Zinc in PDB 5w0u: 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;

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

The structure of Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Dcmp 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 Dcmp (pdb code 5w0u). 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 Dcmp, PDB code: 5w0u:
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 Dcmp


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 Dcmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:0.6 occ:1.00 C B:PHE1081 0.7 79.9 1.0 SG B:CYS1147 0.8 79.2 1.0 CB B:THR1082 0.9 80.0 1.0 CA B:TYR1146 0.9 73.5 1.0 N B:THR1082 0.9 81.5 1.0 CG2 B:THR1082 1.0 74.2 1.0 O B:HOH4001 1.0 75.1 1.0 CB B:PHE1081 1.0 80.3 1.0 N B:TYR1146 1.1 76.5 1.0 C B:TYR1146 1.1 75.4 1.0 CA B:THR1082 1.1 80.7 1.0 N B:CYS1147 1.1 75.5 1.0 CA B:PHE1081 1.4 78.4 1.0 O B:PHE1081 1.6 75.4 1.0 C B:GLU1145 1.7 83.8 1.0 O B:GLU1145 1.8 82.6 1.0 CG B:PHE1081 1.8 87.0 1.0 SG B:CYS1090 1.9 95.2 1.0 CB B:TYR1146 2.0 80.3 1.0 SG B:CYS1087 2.0 81.6 1.0 CA B:CYS1147 2.1 74.5 1.0 CB B:CYS1147 2.1 76.2 1.0 N4 B:DCM2002 2.2 0.1 1.0 O B:ASP1143 2.2 83.6 1.0 ND1 B:HIS1056 2.2 95.9 1.0 CD1 B:PHE1081 2.2 78.6 1.0 OG1 B:THR1082 2.2 82.1 1.0 O B:TYR1146 2.3 79.7 1.0 CB B:ASP1089 2.3 0.4 1.0 N3 B:DCM2002 2.6 77.1 1.0 C B:THR1082 2.6 84.6 1.0 C4 B:DCM2002 2.6 83.8 1.0 N B:PHE1081 2.7 76.3 1.0 CB B:CYS1090 2.7 86.4 1.0 CE1 B:HIS1056 2.8 0.2 1.0 O B:TRP1084 2.8 99.8 1.0 CG B:ASP1089 2.9 0.8 1.0 CD2 B:PHE1081 2.9 81.5 1.0 CG B:TYR1146 3.0 84.1 1.0 CA B:GLU1145 3.1 82.8 1.0 OD2 B:ASP1089 3.1 95.4 1.0 ND2 B:ASN1149 3.1 76.8 1.0 CE1 B:PHE1081 3.1 73.2 1.0 CD2 B:TYR1146 3.2 79.3 1.0 CG B:HIS1056 3.2 0.4 1.0 O B:THR1082 3.2 74.2 1.0 O B:PHE1109 3.3 82.3 1.0 CB B:GLU1145 3.3 89.5 1.0 N B:SER1083 3.4 91.0 1.0 CG2 B:VAL1057 3.4 95.6 1.0 CB B:HIS1056 3.4 0.6 1.0 C B:ASP1143 3.4 81.1 1.0 N B:CYS1090 3.4 97.2 1.0 CE B:MET1139 3.4 80.0 1.0 C B:CYS1147 3.4 76.8 1.0 CE2 B:PHE1015 3.5 73.8 1.0 O B:TYR1028 3.6 75.6 1.0 OD1 B:ASP1089 3.6 0.3 1.0 N B:TRP1148 3.6 74.9 