.0
CB B:ARG1063 3.9 84.3 1.0
CD2 B:TYR100 3.9 95.4 1.0
C B:ILE179 3.9 0.6 1.0
CD1 B:LEU104 3.9 78.3 1.0
CG1 B:ILE334 3.9 86.8 1.0
CD B:PRO82 3.9 89.9 1.0
CB B:TYR1064 3.9 98.5 1.0
CD1 B:TYR100 4.0 0.2 1.0
O B:ARG99 4.0 92.2 1.0
C B:ALA371 4.1 0.4 1.0
O B:TYR177 4.2 0.5 1.0
C B:ASN368 4.2 0.7 1.0
CA B:ARG99 4.2 90.7 1.0
N B:TYR177 4.2 0.7 1.0
CA B:TYR1064 4.2 98.3 1.0
CG B:GLU372 4.2 0.8 1.0
CE1 B:TYR100 4.2 0.5 1.0
CD B:GLU372 4.3 0.1 1.0
CG B:ASN101 4.3 0.0 1.0
CA B:PRO82 4.3 73.0 1.0
CB B:TYR177 4.3 97.8 1.0
N B:GLU372 4.3 0.9 1.0
CD B:LYS103 4.4 1.0 1.0
ND2 B:ASN101 4.4 0.4 1.0
CG B:ARG1063 4.4 94.4 1.0
C B:THR367 4.4 0.5 1.0
CB B:ALA370 4.4 1.0 1.0
CA B:ILE80 4.4 81.0 1.0
C B:GLY175 4.4 0.3 1.0
C B:PRO82 4.4 81.2 1.0
C B:ALA369 4.4 1.0 1.0
CZ B:TYR100 4.5 0.1 1.0
CE2 B:TYR100 4.5 98.1 1.0
O B:PRO82 4.5 86.9 1.0
CD2 B:LEU104 4.5 80.6 1.0
CB B:ARG99 4.5 93.4 1.0
CD1 B:PHE1046 4.5 83.7 1.0
CA B:ASN368 4.5 0.0 1.0
C B:PHE1046 4.5 86.9 1.0
N B:TYR1064 4.6 99.7 1.0
N B:ILE80 4.6 93.7 1.0
CZ B:TYR1031 4.6 77.3 1.0
N B:ALA83 4.6 80.5 1.0
CA B:GLN336 4.7 95.4 1.0
C B:TYR177 4.7 0.4 1.0
C B:ARG1063 4.7 0.5 1.0
CD B:ARG99 4.7 0.5 1.0
CD2 B:TYR177 4.7 98.0 1.0
CA B:LYS176 4.7 0.4 1.0
CA B:TYR177 4.8 0.5 1.0
O B:ARG1063 4.8 0.3 1.0
CE2 B:TYR1064 4.8 92.2 1.0
CD2 B:LEU1049 4.8 80.4 1.0
CA B:ILE334 4.8 80.7 1.0
CA B:ALA369 4.8 0.4 1.0
N B:PHE1046 4.9 89.5 1.0
O B:LEU1060 4.9 85.8 1.0
N B:ILE105 4.9 82.0 1.0
CE2 B:PHE1046 4.9 99.0 1.0
CE B:LYS103 4.9 0.0 1.0
N B:GLN336 4.9 94.6 1.0
OH B:TYR100 4.9 0.4 1.0
CD2 B:TYR1064 4.9 99.0 1.0
N B:ASN368 4.9 0.0 1.0
N B:LYS180 5.0 0.2 1.0
CA B:GLY175 5.0 0.3 1.0
O B:ALA371 5.0 0.7 1.0

Calcium binding site 2 out of 2 in 5w0u

Go back to Calcium Binding Sites List in 5w0u
Calcium binding site 2 out of 2 in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp


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 Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:97.4
occ:1.00
C A:LYS103 0.8 92.1 1.0
O A:THR81 0.9 88.2 1.0
CA A:THR81 0.9 79.7 1.0
CG2 A:ILE179 1.0 0.1 1.0
CB A:THR81 1.2 88.9 1.0
N A:LEU104 1.2 86.6 1.0
N A:ASN101 1.2 87.7 1.0
O A:ALA370 1.3 0.3 1.0
CA A:LYS103 1.3 97.6 1.0
C A:TYR100 1.3 92.9 1.0
CG1 A:ILE179 1.4 0.6 1.0
O A:LYS103 1.5 88.3 1.0
CD1 A:ILE179 1.5 0.4 1.0
C A:THR81 1.5 83.2 1.0
N A:LYS103 1.6 88.7 1.0
O A:ILE80 1.7 79.5 1.0
O A:TYR100 1.9 0.6 1.0
CA A:TYR100 1.9 86.7 1.0
CB A:ILE179 2.0 0.3 1.0
C A:ALA370 2.0 0.1 1.0
N A:TYR100 2.0 82.5 1.0
N A:THR81 2.1 84.6 1.0
OG1 A:THR81 2.1 0.1 1.0
CG2 A:THR81 2.2 88.1 1.0
NE2 A:GLN336 2.3 92.2 1.0
CB A:LYS103 2.4 0.8 1.0
CA A:LEU104 2.4 69.5 1.0
CA A:ASN101 2.4 0.8 1.0
C A:ILE80 2.5 80.6 1.0
N A:GLY102 2.5 0.0 1.0
NH2 A:ARG1063 2.5 0.1 1.0
CE1 A:TYR1064 2.5 0.4 1.0
CG2 A:ILE334 2.5 64.6 1.0
N A:ALA371 2.6 0.5 1.0
CD A:GLN336 2.6 84.5 1.0
CD1 A:TYR1064 2.6 1.0 1.0
N A:PRO82 2.6 81.7 1.0
CG A:GLN336 2.7 99.5 1.0
C A:GLY102 2.8 96.1 1.0
C A:ASN101 2.9 97.5 1.0
OD1 A:ASP1045 2.9 0.9 1.0
CA A:ALA371 2.9 86.2 1.0
CB A:LEU104 2.9 74.7 1.0
CD A:ARG1063 2.9 0.9 1.0
CZ A:ARG1063 2.9 0.3 1.0
CB A:GLN336 3.0 87.5 1.0
CG A:LEU104 3.0 74.2 1.0
O A:THR367 3.0 0.5 1.0
N A:ALA370 3.0 0.2 1.0
O A:ASN368 3.0 0.7 1.0
CA A:ILE179 3.0 0.4 1.0
CD1 A:ILE334 3.1 86.9 1.0
CA A:ALA370 3.1 98.1 1.0
C A:ARG99 3.1 86.3 1.0
OH A:TYR1031 3.1 94.7 1.0
OD2 A:ASP1045 3.2 98.4 1.0
CB A:TYR100 3.2 78.6 1.0
OE1 A:GLN336 3.2 84.9 1.0
CB A:ILE334 3.2 84.7 1.0
CD A:PRO82 3.2 84.4 1.0
C A:LEU104 3.3 74.6 1.0
NE A:ARG1063 3.3 1.0 1.0
CG A:LYS103 3.3 94.0 1.0
CG A:ARG99 3.3 95.8 1.0
CA A:GLY102 3.3 0.7 1.0
NH1 A:ARG1063 3.4 0.5 1.0
O A:LEU104 3.4 84.0 1.0
O A:GLY175 3.4 0.9 1.0
O A:PHE1046 3.4 88.4 1.0
CB A:ASN101 3.4 97.8 1.0
CG A:TYR100 3.5 82.0 1.0
CB A:ALA371 3.5 98.5 1.0
CZ A:TYR1064 3.5 0.1 1.0
O A:ILE179 3.5 95.9 1.0
O A:GLY102 3.5 97.9 1.0
CD1 A:LEU104 3.5 65.8 1.0
OE2 A:GLU79 3.5 0.0 1.0
CG A:TYR1064 3.6 99.2 1.0
CG A:ASP1045 3.6 0.2 1.0
CA A:PRO82 3.6 78.1 1.0
O A:ARG99 3.6 90.6 1.0
CB A:ARG1063 3.6 95.9 1.0
OH A:TYR1064 3.6 0.9 1.0
CA A:ARG99 3.6 81.5 1.0
CB A:TYR1064 3.7 0.6 1.0
