Zinc in PDB 5w1c: Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cytidine

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

The structure of Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cytidine, PDB code: 5w1c 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)	125.46 / 3.18
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.456, 39.824, 155.304, 90.00, 90.27, 90.00
R / Rfree (%)	23.2 / 27

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

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cytidine (pdb code 5w1c). 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 Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cytidine, PDB code: 5w1c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cytidine


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 Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:0.4 occ:1.00 SG B:CYS1147 0.3 90.2 1.0 N B:CYS1147 0.7 73.2 1.0 CA B:THR1082 0.7 86.2 1.0 C B:PHE1081 0.8 72.7 1.0 O B:HOH3001 0.9 0.0 1.0 CB B:THR1082 1.0 79.1 1.0 N B:THR1082 1.0 92.6 1.0 CA B:TYR1146 1.2 83.8 1.0 C B:TYR1146 1.2 74.2 1.0 N B:TYR1146 1.2 84.2 1.0 C B:GLU1145 1.2 93.6 1.0 O B:GLU1145 1.4 92.2 1.0 CB B:PHE1081 1.4 94.8 1.0 CG2 B:THR1082 1.5 84.2 1.0 O B:PHE1081 1.5 73.6 1.0 CB B:CYS1147 1.7 70.1 1.0 N4 B:CTN2002 1.7 0.4 1.0 CA B:PHE1081 1.8 81.8 1.0 SG B:CYS1087 1.8 0.1 1.0 ND1 B:HIS1056 1.8 0.7 1.0 CA B:CYS1147 1.9 83.8 1.0 SG B:CYS1090 2.1 0.2 1.0 O B:ASP1143 2.2 92.8 1.0 C B:THR1082 2.2 94.0 1.0 CG B:PHE1081 2.2 92.2 1.0 O B:TYR1146 2.3 86.3 1.0 C4 B:CTN2002 2.3 94.4 1.0 OG1 B:THR1082 2.4 76.2 1.0 CE1 B:HIS1056 2.4 0.9 1.0 CB B:TYR1146 2.5 81.9 1.0 N3 B:CTN2002 2.6 0.2 1.0 CD1 B:PHE1081 2.6 91.8 1.0 O B:TRP1084 2.6 0.9 1.0 ND2 B:ASN1149 2.7 81.2 1.0 CB B:ASP1089 2.8 96.5 1.0 CA B:GLU1145 2.8 88.0 1.0 CG B:HIS1056 3.0 0.7 1.0 N B:SER1083 3.0 96.0 1.0 O B:THR1082 3.0 90.6 1.0 C B:CYS1147 3.1 81.5 1.0 CB B:CYS1090 3.1 90.6 1.0 N B:PHE1081 3.1 86.5 1.0 CB B:GLU1145 3.1 0.8 1.0 CB B:HIS1056 3.2 0.8 1.0 N B:TRP1148 3.2 68.0 1.0 CE2 B:PHE1015 3.2 84.1 1.0 CD2 B:PHE1081 3.2 69.1 1.0 CG B:ASP1089 3.2 0.8 1.0 CE B:MET1139 3.2 87.5 1.0 O B:TYR1028 3.3 80.0 1.0 CG2 B:VAL1057 3.3 0.2 1.0 OD2 B:ASP1089 3.3 0.9 1.0 CG2 B:THR1027 3.4 0.9 1.0 O B:TYR1144 3.4 93.3 1.0 CG B:TYR1146 3.4 77.0 1.0 