1.0 CZ B:PHE1081 3.6 82.2 1.0 CE2 B:PHE1081 3.7 72.2 1.0 CA B:ASP1089 3.7 96.4 1.0 N B:CYS1087 3.7 92.1 1.0 CB B:CYS1087 3.7 0.8 1.0 CA B:PRO1086 3.7 88.6 1.0 C B:TRP1080 3.8 78.5 1.0 C5 B:DCM2002 3.8 90.3 1.0 CG B:ASN1149 3.8 87.3 1.0 O B:TYR1144 3.8 77.6 1.0 CG2 B:THR1027 3.8 84.6 1.0 N B:GLU1145 3.8 80.3 1.0 CB B:ASN1149 3.8 91.0 1.0 CA B:CYS1090 3.8 82.0 1.0 C B:TYR1144 3.8 81.4 1.0 C2 B:DCM2002 3.8 0.9 1.0 O B:LYS1142 3.9 76.6 1.0 CD1 B:LEU1029 3.9 85.0 1.0 NE2 B:HIS1056 3.9 0.8 1.0 N B:ASP1089 3.9 98.3 1.0 CD1 B:TYR1146 4.0 74.9 1.0 SD B:MET1139 4.0 90.7 1.0 C B:TRP1084 4.0 91.2 1.0 C B:ASP1089 4.1 98.7 1.0 O B:TRP1080 4.1 74.3 1.0 O B:SER1085 4.1 94.9 1.0 CE2 B:PHE1151 4.1 71.8 1.0 CA B:LEU1029 4.1 81.0 1.0 N B:PRO1086 4.2 99.1 1.0 CZ B:PHE1015 4.2 76.2 1.0 CB B:ALA1058 4.2 77.7 1.0 N B:ASN1149 4.2 82.7 1.0 CB B:LEU1029 4.2 78.1 1.0 CA B:ASP1143 4.3 89.2 1.0 C B:SER1085 4.3 94.0 1.0 CD2 B:HIS1056 4.3 0.2 1.0 N B:CYS1030 4.3 74.8 1.0 CD2 B:PHE1151 4.3 76.5 1.0 N B:TYR1144 4.3 78.0 1.0 O2 B:DCM2002 4.4 0.9 1.0 CA B:TYR1144 4.4 86.0 1.0 CE2 B:TYR1146 4.4 87.2 1.0 CA B:CYS1087 4.4 99.0 1.0 N B:ALA1058 4.4 86.0 1.0 O B:CYS1147 4.4 79.7 1.0 OE1 B:GLU1145 4.4 83.0 1.0 C B:PRO1086 4.5 91.2 1.0 OG1 B:THR1150 4.5 75.8 1.0 CB B:CYS1030 4.5 85.2 1.0 O B:CYS1030 4.5 81.7 1.0 N B:TRP1084 4.5 85.2 1.0 CB B:PRO1086 4.5 81.8 1.0 C B:PHE1109 4.5 78.1 1.0 CD2 B:PHE1015 4.5 77.4 1.0 C B:TYR1028 4.6 75.7 1.0 C6 B:DCM2002 4.7 0.0 1.0 SG B:CYS1030 4.7 82.4 1.0 CD B:PRO1086 4.7 90.8 1.0 CG B:LEU1029 4.7 77.4 1.0 OD1 B:ASN1149 4.7 90.2 1.0 CA B:ASN1149 4.7 89.0 1.0 CA B:SER1083 4.7 82.9 1.0 N1 B:DCM2002 4.7 0.6 1.0 CG B:GLU1145 4.8 77.1 1.0 N B:VAL1057 4.8 82.7 1.0 C B:CYS1087 4.8 93.4 1.0 CA B:SER1085 4.8 85.7 1.0 CA B:TRP1148 4.9 70.1 1.0 N B:LEU1029 4.9 76.2 1.0 CB B:VAL1057 4.9 96.4 1.0 CA B:TRP1084 4.9 92.0 1.0 CA B:HIS1056 4.9 0.2 1.0 N B:SER1085 4.9 88.3 1.0 O B:CYS1087 4.9 96.3 1.0 CG B:MET1139 4.9 84.8 1.0 CB B:TRP1080 4.9 81.7 1.0 CA B:THR1110 4.9 84.4 1.0 C B:LEU1029 5.0 84.3 1.0 CA B:TRP1080 5.0 77.0 1.0 CB B:ASP1143 5.0 79.9 1.0 CA B:ALA1058 5.0 79.8 1.0 N B:THR1150 5.0 72.1 1.0 CB B:THR1027 5.0 85.1 1.0 CB B:PHE1109 5.0 75.4 1.0 C B:LYS1142 5.0 78.0 1.0