CG1 A:ILE334 3.7 81.1 1.0
CD1 A:TYR100 3.7 0.4 1.0
C A:PRO82 3.7 77.5 1.0
C A:ILE179 3.8 0.9 1.0
CG A:GLU79 3.9 86.4 1.0
CE1 A:PHE1046 3.9 87.8 1.0
N A:ILE179 3.9 96.9 1.0
CG A:ARG1063 3.9 0.7 1.0
CD2 A:TYR100 3.9 85.5 1.0
C A:ALA371 4.0 99.5 1.0
O A:PRO82 4.0 80.4 1.0
O A:ASN101 4.0 98.8 1.0
C A:ASN368 4.0 0.2 1.0
N A:ALA83 4.0 76.2 1.0
CE1 A:TYR100 4.0 84.8 1.0
CA A:ILE80 4.0 75.2 1.0
CA A:TYR1064 4.0 99.3 1.0
CB A:ARG99 4.0 84.8 1.0
CD2 A:LEU104 4.1 78.3 1.0
CB A:TYR177 4.1 82.8 1.0
C A:THR367 4.1 0.9 1.0
O A:TYR177 4.1 0.6 1.0
CZ A:PHE1046 4.1 0.3 1.0
N A:TYR177 4.1 0.2 1.0
OD2 A:ASP1067 4.2 0.9 1.0
C A:ALA369 4.2 0.6 1.0
CB A:ALA370 4.2 98.0 1.0
CD A:GLU79 4.2 0.3 1.0
N A:GLU372 4.2 0.1 1.0
N A:ILE80 4.3 79.2 1.0
N A:TYR1064 4.3 0.4 1.0
CA A:ASN368 4.4 0.0 1.0
N A:ILE105 4.4 72.3 1.0
CZ A:TYR100 4.4 94.4 1.0
CA A:GLN336 4.4 88.0 1.0
CD2 A:TYR177 4.4 90.9 1.0
CZ A:TYR1031 4.5 91.5 1.0
O A:LEU1060 4.5 90.9 1.0
CE2 A:TYR100 4.5 96.5 1.0
C A:ARG1063 4.6 0.9 1.0
CA A:TYR177 4.6 98.8 1.0
C A:TYR177 4.6 97.4 1.0
C A:GLY175 4.6 0.2 1.0
CG A:ASN101 4.6 0.8 1.0
CD A:ARG99 4.6 0.7 1.0
CE2 A:TYR1064 4.6 0.4 1.0
C A:PHE1046 4.6 87.4 1.0
CA A:ILE334 4.6 83.1 1.0
CD2 A:TYR1064 4.7 96.0 1.0
ND2 A:ASN101 4.7 0.9 1.0
CG A:PRO82 4.7 74.6 1.0
CG1 A:ILE80 4.7 69.4 1.0
CD1 A:PHE1046 4.7 79.2 1.0
CD A:LYS103 4.7 0.0 1.0
N A:ASN368 4.7 0.9 1.0
CE1 A:PHE170 4.7 98.4 1.0
N A:GLN336 4.7 88.1 1.0
CA A:ALA83 4.7 79.4 1.0
CA A:ALA369 4.7 0.0 1.0
O A:ARG1063 4.8 0.8 1.0
CA A:ARG1063 4.8 0.1 1.0
CA A:LYS176 4.8 0.8 1.0
NE A:ARG99 4.8 0.8 1.0
CB A:ALA83 4.8 78.0 1.0
OD1 A:ASN333 4.8 91.7 1.0
CG A:TYR177 4.8 90.4 1.0
O A:ALA371 4.9 0.4 1.0
CB A:ILE80 4.9 75.4 1.0
O A:VAL98 4.9 82.6 1.0
N A:LYS180 4.9 0.5 1.0
N A:ALA369 4.9 0.8 1.0
C A:ASP178 4.9 97.7 1.0
N A:PHE1046 5.0 90.4 1.0
CB A:ASP1045 5.0 0.4 1.0
CB A:PRO82 5.0 77.3 1.0
CD2 A:LEU1060 5.0 0.0 1.0
N A:ARG99 5.0 69.9 1.0

Reference:

Q.Qiao, L.Wang, F.L.Meng, J.K.Hwang, F.W.Alt, H.Wu. Aid Recognizes Structured Dna For Class Switch Recombination. Mol. Cell V. 67 361 2017.
ISSN: ISSN 1097-4164
PubMed: 28757211
DOI: 10.1016/J.MOLCEL.2017.06.034
Page generated: Mon Jul 15 12:41:16 2024

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