C B:ASP1143 3.4 84.3 1.0 C5 B:CTN2002 3.4 0.1 1.0 C B:TYR1144 3.5 91.7 1.0 N B:GLU1145 3.5 96.9 1.0 CE1 B:PHE1081 3.5 89.2 1.0 O B:PHE1109 3.5 88.8 1.0 CB B:CYS1087 3.6 0.6 1.0 CD2 B:TYR1146 3.6 85.8 1.0 CG B:ASN1149 3.6 96.1 1.0 CB B:ASN1149 3.7 96.7 1.0 NE2 B:HIS1056 3.8 0.1 1.0 CZ B:PHE1015 3.8 76.7 1.0 N B:CYS1087 3.8 95.8 1.0 N B:CYS1090 3.8 0.9 1.0 C2 B:CTN2002 3.8 0.5 1.0 CA B:PRO1086 3.8 84.9 1.0 C B:TRP1084 3.8 0.5 1.0 SD B:MET1139 3.9 95.7 1.0 N B:ASN1149 3.9 84.5 1.0 OD1 B:ASP1089 3.9 0.3 1.0 CE2 B:PHE1081 4.0 76.9 1.0 CZ B:PHE1081 4.0 95.0 1.0 CA B:LEU1029 4.0 90.2 1.0 CA B:ASP1089 4.0 0.3 1.0 CD2 B:HIS1056 4.0 0.6 1.0 O B:SER1085 4.1 98.8 1.0 CA B:TYR1144 4.1 88.1 1.0 O B:LYS1142 4.1 95.7 1.0 O B:CYS1147 4.1 90.3 1.0 CB B:LEU1029 4.2 83.2 1.0 CD1 B:LEU1029 4.2 95.7 1.0 OE1 B:GLU1145 4.2 0.3 1.0 CA B:CYS1090 4.2 89.3 1.0 CD2 B:PHE1015 4.2 84.2 1.0 N B:TYR1144 4.2 75.2 1.0 C B:TRP1080 4.2 85.6 1.0 N B:TRP1084 4.2 99.5 1.0 N B:PRO1086 4.2 92.9 1.0 CE2 B:PHE1151 4.2 76.3 1.0 C B:SER1085 4.3 0.3 1.0 N B:ASP1089 4.3 1.0 1.0 N B:CYS1030 4.3 61.9 1.0 C B:TYR1028 4.3 80.1 1.0 CD1 B:TYR1146 4.3 64.6 1.0 CD2 B:PHE1151 4.4 84.2 1.0 C6 B:CTN2002 4.4 0.5 1.0 C B:ASP1089 4.4 0.6 1.0 CA B:SER1083 4.4 97.9 1.0 CA B:CYS1087 4.4 0.5 1.0 CB B:CYS1030 4.4 99.3 1.0 CA B:ASP1143 4.4 93.9 1.0 SG B:CYS1030 4.4 85.0 1.0 CB B:THR1027 4.4 0.4 1.0 CB B:ALA1058 4.5 91.7 1.0 OD1 B:ASN1149 4.5 0.9 1.0 CA B:TRP1148 4.5 75.5 1.0 CG B:GLU1145 4.5 93.6 1.0 N B:ALA1058 4.5 91.2 1.0 O2 B:CTN2002 4.5 0.7 1.0 CA B:ASN1149 4.5 93.5 1.0 O B:TRP1080 4.5 82.0 1.0 C B:PRO1086 4.5 0.4 1.0 CB B:PRO1086 4.5 72.0 1.0 N1 B:CTN2002 4.6 0.6 1.0 CA B:HIS1056 4.6 0.5 1.0 N B:LEU1029 4.6 75.2 1.0 CA B:TRP1084 4.7 0.8 1.0 OG1 B:THR1150 4.7 67.1 1.0 O B:CYS1030 4.7 78.9 1.0 N B:VAL1057 4.7 0.3 1.0 C B:PHE1109 4.7 93.1 1.0 OG1 B:THR1027 4.7 0.3 1.0 C B:TRP1148 4.8 87.3 1.0 C B:SER1083 4.8 0.4 1.0 CG B:LEU1029 4.8 86.1 1.0 CB B:VAL1057 4.8 0.8 1.0 CE2 B:TYR1146 4.8 91.5 1.0 N B:SER1085 4.8 96.3 1.0 CD B:PRO1086 4.8 84.4 1.0 CB B:TRP1148 4.8 88.2 1.0 C B:LEU1029 4.9 86.2 1.0 CA B:SER1085 4.9 99.2 1.0 CD B:GLU1145 4.9 0.5 1.0 C B:CYS1087 4.9 92.8 1.0 CG B:MET1139 4.9 89.1 1.0 N B:THR1150 5.0 70.3 1.0 CB B:TRP1084 5.0 97.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cytidine