Zinc 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 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 Dcmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:0.7 occ:1.00 C A:PHE1081 0.3 82.9 1.0 CA A:TYR1146 0.7 73.1 1.0 C A:TYR1146 0.7 72.0 1.0 SG A:CYS1147 1.0 74.2 1.0 N A:THR1082 1.0 79.2 1.0 N A:CYS1147 1.0 70.8 1.0 CB A:PHE1081 1.0 80.5 1.0 CA A:PHE1081 1.1 75.4 1.0 CG2 A:THR1082 1.1 81.5 1.0 CB A:THR1082 1.3 84.3 1.0 O A:PHE1081 1.4 80.9 1.0 O A:HOH4001 1.4 80.8 1.0 CA A:THR1082 1.4 81.5 1.0 N A:TYR1146 1.7 79.7 1.0 CG A:PHE1081 1.8 87.7 1.0 SG A:CYS1090 1.8 91.3 1.0 CB A:TYR1146 1.9 71.8 1.0 O A:TYR1146 1.9 77.8 1.0 CA A:CYS1147 2.0 73.6 1.0 CB A:ASP1089 2.0 0.5 1.0 N4 A:DCM2002 2.1 0.8 1.0 SG A:CYS1087 2.1 0.1 1.0 O A:GLU1145 2.1 83.6 1.0 CB A:CYS1147 2.2 79.2 1.0 CD1 A:PHE1081 2.3 81.8 1.0 C A:GLU1145 2.3 80.3 1.0 ND1 A:HIS1056 2.3 74.1 1.0 N A:PHE1081 2.3 79.3 1.0 OG1 A:THR1082 2.4 89.1 1.0 CD2 A:PHE1081 2.5 85.2 1.0 CG A:TYR1146 2.6 81.2 1.0 CB A:CYS1090 2.6 87.6 1.0 N3 A:DCM2002 2.6 93.0 1.0 C4 A:DCM2002 2.7 92.3 1.0 O A:ASP1143 2.7 84.8 1.0 CE1 A:HIS1056 2.8 90.8 1.0 CG A:ASP1089 2.8 0.8 1.0 CD2 A:TYR1146 2.8 74.0 1.0 C A:THR1082 2.9 82.2 1.0 OD2 A:ASP1089 3.0 0.2 1.0 O A:TRP1084 3.0 96.9 1.0 CG2 A:VAL1057 3.0 0.3 1.0 N A:CYS1090 3.1 1.0 1.0 CE1 A:PHE1081 3.2 79.4 1.0 CG A:HIS1056 3.3 80.1 1.0 CE2 A:PHE1081 3.3 83.1 1.0 CA A:ASP1089 3.3 1.0 1.0 ND2 A:ASN1149 3.4 83.9 1.0 C A:CYS1147 3.4 72.9 1.0 CA A:PRO1086 3.4 97.8 1.0 O A:PHE1109 3.4 93.5 1.0 CD1 A:TYR1146 3.5 73.7 1.0 OD1 A:ASP1089 3.5 0.2 1.0 C A:TRP1080 3.5 88.8 1.0 CB A:ASN1149 3.5 84.6 1.0 N A:CYS1087 3.5 0.0 1.0 CE2 A:PHE1151 3.6 68.3 1.0 CB A:HIS1056 3.6 99.2 1.0 O A:TYR1028 3.6 76.1 1.0 CZ A:PHE1081 3.6 84.1 1.0 N A:ASP1089 3.6 0.1 1.0 CB A:CYS1087 3.6 0.4 1.0 CA A:CYS1090 3.7 91.5 1.0 C A:ASP1089 3.7 0.7 1.0 CD1 A:LEU1029 3.7 87.3 1.0 CA A:GLU1145 3.7 78.2 1.0 CG A:ASN1149 3.7 87.7 1.0 O A:THR1082 