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 Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:0.6 occ:1.00 SG A:CYS1147 0.4 83.3 1.0 C A:PHE1081 0.4 79.7 1.0 N A:CYS1147 0.5 80.2 1.0 C A:TYR1146 0.7 69.6 1.0 N A:THR1082 0.9 85.6 1.0 CA A:THR1082 1.0 90.9 1.0 CA A:TYR1146 1.0 72.6 1.0 CB A:PHE1081 1.2 92.6 1.0 O A:PHE1081 1.2 70.6 1.0 CB A:THR1082 1.3 91.8 1.0 O A:HOH3001 1.4 0.9 1.0 CG2 A:THR1082 1.5 86.3 1.0 CA A:PHE1081 1.5 81.0 1.0 O A:GLU1145 1.6 93.9 1.0 N A:TYR1146 1.6 80.8 1.0 CA A:CYS1147 1.7 79.5 1.0 CB A:CYS1147 1.7 81.9 1.0 C A:GLU1145 1.7 90.7 1.0 SG A:CYS1087 1.8 0.3 1.0 ND1 A:HIS1056 1.8 98.7 1.0 SG A:CYS1090 1.9 0.7 1.0 O A:TYR1146 1.9 78.2 1.0 CG A:PHE1081 2.1 90.8 1.0 N4 A:CTN2002 2.2 92.2 1.0 CE1 A:HIS1056 2.3 0.0 1.0 CB A:TYR1146 2.4 76.8 1.0 OG1 A:THR1082 2.4 97.2 1.0 C A:THR1082 2.5 92.6 1.0 CB A:ASP1089 2.5 1.0 1.0 O A:ASP1143 2.6 89.3 1.0 C4 A:CTN2002 2.6 0.8 1.0 CD1 A:PHE1081 2.6 89.6 1.0 N3 A:CTN2002 2.7 0.0 1.0 O A:TRP1084 2.7 0.5 1.0 ND2 A:ASN1149 2.8 87.6 1.0 N A:PHE1081 2.8 77.9 1.0 C A:CYS1147 2.9 76.4 1.0 CD2 A:PHE1081 2.9 83.7 1.0 CG A:HIS1056 3.0 0.0 1.0 CB A:CYS1090 3.0 0.8 1.0 CG A:ASP1089 3.1 0.2 1.0 CG A:TYR1146 3.1 69.5 1.0 O A:TYR1028 3.2 80.4 1.0 CA A:GLU1145 3.2 85.6 1.0 N A:SER1083 3.3 88.6 1.0 CG2 A:VAL1057 3.3 0.5 1.0 N A:TRP1148 3.3 70.3 1.0 CE2 A:PHE1015 3.3 86.3 1.0 OD2 A:ASP1089 3.3 0.3 1.0 CB A:ASN1149 3.3 87.5 1.0 O A:THR1082 3.3 96.3 1.0 CG A:ASN1149 3.4 99.2 1.0 CB A:HIS1056 3.4 0.8 1.0 CB A:CYS1087 3.4 0.7 1.0 CD2 A:TYR1146 3.4 81.4 1.0 CG2 A:THR1027 3.4 0.8 1.0 N A:CYS1090 3.5 0.3 1.0 N A:CYS1087 3.5 0.1 1.0 CA A:PRO1086 3.5 84.9 1.0 NE2 A:HIS1056 3.6 0.6 1.0 CE1 A:PHE1081 3.6 90.5 1.0 O A:PHE1109 3.6 99.8 1.0 CB A:GLU1145 3.6 90.7 1.0 N A:ASN1149 3.7 77.4 1.0 O A:TYR1144 3.7 82.4 1.0 C5 A:CTN2002 3.7 0.2 1.0 CE A:MET1139 3.8 87.0 1.0 CA A:ASP1089 3.8 0.1 1.0 CA A:LEU1029 3.8 86.2 1.0 CZ A:PHE1015 