3.7 76.4 1.0 N A:TRP1148 3.8 74.6 1.0 N A:SER1083 3.8 83.6 1.0 CA A:LEU1029 3.8 80.0 1.0 O A:TRP1080 3.8 87.8 1.0 CE2 A:PHE1015 3.9 82.6 1.0 CB A:PRO1086 3.9 88.1 1.0 CD2 A:PHE1151 3.9 71.3 1.0 C5 A:DCM2002 3.9 0.5 1.0 N A:CYS1030 3.9 76.0 1.0 OG1 A:THR1150 3.9 58.8 1.0 CB A:LEU1029 3.9 74.4 1.0 C A:ASP1143 3.9 82.1 1.0 C2 A:DCM2002 3.9 0.6 1.0 N A:PRO1086 4.0 97.6 1.0 CG2 A:THR1027 4.0 89.6 1.0 CE2 A:TYR1146 4.0 81.8 1.0 O A:CYS1030 4.0 78.5 1.0 NE2 A:HIS1056 4.0 91.0 1.0 CB A:CYS1030 4.0 73.6 1.0 CB A:GLU1145 4.1 80.7 1.0 N A:ASN1149 4.1 71.0 1.0 CB A:ALA1058 4.1 86.1 1.0 C A:PRO1086 4.2 0.8 1.0 CE A:MET1139 4.2 81.2 1.0 O A:TYR1144 4.2 74.4 1.0 CA A:CYS1087 4.2 0.3 1.0 O A:SER1085 4.2 0.3 1.0 C A:SER1085 4.2 0.6 1.0 C A:TRP1084 4.2 87.3 1.0 O A:CYS1147 4.3 80.2 1.0 N A:ALA1058 4.3 85.3 1.0 SG A:CYS1030 4.3 69.3 1.0 CZ A:PHE1015 4.3 82.7 1.0 O A:LYS1142 4.4 79.6 1.0 C A:TYR1144 4.4 76.6 1.0 CG A:LEU1029 4.4 79.5 1.0 N A:GLU1145 4.4 75.6 1.0 CD2 A:HIS1056 4.4 82.3 1.0 CA A:ASN1149 4.4 83.0 1.0 SD A:MET1139 4.5 87.1 1.0 O2 A:DCM2002 4.5 0.3 1.0 CD A:PRO1086 4.5 91.4 1.0 C A:CYS1087 4.5 0.0 1.0 CB A:VAL1057 4.5 97.5 1.0 C A:TYR1028 4.5 81.4 1.0 N A:THR1150 4.5 76.1 1.0 CB A:THR1150 4.5 64.2 1.0 C A:LEU1029 4.6 82.2 1.0 CA A:TRP1080 4.6 66.2 1.0 CE3 A:TRP1080 4.6 82.1 1.0 CE1 A:TYR1146 4.6 73.6 1.0 OD1 A:ASN1149 4.6 91.2 1.0 CA A:CYS1030 4.6 71.5 1.0 C A:PHE1109 4.6 84.6 1.0 CB A:TRP1080 4.7 75.0 1.0 O A:ASP1089 4.7 0.8 1.0 N A:LEU1029 4.7 87.2 1.0 O A:CYS1087 4.7 0.7 1.0 CA A:ASP1143 4.7 79.9 1.0 C A:CYS1030 4.7 76.9 1.0 CZ A:PHE1151 4.7 69.4 1.0 CZ3 A:TRP1080 4.8 72.5 1.0 CA A:ALA1058 4.8 89.2 1.0 N A:TRP1084 4.8 92.2 1.0 CA A:SER1085 4.9 92.3 1.0 CD2 A:LEU1029 4.9 84.1 1.0 C6 A:DCM2002 4.9 0.5 1.0 C A:CYS1090 4.9 84.8 1.0 C A:ASN1149 4.9 72.5 1.0 C A:TYR1088 4.9 0.9 1.0 N1 A:DCM2002 4.9 1.0 1.0 N A:VAL1057 4.9 99.1 1.0 CZ A:TYR1146 4.9 88.8 1.0 CA A:TYR1144 5.0 80.6 1.0 N A:TYR1144 5.0 82.2 1.0 N A:TYR1088 5.0 0.9 1.0 CD2 A:PHE1015 5.0 77.2 1.0 CG A:PRO1086 5.0 96.2 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