3.8 80.4 1.0 CE2 A:PHE1081 3.8 86.2 1.0 C A:ASP1143 3.8 80.0 1.0 CE2 A:PHE1151 3.8 81.6 1.0 OD1 A:ASP1089 3.8 0.6 1.0 C A:TYR1144 3.9 86.8 1.0 C2 A:CTN2002 3.9 0.1 1.0 C A:TRP1084 3.9 96.7 1.0 O A:CYS1147 3.9 87.2 1.0 N A:GLU1145 3.9 88.0 1.0 CD2 A:HIS1056 4.0 99.9 1.0 N A:ASP1089 4.0 0.6 1.0 CA A:CYS1090 4.0 85.0 1.0 CD2 A:PHE1151 4.0 87.5 1.0 CB A:LEU1029 4.0 90.2 1.0 C A:TRP1080 4.0 87.3 1.0 N A:CYS1030 4.0 88.6 1.0 CZ A:PHE1081 4.0 92.1 1.0 CD1 A:TYR1146 4.0 64.5 1.0 O A:SER1085 4.1 0.2 1.0 N A:PRO1086 4.1 98.2 1.0 SG A:CYS1030 4.1 93.6 1.0 CD1 A:LEU1029 4.1 88.9 1.0 CB A:CYS1030 4.1 88.8 1.0 CB A:PRO1086 4.2 72.0 1.0 C A:ASP1089 4.2 0.1 1.0 C A:TYR1028 4.2 89.5 1.0 OG1 A:THR1150 4.2 58.9 1.0 C A:SER1085 4.2 0.6 1.0 CA A:ASN1149 4.2 89.0 1.0 SD A:MET1139 4.2 96.3 1.0 C A:PRO1086 4.2 0.2 1.0 CA A:CYS1087 4.2 0.4 1.0 OD1 A:ASN1149 4.3 0.1 1.0 O A:TRP1080 4.3 79.5 1.0 O A:LYS1142 4.3 0.5 1.0 N A:TRP1084 4.4 0.9 1.0 O A:CYS1030 4.4 73.5 1.0 CD2 A:PHE1015 4.4 83.6 1.0 CB A:ALA1058 4.5 90.2 1.0 CE2 A:TYR1146 4.5 95.5 1.0 N A:THR1150 4.5 69.1 1.0 N A:ALA1058 4.5 96.7 1.0 CA A:TRP1148 4.5 72.6 1.0 N A:LEU1029 4.5 89.2 1.0 O2 A:CTN2002 4.5 0.6 1.0 CA A:TYR1144 4.5 85.3 1.0 CB A:THR1027 4.6 0.4 1.0 C A:LEU1029 4.6 93.6 1.0 C6 A:CTN2002 4.6 0.0 1.0 CA A:SER1083 4.6 98.4 1.0 C A:CYS1087 4.6 0.1 1.0 N A:TYR1144 4.6 86.3 1.0 CG A:LEU1029 4.7 83.4 1.0 CD A:PRO1086 4.7 97.7 1.0 C A:TRP1148 4.7 79.3 1.0 CB A:THR1150 4.7 64.5 1.0 CA A:CYS1030 4.7 83.5 1.0 CA A:ASP1143 4.7 81.7 1.0 CB A:VAL1057 4.8 0.9 1.0 N1 A:CTN2002 4.8 0.9 1.0 CA A:TRP1084 4.8 0.9 1.0 C A:ASN1149 4.8 81.3 1.0 C A:PHE1109 4.8 0.3 1.0 OE1 A:GLU1145 4.8 0.2 1.0 CA A:SER1085 4.8 0.5 1.0 N A:VAL1057 4.9 0.7 1.0 CA A:HIS1056 4.9 0.9 1.0 O A:CYS1087 4.9 0.7 1.0 N A:SER1085 4.9 95.0 1.0 C A:SER1083 5.0 0.1 1.0 OG1 A:THR1027 5.0 0.7 1.0 CB A:TRP1148 5.0 73.4 1.0

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